The 4th Joint Spring Conference - Wales Gene Park

The 4th Joint Spring Conference
7-9 March 2016
The City Hall, Cardiff Civic Centre
Abstract Booklet
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Oral Presentations
(Arranged alphabetically by lead author)
Risk factors for the presence of pathogenic APC and biallelic
MUTYH mutations in patients with multiple adenomas
S.W. ten Broeke.1 S.S. Badal 1, T. van Wezel 2, H. Morreau 2, F.J. Hes 1, H.F. Vasen 3,4,
C.M. Tops 1, M. Nielsen 1
1 Department of Clinical Genetics, Leiden University Medical Centre, the Netherlands.
2 Department of Pathology, Leiden University Medical Centre, the Netherlands.
3 The Netherlands Foundation for the Detection of Hereditary Tumours, Leiden, the Netherlands.
4 Department of Gastroenterology, Leiden University Medical Centre, the Netherlands.
[email protected]
Background. Patients with multiple colorectal adenomas may carry germline mutations in the
APC or MUTYH gene. The aims of this study were (1) to assess the proportion of patients with
an APC-mutation or bi-allelic MUTYH mutations in patients with multiple adenomas and (2) to
identify risk factors that predict the finding of mutations.
Methods. We performed mutation analysis of the APC gene and/or MUTYH gene in a
nationwide cohort of 2151 patients ascertained from Dutch family cancer clinics between 1992
and 2015. The following risk factors of a pathogenic germline mutation were analysed using
logistic regression analysis: cumulative adenoma count, age of CRC diagnosis, age of
adenoma detection, family history for CRC and year of mutation analysis.
Results. The presence of APC mutations increases with adenoma count (adenoma count
between brackets): (0) 2%, (1-9) 1%, (10-19) 1%, (20-49) 8%, (50-99) 12%, (100<) 71%. Biallelic MUTYH-mutations were most common in individuals with 50-99 adenomas: (0) 1%, (19) 3% , (10-19) 2%, (20-49) 7 % , (50-99) 16%, (>100) 7% . Adenoma count and younger age
at adenoma detection were associated with a pathogenic mutation. Family history of CRC was
not a predictive factor. A lower age at CRC diagnosis decreased the odds of finding an APC
mutation (OR: 0.45). The detection rate of APC and bi-allelic MUTYH mutations declines from
54% before 2004 to 14% after 2004.
Discussion. Adenoma count and younger age at adenoma detection are the main predictive
factors of finding a mutation. The mutation detection rate of both MUTYH and APC mutations
was very low in patients with <20 adenomas; APC-mutations were most often found in patients
with >100 adenoma and MUTYH-mutations in those with 50-99 adenomas. Adenoma count is
more important in the selection of patients for germline mutation screening than family history
of CRC. Our findings have an important impact on referral policy.
UNC80 mutations lead to Intellectual Disability with persistent
Hypotonia, Encephalopathy, and Growth Retardation, without true
Facial Dysmorphism
Jan Maarten Cobben.1,18 Asbjorg Stray-Pedersen, 2,3,18 Trine E. Prescott, 4,18 Sora Lee, 5
Chunlei Cang, 5 Kimberly Aranda, 5 Sohnee Ahmed, 6 Marielle Alders, 7 Thorsten Gerstner, 8
Kathinka Aslaksen, 9 Martine Tetreault, 10 Wen Qin, 11 Taila Hartley, 11 Shalini N. Jhangiani,
1,16 Donna M. Munzy, 1,16 Maja Tarailo-Graovac, 12 Clara DM van Karnebeek, 13 Care4Rare
Canada Consortium, Baylor Hopkins Centre for Mendelian Genomics, James R. Lupski,
1,14,15,16 Dejian Ren, 5 Grace Yoon. 6,7
(1)Department of Pediatrics; (7)Department of Clinical Genetics, AMC University Hospital, Amsterdam, the
Netherlands (2)Department of Molecular and Human Genetics; (14)Department of Pediatrics; (15)Department of
Molecular and Human Genetics (16) Human Genome Sequencing Centre, Baylor College of Medicine, Houston,
USA (3)Norwegian National Newborn Screening (4)Department of Medical Genetics, Oslo Univeristy Hospital,
Olso, Norway (5)Department of Biology, Univeristy of Pensylvania, Philadelphia, USA (6)Hospital for Sick
Children; (17)Division of Neurology Univeristy of Toronto, Toronto, Canada (8)Department of Pediatrics,
Sorlandet Hospital, Arendal, Norway (10)Department of Human Genetics, McGill Univeristy, Montreal, Canada
(11)The Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Canada (12)Department of Medical
Genetics; (13)Department of Pediatrics, University of British Columbia, Vancouver, Canada (18) These authors
contributed equally to this work.
[email protected]
UNC80 is a large component of the NALCN sodium-leak channel complex that regulates the
basal excitability of the nervous system. Loss-of-function mutations of NALCN cause infantile
hypotonia with psychomotor retardation and characteristic facies (IHPRF). It appears that
UNC80 mutations are associated with a comparable clinical picture: We report four individuals
from three unrelated families with homozygous missense or compound heterozygous
truncating mutations in UNC80 with persistent hypotonia, encephalopathy, growth failure, and
severe intellectual disability. There appears to be no true facial dysmorphism. HEK293T cells
transfected with an expression plasmid containing the c.5098C>T (p.Pro1700Ser) UNC80
mutation found in one individual showed markedly decreased NALCN channel currents
compared to controls.
Our findings further demonstrate the importance of normal basal ionic conductance
components like UNC80, for normal human neurodevelopment.
Strategy to Knockout Type V Collagen Using the CRISPR-Cas9n
System
Andrea Cordaro 1, Paul Nistor 2, C. Maeve Caldwell 2
1 Medical
2
Student, University of Bristol, Bristol, BS8 1TH, United Kingdom
Regenerative Medicine Laboratory, University of Bristol, Bristol, BS8 1TH, United Kingdom
[email protected]
Clustered, regularly interspaced, short palindromic repeat (CRISPR) RNA-guided nucleases
have recently emerged as powerful gene editing tools with high specificity, efficiency and
simple customization. Ehlers-Danlos syndrome is a connective tissue disease in which
deficiency of type V collagen, a component of extracellular matrix, creates morphologically
abnormal collagen fibrils. We present a strategy using the CRISPR-Cas9 nickase (Cas9n)
system to knockout type V collagen in embryonic and iPS cell lines. The Cas9n mutant is a
more specific system compared to its wildtype Cas9 counterpart. Cas9n effects a doublestranded break at a target genomic locus by requiring two simultaneous single-stranded nicks,
thus minimizing off-target mutagenesis. In this strategy, two Cas9ns each complexed with a
20 nucleotide RNA-guide bind to a complementary locus on exon 2 of the col5A1 gene to
create two single-stranded breaks. The exon 2 target locus contains a TAA stop codon that is
out-of-frame. Therefore, a repair single-stranded oligodeoxynucleotide (ssODN) with
homology arms to the target locus is substituted into the exon by homology directed repair
(HDR), causing the TAA stop codon to become in-frame. This allows for the mRNA construct
to be subject to nonsense-mediated decay, inducing a gene knockout. Gene editing was
focused in exon 2 of col5A1 in one embryonic and two iPS cell lines. Two addgene plasmids
were modified for the expression of cas9n and the insertion of RNA guides and two RNA oligos
were created, complementary to the sense and anti-sense target strands of exon 2. A 54
nucleotide repair ssODN was also constructed, with homology arms flanking the site of
alteration. Results were confirmed by gel electrophoresis and sequencing analysis. This
strategy is important for the study of the molecular mechanism of Ehlers-Danlos syndrome in
vitro and as a model for a broad range of specific gene knockouts.
Selectively targeting TSC1/2 deficient cells by exploiting
endoplasmic reticulum stress
D. Mark. Davies. 1,2 Charlotte E. Johnson 2, Rachel Errington 2, Henry, McCann 2, Julian R.
Sampson 2, Andrew R. Tee 2,
1: Department of Oncology, South Wales Cancer Centre, Singleton Hospital, Swansea SA2 8QA, UK.
2: Institute of Cancer and Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
[email protected]
The mammalian/mechanistic target of rapamycin complex 1(mTORC1) pathway is frequently
hyper-activated in tumours of patients with tuberous sclerosis and in sporadic cancers
mTORC1 regulates many processes, such as cell growth, proliferation, metastasis, autophagy,
metabolism and angiogenesis. Recently, mTOR inhibitors, which normalise aberrant
mTORC1 signalling, have been licensed for the treatment of tuberous sclerosis. However, an
alternative approach to normalising mTORC1 signalling is to exploit abnormal cellular stress
that arises from mTORC1 activation. We have demonstrated that TSC1/2 deficient cells exhibit
abnormal endoplasmic reticulum stress and this can be selectively targeted using a clinically
useable drug, nelfinavir. We have further shown that this selective toxicity can be enhanced
by combing nelfinavir with other drugs that target cell survival mechanisms. These drug
combinations represent potential novel approaches to the treatment of tuberous sclerosis and
other tumour predisposition syndromes characterised by hyper activation of mTORC1
signalling, as well as sporadic cancers.
High yield of causative mutations by whole exome sequencing in
selected individuals with childhood cancer
Illja Diets.1 Marjolijn Jongmans 1,2, Esme Wannders 1, Arjen Mensenkamp 1, Marjolijn Ligtenberg 1,
Eveline Kamping 1, Peter Hoogerbrugge 3, Maran Oldenrode-Berends 4, David Koolen 1, Gijs Santen
5, Dylan Mordaunt 6, Antonis Kattamis 7, Agata Pastorczak 8, Anneke Vulto-van Silfhout 1, Eveline de
Bont 9, Jan Loeffen 10, Roland Kuiper 1, Nicoline Hoogerbrugge 1
1 Department of Human Genetics, Radboud University Medical Centre and Radboud Institute for Molecular Life
Science, Nijmegen, the Netherlands.
2 Department of Medical Genetics, University Medical Centre Utrecht, NL
3 Department of Pediartic Oncology, Princes Maxima Centre, The Bilt, NL.
4 Department of Genetics, University Medical Centre Groningen, Groningen, NL
5 Department of Clinical Genetics, Leiden University Medical Centre, Leiden, NL.
6 Department of Genetics and Molecular Pathology, SA Pathology, Women’s and Children’s Hospital, North
Adelaide, Australia.
7 First Department of Pediatrics, Athens University Medical School, Athens, Greece.
8 Department of Pediatrics, Athens University Medical School, Athens, Greece.
8 Department of Pediactrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland.
9 Department of Pediactric Oncology and Hematology, Beatrix Children’s Hospital, University Medical Centre
Groningen, NL.
10 Department of Pediactric Oncology and Hematology, Sophia Children’s Hospital, Erasmus Medical Centre,
Rotterdam, NL
[email protected]
Childhood cancer predisposition shows extensive genetic heterogeneity with currently over
100 predisposing conditions described and likely many to be identified. Recognition of genetic
predisposition in a child with cancer may lead to better treatment choices and surveillance
options.
We applied whole exome sequencing on germline DNA of children and their parents.
These children were diagnosed with cancer and had at least one of the following features:
intellectual disability (ID) or congenital anomalies, adult type of cancer, a family history for
childhood cancer or multiple primary malignancies. All included cases remained undiagnosed
after consultation by a clinical geneticist and often multiple genetic tests.
Analysis of the first 25 patients resulted in a high yield of causative mutations (Table 1).
Five patients carried mutations in the known cancer genes TP53, DICER1 (n=3) and ETV6. In
three children, exome sequencing revealed syndromes that likely contributed to their
malignancy (EP300 based Rubinstein Taybi syndrome in a girl with AML; ARID1A based Coffin
Siris syndrome and ACTB based Baraitser Winter syndrome in two boys with ALL). In addition,
we identified novel candidate genes for childhood cancer. For instance, in a girl with lymphoma
and congenital anomalies of the kidney (CAKUT) and uterus a de novo E4F1 mutation
(p.Arg90*) was found, which could explain both conditions. E4F1 is a binding partner of
HNF1β, a gene known to be involved in CAKUT. In addition, E4F1 is a key posttranslational
regulator of p53.
Our study shows the value of exome sequencing in the field of childhood cancer
predisposition, both to facilitate the diagnosis of known syndromes as well as to trace novel
genes involved in cancer susceptibility.
Table 1. Results of whole exome sequencing of the first 25 patients
Solved
Strong candidate
gene found
1. ID/congenital anomalies
4
3
2. Multiple primary cancers
2
3
3. Family history
3
2
4. Adult type of cancer
0
1
Total
9
9
No candidate
gene found
4
1
2
0
7
Analysis or
validation ongoing
10
3
6
1
20
Total (%)
21 (46.6)
9 (20)
13 (28.9)
2 (4.4)
45 (100)
SMAD2 Mutations are associated with arterial aneurysms
and dissections
Dimitra Micha 1, Dong-chuan Guo 2, Yvonne Hilhorst-Hofstee 3, Fop van Kooten 4, Dian
Atmaja 1,5, Eline Overwater 1,6, Ferdy K. Cayami 1,5, Ellen S. Regalado 2, Jiddeke M. van de
Kamp 1, Rene van Uffelen 7, Hanka Venselaar 8, Sultana M.H. Faradz 5, Gerrit Vriend 8,
Marjan M. Weiss 1, Erik A. Sistermans 1, Alessandra Maugeri 1, Dianna M. Milewicz 2,
Gerard Pals 1, Fleur S. van Dijk 1,9,10
1 Department of Clinical Genetics, Centre for Connective Tissue Research, VU University Medical Centre, P.O.
Box 7057, 1007 MB Amsterdam, NL.
2 Department of Internal Medicine, University of Texas Health Science Centre at Houston, Houston, Texas, USA.
3 Department of Clinical Genetics, Leiden University Medical Centre, PO Box 9600 2300 RC, Leiden, NL
4 Department of Neurology, Erasmus Medical Centre, PO Box 2040, 3000 CA, Rotterdam, NL.
5 Centre for Biomedical Research, Faculty of Medicine, Diponegoro University Jln Prof H Soedarto, P.O. Box
1269, Semarang, Central Java, Indonesia.
6 Department for Clinical Genetics, Academic Medical Centre, P.O. Box 22660, 1100 DD, AmsterdamNL
7 Department for Respiratory Medicine, Albert Schweitzer Hospital, 3318 AT Dordrecht, NL
8 Centre for Molecular and Bimolecular Genetics (CMBI), P.O. Box 9101, 6500 HB, Nijmegen, NL
*Correspondence: [email protected]
9 Department of Clinical Genetics, University Medical Centre Groningen, P.O. Box 30.001, Groningen, NL
10 North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Harrow, UK.
[email protected]
We report three families with arterial aneurysms and dissections in which variants predicted to
be pathogenic were identified in SMAD2. Moreover, one variant occurred de novo in a proband
with unaffected parents. Recently, a fourth variant was identified. SMAD2 is a strong candidate
gene for arterial aneurysms and dissections given its role in the TGF-β signaling pathway.
Furthermore, although SMAD2 and SMAD3 probably have functionally distinct roles in cell
signaling, they are structurally very similar. Our findings indicate that SMAD2 mutations are
associated with arterial aneurysms and dissections and are in accordance with the observation
that patients with pathogenic variants in genes encoding proteins involved in the TGF-β
signaling pathway exhibit arterial aneurysms and dissections as key features.
Characterising STAT3 signaling as a therapeutic target for
vascularized tumours and Tuberous sclerosis
K.M. Dodd, E. Rad, N.T.F Green, A.R. Tee
Cancer and Genetics, Institute of Medical Genetics, Heath Park, Cardiff, CF14 4XN, UK.
[email protected]
Tuberous sclerosis (TSC) is a rare inherited tumour-predisposition disorder affecting
approximately 1 in 10,000 live births. Mutation to either the TSC1 or TSC2 genes results in the
development of benign tumours in multiple organ systems. The tumours which present with
TSC are heavily vascularized due to constitutive activation of the mammalian target of
rapamycin signaling (mTOR) pathway. Cell line models for TSC therefore provide a useful
model for studying the process of tumour angiogenesis and the mTORC1 signalling pathway,
which is thought to be upregulated in a number of sporadic cancers as well as TSC.
We utilize cell line models for TSC to investigate key signaling mechanisms driving the activity
of HIF-1α, a hypoxia induced transcription factor which promotes vascularization, increased
glucose metabolism, metastasis and cell survival. Elevation of HIF is reported in a number of
different cancer cell types, and is downstream of several tumour suppressors and oncogenes,
making it an appealing therapeutic target for both a number of sporadic cancers and TSC.
We demonstrate that inhibition of STAT3 with the curcumin analogue FLLL31 can block the
migration of TSC associated (AML) angiomyolipoma-derived cell lines, this inhibition is further
enhanced by co-treatment with the mTOR kinase inhibitor KU-0063794, indicating that STAT3
drives migration of these cells via mTOR-dependent and -independent mechanisms.
Furthermore, knockdown of STAT3 in these AML-derived cells also significantly reduced
average tumour spheroid volume in soft agar.
Further investigation into this signalling pathway has revealed that the transcription factor NfkB is also upregulated in TSC2-/- cell lines and is driving STAT3 activity in this setting. Our
results demonstrate that TSC-loss induces expression of a network of transcription factors
promoting tumour growth, including STAT3, Nf-KB and HIF-1α.
Our data indicates that targeting NF-kB/STAT3 in combination with mTORC1 may enhance
the anti-tumourigenic efficacy of rapalogues currently utilised in cancer therapy.
To demonstrate the wider implications of this work, we replicated this work in cell line models
for neurofibromatosis type 1 (NF-1). Results indicate that STAT3 knockdown or inhibition with
FLLL31 can block cell migration and invasion, as well as tumour spheroid formation of cell
lines derived from NF-1 associated malignant peripheral nerve sheath tumours (MPNSTs).
This work indicates that STAT3 may be an appealing therapeutic target for a wide range of
tumour types.
Understanding mechanisms behind renal cancer development
E.A.Dunlop 1, M. Naven 2, S. Rundel 1,2, K. Ashelford 2, S. Edkins 2, J.R. Sampson 1, A.R.
Tee 1.
1 Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
2 Wales Gene Park, Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
[email protected]
The genetic condition, Birt-Hogg-Dubé (BHD) Syndrome is characterised by the development
of fibrofolliculomas, lung cysts and renal cancer. Renal cancer is the most life-threatening
manifestation of BHD syndrome and is estimated to affect up to one third of BHD patients. In
contrast to other monogenic disorders which cause renal cancer, the renal tumours associated
with BHD syndrome are histologically diverse, with chromophobe, hybrid
chromophobe/oncocytoma, clear cell, oncocytoma and papillary subtypes all observed. The
average age of onset of renal cancer in BHD patients is 50 years (Shuch et al., 2014), over 13
years younger than the average onset of sporadic renal cancer.
Folliculin (FLCN) is the tumour suppressor gene responsible for BHD syndrome. We have
previously shown that loss of FLCN results in PGC-1α-mediated mitochondrial biogenesis and
increased ROS production (Yan et al., 2014). We hypothesise that renal cancer development
occurs earlier in BHD patients than in the general population due to accelerated genetic
damage which may be in part due to elevated levels of ROS caused by loss of FLCN function.
The random nature of the increased genetic damage, increased genetic instability or
decreased DNA repair occurring in FLCN-deficient cells could account for the different
histological tumour subtypes observed in BHD patients.
As it takes time for these genetic changes to occur and renal cancer to develop in BHD
patients, we wanted to investigate how the genetic landscape of FLCN-deficient cells alters
over time. We monitored FLCN-expressing and –deficient human kidney cells immediately
following FLCN-knockdown and following one year of continuous tissue culture. We then
assessed these cells for alterations in DNA damage markers by western blotting and for
changes in gene expression through RNAseq using next generation sequencing technology.
We found that after one year in culture, FLCN-deficient cells harbour elevated levels of DNA
damage compared to control cells. They also exhibit a markedly different gene expression
profile. We observe gene expression changes previously linked to FLCN loss, such as
are over-represented in the dataset, which fits with the reported role of FLCN in cell-cell
adhesion. Further analysis of the genetic changes observed following long-term FLCN
knockdown will give us a better understanding of mechanisms underlying renal cancer
development.
Prostate cancer genome-wide association study from 89,000 men
using the OncoArray chip identifies more than 30 novel prostate
cancer susceptibility loci.
Rosalind A. Eeles 1. Fredrick R. Schumacher 2, Ali A. Al Olama 3, Sonja I. Berndt 4, Fredrik
Wikland 5, David V. Conti 2, Mahbubl Ahmed 1, Sara Benlloch 3, Kenneth Muir 6, Artitaya
Lophatananon 6, Douglas F. Easton 3, Peter Kraft 7, Stephen J. Chanock 4, Brian E.
Henderson 2, Zsofia Kote-Jarai 1, Christopher A. Haiman 2. On Behalf of the Elucidating Loci
Involved in Prostate Cancer Susceptibility (ELLIPSE), Prostate Cancer Assoccation Group to
Investigate Cancer Associated Alterations (PRACTICAL), Cancer of the Prostate in Sweden
(CAPS), Breast and Prostate Cancer Cohort Consortium (BPC3) and Prostate Cancer
Genome-wide Association Study of Uncommon Susceptibility loci (PEGASUS)
1 The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK.
2 University of South California, USA.
3 University of Cambridge, UK.
4 NIH, USA.
5 Karolinska, Stockholm, Sweden.
6 University of Manchester, UK.
7 University of Harvard, USA.
[email protected]
Genome-wide association studies (GWAS) and fine-mapping efforts have identified 112 loci
associated with prostate cancer susceptibility to date. Combined multiplicatively, these loci
explain 33% of the familial relative risk for prostate cancer among populations of European
ancestry. In order to identify novel prostate cancer susceptibility loci we conducted a GWAS
involving 53,000 prostate cancer cases and 36,000 controls using the OncoArray that includes
a 260K GWAS backbone and a custom portion of 310K SNPs developed from previous GWAS
and fine-mapping studies of multiple cancer types (http://epi.grants.cancer.gov/oncoarray/).
Following standard quality control procedures, the prostate cancer OncoArray genotyped data
were imputed using the October 2014 release of the 1000 genomes project data as a reference
and analysed by participating study for overall and advanced prostate cancer using logistic
regression. The study-specific results were combined using inverse variance fixed effect metaanalysis. Regions surrounding previously associated variants (+/- 500kb of the reported index
variant) were excluded to identify novel associations. In the OncoArray meta-analysis, we
identified more than 30 novel loci significantly associated (P<5.0x10-8) with overall prostate
cancer risk, including loci associated with advanced (Gleason ≥8, death from prostate cancer,
PSA>100, or disease stage “Distant – outside the pelvis”), or early-onset (≤55 years of age)
prostate cancer. These results provide further insight into the underlying mechanisms of
prostate cancer carcinogenesis and will improve the utility of genetic risk scores for targeted
screening and prostate cancer prevention. It is expected that these results combined with fine
mapping analyses will yield a genetic profile of about 150 SNPs for large scale genotyping in
such translational studies in 2016.
Use of multiple SNP testing to predict breast cancer risk in a
familial screening clinic
D.G. Evans *1,2, A. Brentnall *3, H. Byers 2, E. Harkness 1, P. Stavrinos 2, A. Howell 1, W.
Newman 1, J. Cuzick 3.
1 Genesis Breast Cancer Prevention Centre and Nightingale Breast Screening Centre, Univeristy Hospital of
South Manchester, Southmoor Road, Wythenshawe, Manchester, M23 9LT, UK.
2 Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, University of
Manchester and Central Manchester Foundation Trust, Manchester, M13 9WL. UK.
3 Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London,
London, EC1M 6BQ, UK.
[email protected]
Introduction: Familial-risk clinics have been set up across the developed world to offer
intensive screening and preventive strategies. Whilst genetic testing for BRCA1/2 provides
important risk information for a minority of women, use of common genetic variants associated
with variation in breast cancer risk has not yet been implemented but may have relevance to
a much larger number of women.
Methods: A case-control study was designed to assess the effects of the first 18 single
nucleotide polymorphisms identified through genome wide association studies on breast
cancer incidence. Pre-defined polygenic risk scores for the general population (SNP18),
BRCA1 (SNP3) and BRCA2 carriers (SNP13) were obtained by multiplying normalised risk
estimates for each allele to provide an overall score. The observed / expected odds of breast
cancer was estimated by logistic regression and discrimination was measured by the area
under the receiver operating characteristic (AUC). A prospective sub-sample was used to
assess women without breast cancer at entry to the clinic, and analysis of the non-BRCA
carriers was also tested after adjustment for expected absolute risk from the Tyrer-Cuzick
model.
Results. SNP18 genotyping was performed in 2,055 samples including 451 women with breast
cancer (364 prospective). SNP18 was a predictor in the non-BRCA1/2 group (inter-quartile
range odds ratio 1.55 (95%CI 1.30-1.87), AUC 0.59 (0.55-0.62), O/E 96%). The risk ratio from
upper to lower quintile of polygenic risk score was 2.1 fold. Findings were similar for women in
the prospective sub-sample, and unaffected by adjustment for risk from classical risk factors.
There was some evidence to support the use of SNP3 (BRCA1 carriers, AUC 0.62 (95%CI
0.55 – 0.70)) and SNP12 (BRCA2 carriers, AUC 0.55 (0.48-0.62)), but the general population
weights in SNP18 performed worse for these groups (BRCA1 AUC 0.52 (0.44–0.59), BRCA2
AUC 0.53 (0.45- 0.60)).
Conclusion SNP18 is ready to be used to refine risk assessment for women already at
increased risk due to their family history, without BRCA1/2 mutations. Different weightings are
required for women with BRCA1/2 mutations.
A network analysis of genes with de novo mutations in
polymicrogyria patients
Katherine A. Fawcett 1, David Sims 1, Thomas Cushion 2, Daniela T. Pilz 2,3,
Andrew E. Fry 2,4.
1 MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department
of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK.
2 Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN.
3 Clinical Genetics, West of Scotland Genetic Services, Queen Elizabeth University Hospital, 1345 Govan Road,
Glasgow, G51 4TF.
5 Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
[email protected]
Polymicrogyria (PMG) is a clinically and genetically heterogeneous malformation of cortical
development characterised by excessive small gyri and disruption of normal cortical layering.
In recent years a range of single gene and chromosomal disorders have been identified in
PMG patients. This has led to improved knowledge of the disease and the biological pathways
underlying normal brain development. However, in the majority of cases the cause of PMG
is still unknown. We exome sequenced 57 parent-offspring trios (PMG patients and their
unaffected parents) and identified 68 de novo variants, of which six were in known
polymicrogyria genes. We assessed whether the de novo variants hit genes demonstrating
higher than expected levels of mutational constraint within healthy human populations. We
also exploited gene networks constructed using gene annotation, gene co-expression and
protein-protein interaction datasets to examine the connectivity between these genes and
known PMG genes. We found that genes in which the de novo variants resided were enriched
for constrained genes (genes that carry fewer-than-expected missense variants in a control
population). Furthermore, genes carrying de novo variants in PMG patients were more
connected to each other within gene networks than would be expected by chance. Novel genes
carrying predicted deleterious de novo variants were significantly clustered within the
networks. Moreover, a subset of the candidate genes were individually more connected to
known PMG genes than expected by chance. We found that, after excluding pathogenic
mutations in known PMG genes, there remained a trend towards enrichment of constrained
genes suggesting that further genes causing PMG remain to be identified. However, the
paucity of genes hit in multiple patients in our exome data is further evidence that PMG is a
genetically heterogeneous disorder. Sequencing of additional patient cohorts and/or analysis
of variants in relevant functional models will be necessary to confirm a causative role for the
novel variants identified in our study.
Visualising phenotypic and genomic relationships with DECIPHER
– A community endeavour to map the Clinical Genome
Firth HV, Bevan AP, Brent S, Hutton B, Perrett D, Swaminathan G, Wright CF, Hurles, ME.
1Wellcome
2
Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA UK
Dept of Medical Genetics, Cambridge University Hospitals Foundation Trust, Cambridge CB2 2QQ UK
[email protected]
DECIPHER (http:///decipher.sanger.ac.uk) was established in 2004 to serve the genetics
community and has grown to become a major global platform for the visualization of phenotypic
and genomic relationships. DECIPHER is unique in displaying all scales of genomic variation,
from single base pair to megabases is size, in a single interface and has now developed an
exciting visualisation of phenotypic relationships.
DECIPHER promotes flexible data-sharing; it enables the extent of sharing to be tailored so
that it is proportionate to the clinical or scientific need to facilitate diagnosis or discovery.
DECIPHER is a global community with 242 projects (9 in the Netherlands and 70 in the UK).
There are 6 consortia within DECIPHER enabling more limited sharing (including the DDD
consortium linking all 23 UK Clinical Genetics services and the NHS consortium). More than
32,000 patient records are shared via consortia, including >110,000 phenotypes and their
associated genomic variants. There are >18,500 patient records with open-access consent
that are searchable via the openly available search engine on the homepage that enables
searching of phenotype terms and genomic coordinates using single terms or more advanced
searches. Search is customized and for logged-in users will also include any data in project or
consortia of which they are members. Since its inception, DECIPHER has facilitated more than
900 publications in the peer-reviewed scientific literature.
DECIPHER has facilitated key exchanges between UK and Dutch clinical geneticists enabling
closer interaction between the two communities. Over recent years, DECIPHER has widened
its remit from developmental disorders to Rare Disease, including hereditary cancer.
DECIPHER is a pioneering partner in the Global Alliance for Global Health (GA4GH) initiative
and has been driving development of the Matchmaker exchange Application Programming
Interface (API) enabling a query initiated in DECIPHER to also search connected databases
(currently PhenomeCentral and GeneMatcher).
A major development in DECIPHER for 2016 is the Phenotype browser built using Human
Phenotype Ontology (HPO) terms enabling the relationship between phenotypes, genes and
genomic variants to be explored and analysed computationally and the rich patient resource
in DECIPHER to be visualised and queried from both a phenotypic and genomic perspective.
A demonstration will be given during the presentation.
The Development of a Clinical Screening Instrument for Tumor
Predisposition Syndromes in Childhood Cancer Patients: protocol
for a prospective, observational, multi-center study (TuPS)
Saskia M.J. Hopman 1,2, Floor A.M. Postema 2, Corianne A.J.M de Borgie 3, Johannes H.M.
Merks 2, Raoul C.M. Hennekam 4.
1 Department of Genetics, University Medical Centre Utrecht, the Netherlands
2 Department of Pediatric Oncology, Emma Children’s Hospital/ Academic Medical Centre Amsterdam, the Netherlands
3 Clinical Research Unit, Clinical Methodology, University of Amsterdam, the Netherlands
4 Department of Pediatrics, Emma Children’s Hospital/ Academic Medical Centre, Amsterdam, the Netherlands
[email protected]
Background
Identification of a tumor predisposition syndrome (TPS) in patients who have cancer in
childhood is paramount for optimal care. A screening instrument may serve as a standard
screen for genetic counselling. It can guarantee that in each child with cancer the presence of
a TPS is considered. Such a screening instrument should be based on the manifestations of
known TPS. We have developed a screening instrument consisting of 2D and 3D picture series
and a screening form for manifestations not visible in the picture series1. The screening
instrument can be completed by a research nurse, genetic counsellor or treating physician and
remotely reviewed by a clinical geneticist.
Here we describe the protocol for the TuPS study, a prospective multi-center study for
validation of the screening instrument.
Aim
1: To assess prospectively the clinical validity (focusing on sensitivity) of an observational
screening instrument for tumor predisposition syndromes in childhood cancer patients.
2: To use 3D facial analyses in childhood cancer patients to identify additional (patterns of)
morphological abnormalities with predictive value to improve the screening instrument.
Outcome measurements
For aim 1, the primary outcome measurement in the assessment of the screening instrument
will be sensitivity. A sensitivity of 94% or higher will be considered as clinically relevant. The
secondary outcome measurements are the specificity, positive predictive value, negative
predictive value, the inter-observer variability and the separate contribution of all aspects of
the tool separately to the decision of the clinical geneticist when assessing the tool. For aim 2
the outcome measurement will be positive predictive value of individual morphological
abnormalities and their weight within the overall assessment of the instrument.
Methodology and design
All children newly diagnosed with a childhood cancer in the Netherlands within a period of 2
years (sample size 1000 patients) will be evaluated by two clinical geneticists using the
screening instrument. Children with a positive screening result (suspected for a TPS) will follow
regular clinical genetic diagnostics. From the series of patients with a negative screening result
(not suspected for a TPS), a random sample of patients will be assigned to additional full
clinical genetic evaluation in order to determine false negatives.
1:
Hopman et al. Eur J Cancer. 2013 Oct;49(15):3247-54
Remark: the development of the screening instrument was submitted as an abstract and selected for a poster for
the UK-NL joint meeting 2014.
NF1 genetic testing: where have we got to?
D.G. Evans 1,2, N. Bowers 2, E. Burkitt-Wright 2, S. Garg 2, V. Scott-Kitching 2, M. PenmanSplitt 3, A. Dobbie 4, E. Howard 2, J. Ealing 2, G. Vassalo 2, A.J. Wallace 2, Northern UK NF1
Research Network, S.M. Huson 2
1 Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester Academic Health Sciences Centre (MAHSC),
Institute of Human Development, University of Manchester; 2 Neurofibromatosis Centre, Manchester Centre for Genomic
Medicine, St Mary’s Hospital, Central Manchester University Hospital NHS Foundation Trust Manchester, M13 9WL, UK; 3
Northern Genetic Service, Centre for Life, Newcastle; 4 Yorkshire Genetic Service, Chapel Allerton Hospital, Leeds.
[email protected]
Introduction – The NHS has commissioned a national complex NF1 service since 2009. As
part of the service we provide an RNA based mutation analysis for NF1, a DNA based analysis
for SPRED1 and melanocyte/schwann cell culture to assist in counseling mosaic patients. We
present the outcomes of testing and discuss their implications for future practice.
Methods – The RNA based technique used was that developed by Messiaen and colleagues
(Human Mutation 2000; 15:541-5).The outcome of testing of individuals from 04/09 to 12/15
were analyzed. Mutation detection rates depending on family history and clinical presentation
(whether they met NIH diagnostic criteria or had a pigmentary phenotype) were compared.
Statistical anaslysis was carried out using chi square testing with two tailed Fisher’s exact test.
Results- RNA analysis was carried out on 361 NF1 affected individuals who fulfilled NIH
criteria with at least one non pigmentary criterion. Potentially causative variants in the NF1
gene were identified in 166/171 (97.08%-95% CI 94.56-99.6%) of familial cases compared to
182/190 (95.8%-95% CI 92.93-98.65%) of sporadic samples (p=0.58). A total of 41/348
(11.8%) of samples had mutations only classifiable with RNA analysis. Of the thirteen cases
with no identified mutation two had a dysembryoplastic neuroepithelial tumour (DNET)
identified on MRI of the brain both associated with epilepsy. The presence of DNET in 2/13
(15%) negative screens versus 2/348 (0.6% -Relative Risk of 0.004) with mutations is highly
significant (p=0.007).44/71 individuals (62%) aged <20 with 6+ CAL and no non pigmentary
NF1 criterion had an RNA sample assessed. Six of this group (10.5%) had SPRED1 mutations.
Missense mutations in the NF1 gene were found more frequently than SPRED1 mutations in
patients with pigmentary only phenotypes regardless of family history. Furthermore the
mutation type was significantly different in those with pigmentary only phenotypes with 76.5%
(13/17 in this analysis) of cases having non-truncating mutations compared with only 13.6%
(17/125) of cases with neurofibromas. Six individuals with mosaic NF1 and negative analysis
on lymphocytes have undergone biopsy of CAL patches, five for genetic counselling and one
for diagnostic purposes. The causative mutation has been found in 3/3 where results are
available at time of submission. In exceptional cases, clinical assessment challenged the initial
laboratory report and was correct.
Conclusion – RNA based testing has proven to be more specific and sensitive than DNA
based techniques. The detection rate in sporadic and familial cases was similar- the only
mosaic cases detected all had a segmental phenotype. Using the detection rates reported
here, a normal RNA based test gives only a 1/9 likelihood of still having NF1 compared with a
1/6 chance using DNA based NF1 testing. The improved detection of RNA based techniques
combined with increasing clinical indications (clinically relevant genotype-phenotype
correlation, cord blood testing vs. clinical follow-up to allow early diagnosis of affected
individuals, PGD and free foetal DNA testing for pregnancies with affected Fathers) mean we
offer mutation testing to all newly diagnosed individuals and families with no previous mutation
analysis.
Experience of participation in a therapeutic drug trial for neonatal
patients with X-linked Hypohidrotic Ectodermal Dysplasia (XLHED)
A.Kamath 1 ,I. Tully 1, P. Kandaswamy 2, N. Thomas 2, K. Burke 2, A. Clarke 1,3
1 Institute of Medical Genetics, University Hospital of Wales, CF14 4PY, UK
2 Department of Paediatrics, University Hospital of Wales, CF14 4PY, UK
3 Cardiff University, Cardiff, CF10 3XQ, UK
[email protected]
Background:
X-linked Hypohidrotic Ectodermal Dysplasia (XLHED), the most common ectodermal dysplasia
is caused by Ectodysplasin A (EDA) gene mutations. The EDA Receptor (EDAR) binds
specifically the A1 isoform of EDA (EDA-A1) for signal transmission.1 Affected males present
with abnormalities of the skin, teeth, hair and secretory glands.
Methods:
A phase two, open-label trial has recruited ten cases to assess the safety, pharmacokinetics
and immunogenicity of postnatal administration of EDI200. This is a fully humanized EDA-A1
replacement molecule, linked to a human IgG/Fc sequence. Male infants, recruited between
48 hours and 14 days of age, with a genetically confirmed diagnosis of XLHED, are eligible to
receive five doses over 14 days. We report on the experience of recruiting and treating two
neonatal patients out of ten (globally).
Both at-risk males were identified antenatally, following confirmation of maternal carrier status,
conferring 50% risk. The infants were admitted to the Children’s Hospital at about one week of
age for a 21-day period, following confirmation of the genetic diagnosis.
The treatment was administered in 5 doses. Blood, urine tests and skin biopsies were taken
to monitor the effects of the treatment. Immunogenicity and pharmacokinetics were measured
after the first and final doses. Clinical reviews including ophthalmology, dermatology and
neurodevelopmental assessments were undertaken.
Results:
There were no apparent complications from the treatment in either patient. Both patients are
being followed-up according to the protocol.
Discussion:
In utero administration of the preparation has shown promising outcomes in animal models.2
Therefore, the next step, which may be more effective at ameliorating the effects of this
condition, would be to attempt prenatal therapy if there are no apparent ill effects of the
treatment in human neonates.
REFERENCES
1. YanM,WangLC, Hymowitz SG, Schilbach S, Lee J, Goddard A, de VosAM, Gao WQ, Dixit VM. 2000. Two-amino acid
molecular switch in an epithelial morphogen that regulates binding to two distinct receptors. Science 290:523–527.
2. Gaide O, Schneider P. 2003. Permanent correction of an inherited ectodermal dysplasia with recombinant EDA. Nature
Medicine 9 (5): 614-618
Technological innovation in hereditary cancer risk assessment
A.Kulkarni 1, A. Kenney 2, V. Tripathi 1, C. Compton 1, S. Rose 1, E. Haque 1, L. Izatt 1,
D. Ruddy 1, E. Clement 1, A. Shaw 1
1 Guy’s Regional Genetics Service, Guy’s Hospital, London, SE1 9RT, England
2 UBQO Limited, London, SW4 0AL, England
[email protected]
Guy’s Cancer Genetics guidelines are used across Southeast London, Kent & East Sussex
and updated in line with national standards. However they are currently presented in ‘noninteractive’ 'pdf' format that is not always readily accessible. It is also difficult to ensure
clinicians are using the most recent version of the guidelines.
The Cancer Genetics application (App), developed by Guy’s Clinical Genetics department and
UBQO with funding from Guy’s and St Thomas’ Charity, provides streamlined hereditary
cancer risk assessment and referral guidance for clinicians.
The aim is to address inequity in referrals and improve patient access to our service by
targeting several key factors, including clinicians’ limited understanding of hereditary cancer,
lack of time, confusion about where to refer patients and use of outdated guidance.
The App contains a risk assessment tool and succinct reference guide, enabling clinicians to
easily decide who requires genetic assessment of their cancer risk and who can be managed
in primary or secondary care. Patients thereby have quicker access to cancer surveillance,
genetic counselling, pharmaco-prevention and surgical options.
Cancer Genetics is freely available on iOS and android platforms and via a public website. It
is certified as a Class 1 medical device and a secure content management system allows quick
central updates.
We will present the development process, user feedback and integration of the App into
primary and secondary care. Our goal is that Cancer Genetics will promote timely, evidencebased management of those at risk of hereditary cancer.
Informing family members in hereditary tumour syndromes
Fred H. Menko, Annelien L. Bredenoord, Imke Christiaans, Lutgarde C.P. Govaerts,
Marjolein Kriek, Mere C. van Maarle, Renske Oegema, M. Corrette Ploem, Fleur Vansenne,
Margreet G. Ausems, Frederik J. Hes, Suzanna G.M. Frints, Jasper J. van der Smagt
Correspondence: Fred H. Menko, clinical geneticist, Family Cancer Clinic, Antoni van Leeuwenhoek, Netherlands
Cancer Institute, Amsterdam, the Netherlands
[email protected]
National and international guidelines have been set up on informing at-risk relatives in families
with hereditary tumour syndromes. However, unfortunately, in clinical practice relatives not
rarely present with symptomatic cancer since they were either not informed or refrained from
DNA testing and surveillance.
In the Netherlands, in 2015, a front-page newspaper item on this issue has led to public interest
in our ongoing debate with patient advocate organisations on current guidelines, the duties of
patients and geneticists and the pros and cons of contacting family members initiated by the
clinical genetics centres. In addition, the compilation of pedigrees and family data bases is a
subject of debate, since under current Dutch legislation the family members involved might
have a right to be informed that their personal data have been registered.
Several ongoing projects are aimed at improving the procedure in which probands inform their
relatives. In addition, it is a matter of debate if genetics centres could take on a proactive role
and directly contact relatives at risk of disease. A new form of organisation would be needed
if such a proactive role would seem to be the best way to proceed.
The issue is pressing due to the changing landscape of DNA diagnostics with an expected
increase in DNA testing due to next generation sequencing and testing for the purpose of
treatment decisions.
We discuss legal, ethical and social issues of informing at-risk relatives and the option of
research projects aimed at the evaluation of various models suitable for implementation in
clinical practice.
Heterozygous KIDINS220/ARMS nonsense variants cause spastic
paraplegia, intellectual disability, nystagmus, and obesity
Dragana Josifova 1, Glen Monroe 2, Federico Tessedori 2,7*, Esther de Graaff 3, Bert van der
Zwaag 2, Sarju Mehta 4, The DDD Study 5, Magdalena Harakalova 2, Karen Duran 2, Sanne
Savelberg 2, Ies Nijman 3, Heinz Jungbluth 6, Casper Hoogenraad 3, Jeroen Bakkers 7,9, Nine
Knoers 2, Helen Firth 4,5, Phil Beales 8, Gijs van Haaften 2**, Mieke van Haelst 2**#
1 Department of Clinical Genetics, Guys’ and St Thomas’ Hospital, London SE1 7EH, UK.
2 Department of Medical Genetics and Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht
3584 CX, NL
3 Division of Cell Biology, Faculty of Science, University of Utrecht 3584 CH, NL
4 Department of Clinical Genetics, Cambridge University NHS Foundation Trust, Addenbrooke’s Hospital,
Cambridge CB2 0QQ
5 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1RQ, UK.
6 Department of Paediatric Neurolog, Evelina Children’s Hospital, Guys’ and St Thomas’ Hospital NHS
Foundation Trust, London SE1 7EH, UK; Randall Division of Cell and Molecular Biophysics, Muscle Signaling
Section, and Department of Basic and Clinical Neuroscience, IoPPN, King’s College, London, WC1N 1EH, UK.
7 Hubrecht Institute-KNAW and University Medical Centre Utrecht, Utrecht 3584 CT, NL
8 Genetics and Genomes Medicine Program, UCL Institute of Child Health, London WC1N 1EH, UK.
9 Department of Medical Physiology, University Medical Centre Utrecht, Utrecht 3584 CX, NL
*/** The authors wish it to be known that, in their opinion, the first three authors and the last two authors should be
regarded as joint authors.
# Corresponding author: Mieke M. van Haelst – [email protected]
[email protected]
We identified de novo nonsense variants in KIDINS220/ARMS in three unrelated patients with
spastic paraplegia, intellectual deficit, nystagmus, and obesity. KIDINS220 (Kinase D
ineracting substrate of 220 kDa), also known as ARMS (Ankyrin Repeat-rich Membrane
Spanning) is an essential scaffold protein coordinating neurotrophin signal pathways in
neurites and controls axonal and dendritic maturation. The spatiotemporal expression of
different KIDINS220 isoforms is finely tuned in the mammalian brain, and knockout Kidins220
animals show developmental central nervous system anomalies.
Molecular analysis of patients’ variants confirmed expression and translation of truncated
transcripts. These transcripts are similar to recently characterized alternative terminal exon
splice isoforms of KIDINS220 that function in a dominant negative manner on full-length (wildtype) KIDINS220 by aberrant localization in intracellular puncta in the cell body instead of
neurite tips. In Zebrafish, functional tissue-specific expression studies in motor neurons using
the wild-type or p.(Trp1350*) variant resulted in spasms.This was more evident in embryos
expressing the mutant KIDINS220, confirming a functional link between spasticity and
disruption of KIDINS220 levels and/or function.
Our patients manifest similarities with MOMO Syndrome (Macrosomia, Obesity, Macrocephaly
and Ocular abnormalities; OMIM 157980), however prenatal ventricular dilatation and spastic
paraplegia are not features of this condition. KIDINS220 Sanger sequencing of ten MOMO
patients did not yield any variants. We therefore suggest that our patients have a distinct
syndrome characterized by Spastic paraplegia, Intellectual disability, Nystagmus and Obesity
(SINO).
In conclusion, we show here that de novo heterozygous truncating KIDINS220 variants cause
SINO syndrome. This is the first report of KIDINS220 variants causing a human disease.
Classification and clinical management of Variants of Uncertain
Significance in high penetrance cancer predisposition genes
S. Moghadasi 1, D.M. Eccles 2, P. Devilee 3, M.P.G. Vreeswijk 3, C.J. Asperen 1
1 Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2333ZA, the Netherlands
2 Faculty of Medicine, University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital,
Southampton, SO16 5YA, UK.
3 Department of Human Genetics, Leiden University Medical Centre, Leiden, 2333ZC, the Netherlands.
[email protected]
In 2008, the International Agency for Research on Cancer (IARC) proposed a system for
classifying sequence variants in highly penetrant breast and colon cancer susceptibility genes,
linked to clinical actions. This system uses a multifactorial likelihood model (MLM) to calculate
the posterior probability that an altered DNA sequence is pathogenic. Variants between 5%94•9% are categorized as variants of uncertain significance (VUS) (class 3). This interval is
wide and includes variants with a substantial difference in pathogenicity. We think that carriers
of class 3 variants would benefit from a fine-tuning of this classification.
To improve the clinical utility of the current classification system, we suggest a pragmatic
adaptation to clinical practice. Our suggestion is that the laboratory specialists divide VUS
class 3 into two subgroups: class 3A with a posterior probability of 0•05 to 0•499 and class 3B
with a posterior probability of 0•5-0•949. We propose to communicate and test family members
when the posterior probability of pathogenicity of a VUS is higher than 0•5 (i.e. category 3B)
but no communication of variants in class 3A unless there is clinical benefit for counselee or
for research.
The purpose of the recommendations is to improve the clinical management of the counselees
by a more precise classification of the variants without causing unnecessary stress for the
counselees or additional costs for the health care system, while minimizing the risk of missing
pathogenic mutations in clinical practice.
Our recommendations for classification and communication of the variants:
Class
Posterior probability
Description
Our suggestion for communication with
counselees
Class 1
<0·001
Clearly not
pathogenic
Do not communicate
Class 2
0·001-0·049
Unlikely to be
pathogenic
Class
3A
Class
3B
0·05-0·499
0·050·949
Class 3
Class 4
0·95-0·99
Class 5
>0·99
VUS
0·5-0·949
Do not communicate
(unless there is clinical benefit for counselee or
for research)
Do NOT communicate
(unless there is clinical benefit for
counselee or for research)
Do communicate
Likely to be
pathogenic
Clearly
pathogenic
Do communicate
Do communicate
De novo loss of function mutations in USP9X cause a female
specific recognizable syndrome with developmental delay and
distinct congenital malformations
Margot R.F. Reijnders 1,21, Vasilio Zachariadis 2,21, Brooke Latour 1,3,21, Lachlan Jolly 4,21, Grazia M.
Mancini 5, Rolph Pfundt 1, Ka Man Wu 1, Conny M.A. Van Ravenswaaji-Arts 6, Hermine E. VeenstraKnol 6, Britt-Marie M. Anderlid 2,7, Stephen A. Wood 8, Sau Wei Cheung 9, Angela Barnicoat 10, Frank
Probst 9, Pilar Magoulas 9, Sue Price 13, Alice S. Brooks 5, Helena Malmgren 2,7, Arja Harila-Saari 11,
Carlo M. Marcelis 1, Maaike Vreeburg 12, Emma Hobson 13, V. Reid Sutton 9, Zornitza Stark 14, Julie
Vogt 15, Nicola Cooper 16, Jiin Ying LIM 17, Angeline Hwei Meeng LAI 17, Deepti Domingo 18, Bruno
Reversade 19, The DDD Study, Jozef Gecz 4, Christian Gilissen 1, Han G. Brunner 1,12, Usha Kini 20,
22, Ronald Roepman 1, 22*, Ann Nordgren 2, 7, 22, Tjitske Kleefstra 1, 22*.
1 Dept of Human Genetics, Radboud University Medical Centre, 6500 HB Nijmegen, NL.
2 Dept of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institute, 171 76 Stockholm, Sweden.
3 Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre 6500 HB Nijmegen, NL.
4 Neurogenetics, School of Medicine and the Robinson Research Institute, SA 5006 the University of Adelaide, Australia.
5 Dept of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, NL.
6 University of Groningen, University Medical Centre of Groningen 9700 RB Department of Genetics, Groningen, NL.
7 Dept of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden.
8 The Eskitis Institute for Drug Discovery, Griffith University, QLD 4111 Brisbane, Australia.
9 Dept for Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
10 Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
11 Dept of Women’s and Children’s Health, Karolinska University Hospital, 171 76 Stockholm, Sweden.
12 Dept of Clinical Genetics, Maastricht University Medical Centre, 6202 AZ Maastricht, NL.
13 Dept of Clinical Genetics, Chapel Allerton Hospital, Leeds, LS7 4SA, UK.
14 Victorian Clinical Genetics Service, Murdoch Children’s Research Institute, Melbourne, VIC 3052 Australia.
15 West Midlands Regional Genetics Service, Clinical Genetics Unit, Birmingham Women’s Hospital, B15 2TG, UK.
16 Clinical Genetics Unit, Birmingham Women’s NHS Foundation Trust, Mindelsohn Way, Edgbaston, B15 2G, UK.
17 KK Women’s and Children’s Hospital, 229899 Singapore, Singapore.
18 School of Biological Sciences, the University of Adelaide, Adelaide 5000, Australia.
19 Institute of Medical Biology, A (*) STAR, 138648 Singapore, Singapore.
20 Dept of Clinical Genetics, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK.
21, 22 These authors contributed equally
[email protected]
Mutations in over a hundred genes have been reported to cause X-linked recessive intellectual
disability (ID) mainly in males. In contrast, the number of identified X-linked genes in which de
novo mutations specifically cause ID in females is limited. Here, we report seventeen females
with de novo loss of function mutations in USP9X, encoding a highly conserved
deubiquitinating enzyme. The females in our study have a specific phenotype that includes
ID/developmental delay (DD), characteristic facial features, short stature and distinct
congenital malformations comprising choanal atresia, anal abnormalities, post-axial
polydactyly, heart defects, hypomastia, cleft palate/bifid uvula, progressive scoliosis and
structural brain abnormalities. Four females from our cohort were identified by targeted genetic
testing as their phenotype was suggestive for USP9X mutations. In several females pigment
changes along Blaschko lines and body asymmetry were observed which is likely related to
differential (escape from) X-inactivation between tissues. Expression studies on both mRNA
and protein level in affected female-derived fibroblasts showed significant reduction of USP9X
level, confirming the loss of function effect of the identified mutations. Given that some features
of affected females are also reported in known ciliopathy syndromes, we examined the role of
USP9X in the primary cilium and found that endogenous USP9X localizes along the length of
the ciliary axoneme, indicating that its loss of function could indeed disrupt cilium-regulated
processes. Absence of dysregulated ciliary parameters in affected female-derived fibroblasts
however points towards spatiotemporal specificity of ciliary USP9X (dys-)function.
Imprinting: the Achilles heel of trio-based Exome sequencing
G.W.E. Santen 1, MAGEL2 Consortium, A. van Haeringen 1, E, Aten 1
1 Department of Clinical Genetics, Leiden University Medical Centre, Leiden, 2300 RC, the Netherlands.
[email protected]
The possibilities and application of molecular genetic diagnostics have increased immensely
in the past decade, particularly in the field of rare intellectual disability (ID) syndromes. A
frequently cited reason for parents to perform genetic diagnostics is to know their recurrence
risk (RR) for a future pregnancy. The vast majority of ID has been shown to be caused by de
novo mutations and thus results in a low RR. Mutations and chromosomal deletions in
imprinted regions, although a rare cause of ID may result in a 50% RR.
Next generation sequencing is rapidly replacing classical molecular diagnostics. It has been
shown that trio-based sequencing is an efficient way of finding causal mutations. None of the
published large exome sequencing studies however report taking familial imprinted mutations
explicitly into account in their filtering strategy, and imprinted causes of ID have not been
identified in these studies.
We encountered a large family with 14 affected individuals from 5 nuclear families in two
generations. All patients had severe intellectual disability and many of them displayed
camptodactyly and hypotonia. There were dysmorphic features, but no syndromic diagnosis
could be made by experienced clinical geneticists. Four of the patients died at young age due
to various complications. Exome sequencing did not reveal any pathogenic mutation using
standard analyses, but when the extraordinary pedigree of this family was taken into account
a paternally inherited pathogenic frameshift mutation in MAGEL2 was identified.
MAGEL2 is located in the imprinted Prader-Willi/Angelman region on chromosome 15. De
novo truncating mutations in MAGEL2 on the paternal allele have been shown to cause a
Prader-Willi-like phenotype in 4 patients. The diagnosis of Prader-Willi was considered in one
of our patients, although it was not in the differential diagnosis for the other patients.
It is worrisome to realize that the causative mutation was only identified because of the
extended pedigree of this family and would have been missed otherwise Clearly, this issue
only arises when trio exome sequencing is performed, and not when only the affected
individual is sequenced. To further investigate the scope of this potential pitfall we have looked
for putatively truncating mutations in MAGEL2, UBE3A and KCNK9 in the ExAc database
(accessed June 10th 2015) consisting of ~120.000 alleles. We identified 6 likely pathogenic
alleles leading to an estimated carrier frequency of ~1/10.000. We therefore recommend that
any trio-based sequencing analysis pipeline takes imprinted genes explicitly into account,
displaying all variants, inherited or not, in this relatively limited number of genes.
SMC1A truncating mutations are associated with a severe epilepsy
phenotype which is distinct from de Lange syndrome.
Suresh Somarathi 1, Joseph Symonds 2, Ajoy Sarkar 3, Tara Montgomery 4, Alan Donaldson
5, Anne Lampe 6, Peter Turnpenny 7, Shelagh Joss 2, Kay Metcalfe 1
1 Department of Genomic Medicine, Saint Mary’s Hospital Central Manchester University Hospitals NHS Foundation Trust,
Manchester Academic Health Science Centre, Manchester M13 9WL, UK.
2 West Scotland Genetics Service, Level 1, Laboratory Medicine Building, South Glasgow University Hospital, 1345 Govan
Road, Glasgow G51 4TF, UK.
3 Department of Clinical Genetics, Nottingham City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, UK 2
4 Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK.
5 Department of Clinical Genetics, University Hospital Bristol NHS Trust, Saint Michael’s Hospital, Bristol, UK.
6 South East of Scotland Clinical Genetics Service, Molecular Medicine Centre, Western General Hospital, Edinburgh, UK.
7 Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree) Exeter, UK.
[email protected]
Background
In frame mutations and missense mutations in the SMC1A gene (Structural Maintenance of
Chromosomes 1A), which is a cohesion complex gene are reported to be responsible for about
4 to 6% of cases of Cornelia de Lange Syndrome (CDLS). Children affected with CDLS have
distinct facial features, developmental delay, prenatal and postnatal growth retardation,
abnormalities of hands and feet with variable involvement of other organs. Frameshift and
nonsense mutations in SMC1A were not reported in association with CDLS previously and
were assumed to be lethal. More recently loss of function mutations in the SMC1A gene have
been reported in the literature (Goldstein JH et al., 2015; Lebrun N et al., 2015).
Aim
We report a series of 8 cases (7 cases from DDD study and another one who is a deceased
twin of one of the subjects) in whom de novo loss of function mutations were identified including
frameshift and nonsense mutations in the SMC1A gene. We analysed their clinical features to
expand the clinical phenotype of these truncating types of SMC1A mutations.
Discussion
All the 7 cases have epilepsy and presented with clusters of epileptic seizures which are of
multiple types and in some, showed poor response to treatment with anti-epileptic medication.
Abnormalities of limb development were noticed in 3 subjects, which included clinodactyly and
camptodactyly of fingers, 1-2 toe syndactyly of toes and deviation of halluces at metatarsophalangeal joints. Mild facial asymmetry with unilateral ptosis was present in 1 subject. Deep
set eyes with downward sloping palpebral fissures and widely spaced teeth were present in 1
subject. Ventricular septal defect (VSD) and Atrial septal defect (ASD) were present in 1
subject and a small intra-atrial connection was present in another subject. Hypotonia and
cortical visual impairment were present in 2 subjects. One subject had bifid T6 Vertebra and
choanal atresia. Symmetrical growth retardation and developmental delay was present in all
the subjects.
Conclusion
The clinical phenotype of the patients with loss of function mutations in SMC1A appears to be
different to the typical features of CDLS and appears to be a distinct clinical entity. It is
important to note that none of these subjects were considered to have CDLS prior to the results
from the DDD study. These observations are also supportive of SMC1A as a candidate gene
in some patients with clusters of seizures and severe epilepsy.
Compound heterozygous NEK1 variants in two siblings with oralfacial-digital syndrome type II (Mohr syndrome)
Marijn F. Stokman* 1,2, Glen R. Monroe* 1,2, Isabelle F.P.M. Kappen* 1,3, Paulien A. Terhal 1,
Marie-Jose H. van den Boogaarde 1, Sanne M.C. Savelberg 1,2, Lars T. van der Veken 1,
Robert J.J. van Es 4, Susanne M. Lens 2,5, Rutger C. Hengeveld 2,5, Marijn A. Creton 4, Nard
G. Janssen 4, Aebele B. Mink van der Molen 3, Michelle B. Ebbeling 6, Rachel H. Giles 7,
Nine V. Knoers 1,2, Gijs Van Haaften 1,2 (* Shared First Authors)
1 Department of Genetics, University Medical Centre Utrecht, Utrecht, 3584 EA, the Netherlands
2 Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands
3 Department of Plastic Surgery, University Medical Centre Utrecht, Utrecht 3584 CX, the Netherlands
4 Department of Oral and Maxillofacial Surgery and Special Dental Care, University Medical Centre Utrecht,
Utrecht, 3584 CX, the Netherlands
5 Department of Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, 3584 CG, the
Netherlands
6 Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, 3584 CX, the Netherlands
7 Department of Nephrology and Hypertension, Regenerative Medicine Centre, University Medical Centre
Utrecht, Utrecht 3584 CT, the Netherlands
[email protected]
Background The oral-facial-digital (OFD) syndromes comprise a group of related disorders
with a combination of oral, facial and digital anomalies. Variants in several ciliary genes have
been associated with subtypes of OFD syndrome, yet in most OFD patients the underlying
cause remains unknown.
Objective To investigate the molecular basis of two brothers with OFD type II, Mohr syndrome.
Methods We performed single nucleotide polymorphism (SNP)-array analysis on two brothers
with features of OFD type II and their healthy parents to identify homozygous regions and
candidate genes. Subsequently, we performed whole exome sequencing (WES) on the family.
Candidate variants were confirmed with Sanger sequencing and alternative splicing was
assessed with cDNA analysis. Immunocytochemistry was used to assess cilia number and
length.
Results Using WES we identified compound heterozygous variants in the NIMA (Never in
Mitosis Gene A) - Related Kinase 1 gene (NEK1). The novel variant c.464G>C disturbs normal
splicing in an essential region of the kinase domain. The nonsense variant c.1226G>A,
p.Trp409*, results in nonsense-associated alternative splicing, removing the first coiled-coil
domain of NEK1. Patient-derived fibroblasts showed severely reduced ciliation compared to
control fibroblasts (18.0% vs. 48.9%, p<0.0001). There was no significant difference in cilia
length.
Conclusions We identified compound heterozygous deleterious variants in NEK1 in two
brothers with Mohr syndrome. Ciliation in patient fibroblasts is drastically reduced, consistent
with a ciliary defect pathogenesis. Our results establish NEK1 variants involved in the etiology
of a subset of patients with OFD syndrome type II and support the consideration of including
(routine) NEK1 analysis in patients suspected of OFD.
Genetic studies in Noncompaction Cardiomyopathy using Next
Generation Sequencing
L.A. Verlooij 1, J.P. van Melle 2, R.A. de Boer 2, M.P. van der Berg 2, J.D.H. Jongbloed 1, Y.M.
Hoedemaekers 1.
1 Department of Clinical Genetics, University Medical Centre, Groningen, 9700 RB, the Netherlands.
2 Department of Cardiology, University Medical Centre, Groningen, 9700 RB, the Netherlands
[email protected]
Background: Noncompaction cardiomyopathy (NCCM) is a myocardial disease,
characterized by a thickened left ventricular wall with a two-layered structure, consisting of a
thin compact epicardial layer and an excessively thickened non-compact endocardial layer.
NCCM is genetic in 67% of the patients, yet in 50% of familial NCCM no genetic defect has
been identified. Next Generation Sequencing (NGS) techniques now allow analysis of a large
number of cardiomyopathy genes simultaneously, which may yield a higher mutation detection
rate.
Goal: The aim of this study is to delineate the prevalence and spectrum of genetic defects in
NCCM patients in a tertiary referral Center in the Northern part of the Netherlands (Groningen),
using NGS and thereby evaluating its value in diagnosing a genetic defect in NCCM.
Methods: NGS was performed in 61 of 86 patients. The other 25 patients were (previously)
tested for two to nine genes with Sanger sequencing.
Results: In 30 of 86 patients (35%) a genetic defect (class 5 or 4) was detected by NGS.
Eighteen (58%) of the genetic defects were found in sarcomeric genes. Mutations in MYH7
were the most common genetic defect (32%), followed by MYBPC3 (19%) and TTN (13%)
(figure 1). NGS identified a large group of class 3 variations, 67% of the identified genetic
defects, in 18 of 61 patients (30%) (figure 2).
Conclusions: The prevalence of genetic defects in NCCM identified with NGS is comparable
to the prevalence described previously. However, with NGS a large group of class 3 variations
was identified. Part of these mutations may be re-classified as class 4 or 5 defects in the future,
which may result in a higher mutation detection rate and spectrum of genetic defects in NCCM.
Sarcomere mutations remain the most common identified genetic cause for NCCM. MYH7
(32%) MYBPC3 (19%) TTN (13%) DSP (6%) MYPN (6%) Other (23%) 02468 10 12 14 16 2
to 9 genes NGS 55 genes NGS 60 genes Class 5 Class 4 Class 3
Fetal imaging in the diagnosis of skeletal dysplasias and
craniosynostosis – a case series
V. Ward 1, M. Irving 1, A. Beleza 1, S. Sankaran 2, G.J. Lee 3, C. Ridout 4, C. Ogilvie 5, K.
Mann 5, D. Shears 6, J. Carmichael 7, M. Holder-Espinasse 1
1 Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK.
2 Maternal-Fetal Medicine, Guy’s and St Thomas’ NHS Foundation Trust, London, UK.
3 Neonatology, Guy’s and St Thomas’ NHS Foundation Trust, London, UK.
4 Molecular Genetics, Viapath, Guy’s and St Thomas’ NHS Foundation Trust, London, UK.
5 Genetics Laboratories, Guy’s and St Thomas’ NHS Foundation Trust, London, UK.
6 Clinical Genetics, Oxford University Hospital NHS Foundation Trust, Oxford, UK.
7 Paediatric Radiology, Guy’s and ST Thomas’ NHS Foundation Trust, London, UK.
[email protected]
There are more than 450 skeletal dysplasias ranging in severity and the degree of associated
complications, and although individually rare, collectively they have a birth incidence of around
1 in 5000. Prenatal diagnosis is most often prompted by the finding of short long bones on
routine ultrasound scanning or in cases with a family history of skeletal dysplasias. Specific
diagnosis can be difficult and relies on clinical, radiological and molecular criteria.
Craniosynostosis, the premature fusion of the cranial sutures, has a prevalence of 1 in 2000
and around 15% of these are syndromic and are associated with other anomalies. Prenatal
ultrasound diagnosis of craniosynostosis can be difficult and so a definite diagnosis relies on
DNA testing.
The use of fetal MRI and fetal CT scan imaging has advantages over ultrasound imaging and
can provide excellent tissue resolution and a greater field of view. Detailed imaging allows for
a clear differential diagnosis to be established as early as possible, enabling further
investigations such as molecular diagnostic testing to be considered to achieve a more precise
diagnosis. This can allow for the distinction between lethal and non lethal dysplasias, and
permit further discussions with parents around the prognosis and further management of these
conditions.
We report 4 prenatal cases of Saethre-Chotzen and Carpenter syndromes,
Hypochondrogenesis, and Metatropic dysplasia with their clinical, radiological and molecular
features. We show the first UK case where fetal CT scan was performed as well as fetal MRI
images to demonstrate the importance of fetal imaging in helping to reach a prenatal diagnosis
and the impact it has on subsequent clinical management.
Poster Presentations
Poster Presentations, displayed alphabetically by lead author
1. Adrenocortical carcinoma in association with Birt-Hogg-Dube Syndrome
J. Adlard. A. Anthoney, H. Lindsay, R. Robinson, R, Charlton, A. Kraus
2. Concurrent BRCA1 and PALB2 mutations identified on cancer gene panel testing
J.Adlard. N. Camm, L. Mavrogiannis, S. Shepherd, R. Charlton.
3. RET variant p.Tyr791Phe: Low risk, but not no risk?
J.Adlard. S. Gilbey, M. Lansdown, R. Brown, L. Mavrogiannis, R. Charlton.
4. A novel missense mutation in TRPV4 causing Spondometaphyseal Dysplasia,
Kozlowski type and Metatropic Dysplasia
R.A. Akilapa D.S Johnson , S.M. Kirwin
5. Results of a National Audit of Screening Advice given to Adults with PTEN
Hamartoma Syndrome
A.F. Brady , A. Taylor , K.L. Lachlan
6. Histological & molecular hallmarks of PMS2 associated tumours
S.W. ten Broeke. T. van Wezel , E. Gomez Garcia , L.P. van Hest , T.G.W. Letteboer , J.W. OlderodeBerends , Th.A. van Os , L. Spruijt , J.F.J. Tromp , J.T.Wijnen , H. Morreau , M. Nielsen
7. Rib Anomalies in People with Congenital Heart Disease
D.L. Brown, I.J. Wilson, M.J. Wright, J.J. O’Sullivan, J.A. Goodship,
C. Gowdy
8. Perlecan (HSPG2) Mutations associated with Rolland Desbuquois Dyssegmental
Dysplasia
E. Clement, A. Calder, T. Cullup, E. Rosser
9. Antenatal diagnosis of Mosaic Trisomy 13: Dilemmas in management
E. Craft, T. Mousa, A.O. Akuma, F. Bulock, P.Vasudevan
10. The utility of a Carrier Register to provide long term follow up for carriers of
inherited cancer syndromes
A.Dane, J. Wiggins, C. Moss., Z. Kemp, A. George
11. Are online personal health records useful for patients with genetic conditions to
share information with family members?
Selina Goodman, Professor Heather Skirton & Professor Ray Jones
12. A unique case of a mosaic genome-wide uniparental isodisomy in a newborn with
Beckwith-Wiedemann syndrome
Saskia M.J. Hopman, P.F.R. Hochstenbach, A.A. Verrijn Stuart , J.C. Giltay , L.T. van der Veken
13. Compound heterozygosity for two novel mutations in NTHL1 in an individual with
adenomatous polyposis and multiple tumours
S. Kenwrick, O. Spasic-Boskovic, A. Taylor, K. Brugger, H. Rai, S. Abbs, J. Wyke, M. Tischkowitz, E.
Maher, J. Whitworth
14. Brain-thyroid-lung syndrome in a child caused by a deletion on chromosome 14
proximal of the NKX2.1 gene locus
Mira Kharbanda, Sunia Khadouma, Jeremy Jones, Malcolm Donaldson,
Joachim Pohlenz, Pia Hermanns
15. Mast syndrome (SPG21), a rare but recognizable phenotype
Anneke Kievit, Esther Brusse, Margriet Collée, Erik-Jan Kamsteeg,
Rick van Minkelen
16. KBG Syndrome: an emerging cause of developmental delay
K.J. Low, T.Ashraf, N.L.E Canham, J. Clayton-Smith, C. Deshpande, A. Donaldson, R.B. Fisher, F.A.
Flinter, N.C Foulds, K. Gibson, I. Hayes, A. Hills, S.E. Holder, M.D. Irving, S. Joss, E.C. Kivuva, K. Lachlan,
A.C. Magee, V.P.M. McConnell, M. McEntagart, K. Metcalfe, T. Montgomery, R.A. Newbury-Ecob, F.J.
Stewart, P.D. Turnpenny, J. Vogt, M. Williams , DDD Study, S.F. Smithson
17. Retrospective analysis of the prevalence of Beckwith-Wiedermann Syndrome in
Northern Ireland
R. Moore 1, D.Donnelly
18. Three generation family with atypical interstitial deletion within chromosome
22q11.21
R. Moore, V. McConnell
19. GSK2126458, a dual PI3K/mTOR inhibitor, is less effective than rapamycin for
treatment of renal lesions in a genetically engineered Tsc2+/- mouse model
Kalin Narov, Paulina Samsel, Jian Yang, Ashley Jones, Julian Sampson, Ming Hong Shen
20. Feingold syndrome with no Tracheo-oesophalgeal atresia
C. Powell, E. Craft, P. Vasudevan
21. Genetic mechanisms associated with tuberous sclerosis and tuberous sclerosis-like
phenotypes
Meera Raja, Gemma Sharman, Laura Thomas, Angharad Walters, Peter Giles, Kevin Ashelford,
Matthew Mort, James Colley, Julian Sampson
22. Histiocytoid Cardiomyopathy and Microphthalmia and Linear Skin Defects
Syndrome: Phenotypes linked by truncating variants in NDUFB11
Gillian Rea, James S. Ware, Tessa Homfray, Jan Till, Ferran Roses-Noguer, Rachel Buchan, Sam
Wilkinson, Alicja Wilk, Roddy Walsh, Shibu John, Shane McKee, Fiona J. Stewart, Victoria Murday,
Robert W. Taylor, John Baksi, Piers Daubeney, Sanjay Prasad, Paul J.R. Barton, Stuart Cook
23. Audit of Tuberous Sclerosis Diagnostic assessment and surveillance in the Northern
Region.
Richardson, A. Henderson
24. A Clinical Audit of a Lynch Syndrome Referral Protocol
Peter Risby, Dr. Verna Lavender
25. A single centre experience of tumour immunohistochemistry and mutation analysis
in the investigation of Muir Torre Syndrome
Katherine Schon, Ed Rytina, James Drummond, Stephen Abbs, Marc Tischkowitz
26. Genetic Mechanisms in Colorectal Polyposis
Dr. E. Short, Dr. L. Thomas, Dr. P. Giles, Dr. J. Colley, Dr. K. Ashelford, Dr. M. Mort, Prof. J. Sampson.
27. Genetic Weight Watching
C.T.R.M Stumple, D.A. Schott, T. Rinne, M.M. van Haelst, M.F. Stokman, E.C.M Mariman
28. Exome sequencing reveals distinct molecular mechanisms of duodenal and
colorectal tumorigenesis in familial adenomatous polyposis and MUTYH-associated
polyposis
Laura E. Thomas, Joanna Hurley, Sian Jose, Kevin Ashelford, Matthew Mort, Shelley Idzizazyczk, Julie
Maynard, Helena Leon Brito, Manon Harry, Angharad Walters, Sarah Jane Walton, Sunil Dolwani,
Geraint Williams, Meleri Morgan, Susan Clark, Julian R. Sampson
29. Skin lesions and arthralgias in a large pedigree with a partially anakinra-responsive
and possibly IL-18 driven NLRC4-related autoinflammatory disease
C.M.L. Volker-Touw, H.D. de Koning, T. van Kempen, K. Oberndorff, J. Giltay, C.G.F. de Kovel, M. Boes,
M.A.M. van Steensel, G.T.J. van Well, A. Simo, J. Frenkel, M.E. van Gijn
30. Audit of BRCA gene testing and demand for risk reducing mastectomy in Essex
E. Williams, B. Hoskins, V. Ramakrishnan, L. Side
Adrenocortical carcinoma in association with Birt-Hogg-Dube
Syndrome
J. Adlard. A. Anthoney, H. Lindsay, R. Robinson, R, Charlton, A. Kraus.
Yorkshire Regional Genetics Service and Leeds Teaching Hospitals NHS Trust, LS7 4SA, UK.
[email protected]
Case
The proband was a woman who had undergone left adrenalectomy at 42 years for a virilising
adrenocortical tumour with raised testosterone levels and hirsuitism. Mitotic activity was low,
but there was histological concern for an adrenal carcinoma, and the tumour recurred 4 years
later. She had a past medical history of lung cysts and eight episodes of pneumothorax. No
abnormal skin lesions were identified, but her sister was reported to have had skin lumps and
a renal cyst. Her parents were smokers and had died of lung cancer in their 50s/60s.
Genetic testing was performed on a panel test. A frameshift FLCN mutation c.1250del;
p.Phe417fs was identified consistent with Birt-Hogg-Dube syndrome. Her 24 year-old son
carries the same mutation. He does not have skin lesions and a renal ultrasound was normal.
However, he had respiratory symptoms and was found to have right lung bullae.
Discussion
Adrenal tumours have very rarely been described in patients with Birt-Hogg-Dube syndrome
of non-secretory and oncocytic subtype (Raymond et al 2014). Our case supports and extends
a phenotype of adrenal tumours in Birt-Hogg-Dube syndrome. Adrenal tumours are recognised
in other syndromes including Lynch, MEN1 and Li Fraumeni for which our patient screened
negative.
Concurrent BRCA1 and PALB2 mutations identified on cancer gene
panel testing
J.Adlard. N. Camm, L. Mavrogiannis, S. Shepherd, R. Charlton.
Yorkshire Regional Genetics Service and Leeds Teaching Hospitals NHS Trust, LS7 4SA, UK.
[email protected]
Case
The proband was diagnosed with ER positive, HER2 negative unilateral ductal breast cancer
at 65 years. She had a family history meeting local criteria for BRCA1 and BRCA2 mutation
testing which did not identify any pathogenic mutation.
10 months later, the proband's daughter was diagnosed with ER positive, HER2 negative
unilateral ductal breast cancer at the age of 32. She was offered a wider panel test of breast
cancer-associated genes which identified two pathogenic mutations: BRCA1 c.4165_4166del;
p.Ser1389X and PALB2 c.2052del; p.Arg686fs.
The proband's husband had one paternal first cousin affected with breast cancer in her 50s.
Testing confirmed he carries the BRCA1 mutation and his wife, the PALB2 mutation
Discussion
Families with coincident BRCA1/2 and PALB2 mutations are rare (Ancot et al 2015; Downs et
al 2015). It is likely that the risk for double heterozygotes is similar to the risk of the more
penetrant gene (BRCA1) with some additional disease-specific risk (e.g. pancreas) from the
other gene (PALB2). This case demonstrates potential value of extending breast cancer gene
testing to panels, which provided likely explanations for the cancer history on both sides of the
family. Further details of the pedigree, testing and management will be presented.
RET variant p.Tyr791Phe: Low risk, but not no risk?
J.Adlard. S. Gilbey, M. Lansdown, R. Brown, L. Mavrogiannis, R. Charlton.
Leeds Teaching Hospitals NHS Trust, Leeds LS7 4SA, UK.
[email protected]
Cases
We have identified two unrelated men diagnosed with isolated phaeochromocytoma in their
40s/50s as carrying the controversial RET gene variant c.2372A>T; p.Tyr791Phe. This variant
was included in the European Molecular Genetics Quality Network laboratory assessment
scheme in 2012. 65.5% of laboratories reported the variant as relevant for developing
medullary thyroid cancer and 15% as a potential but debated risk, with the information to be
used with caution. However, some research paper authors (Erlic et al 2010, Toledo et al 2015)
have suggested that it has no pathogenic effect.
Both of our probands have had thyroid problems. The first had a left thyroid lobectomy prior to
genetic testing for a multinodular goitre with no evidence of C-cell hyperplasia. The second
proband had elevated serum calcitonin detected and abnormal thyroid imaging; total
thyroidectomy was performed, with histology showing multinodular goitre and widespread Ccell hyperplasia.
Discussion
The general population heterozygote frequency of this variant is about 0.8%. As MEN2 is rare
(~1 in 35,000-100,000), the variant cannot be highly penetrant. However, the identification of
both phaeochromocytoma and C-cell hyperplasia in an individual with RET p.Tyr791Phe is
against this variant being completely benign. Further details and discussion will be presented.
A novel missense mutation in TRPV4 causing Spondometaphyseal
Dysplasia, Kozlowski type and Metatropic Dysplasia
R.A. Akilapa 1 D.S Johnson 1, S.M. Kirwin 2
1 Sheffield Children’s Hospital NHS Foundation Trust, Sheffield, S10 2AH. UK.
2 Molecular Diagnostics Laboratory, 1600 Rockland Road, Wilmington, DE 19803, USA.
[email protected]
TRPV4 is a protein coding gene, important for calcium ion permeability. The encoded Nonselective cation channel is thought to be regulated by a calmodulin-dependent mechanism.
Mutations in the gene are causative of a heterogeneous group of disorders including
Spondometaphyseal Dysplasia Kozlowski type, Metatropic Dysplasia, Hereditary Motor and
Sensory Neuropathy type IIC and Autosomal Dominant Bracyolmia. We report on a family
harbouring a novel TRPV4 missense mutation in exon 16, that to our knowledge has not been
previously published or recorded in the NCBI SNP or 1000 genome databases. The proband
presents with clinical features consistent with a diagnosis of Spondomtephyseal Dyplasia
Kozslowski type. Further family studies confirmed the mutation to be present in the proband’s
daughter. X-rays were consistent with a diagnosis of Metatropic Dysplasia. The absence of
this missense variation in unaffected family members adds further evidence to the
pathogenicity of the mutation found. This report demonstrates the heterogeneity of pathology
caused by identical mutations in TRPV4. It also broadens our understanding of this particular
region of the gene, in particular the importance in calcium/calmodulin signalling which is known
to be influenced by this domain.
Results of a National Audit of Screening Advice given to Adults with
PTEN Hamartoma Syndrome
A.F. Brady 1, A. Taylor 2, K.L. Lachlan 3
1 North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Watford Road,
Harrow, HA1 3UJ.
2 Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge, CB2 0QQ.
3 Wessex Clinical Genetics Service, University Hospitals Southampton NHS Trust, SO16 5YA.
[email protected]
We report the results of a national audit of screening advice given to adult patients with PTEN
Hamartoma syndrome. Screening guidance was proposed by the Pan Thames Cancer
Genetics Group and reviewed at the Spring Cancer Genetics Group meeting 2015.
Patients were included in the audit if they had a PTEN mutation (or likely pathogenic variant)
or are at 50% risk, were 16 years or older at time last advice given, with most recent advice
given between August 1st 2010 and August 1st 2015.
The audit aimed to establish a baseline for practice in the UK with a view to completing the
audit loop in five years time.
Histological & molecular hallmarks of PMS2 associated tumours
S.W. ten Broeke.1 T. van Wezel 2, E. Gomez Garcia 3, L.P. van Hest 4, T.G.W. Letteboer 5, J.W.
Olderode-Berends 6, Th.A. van Os 7, L. Spruijt 8, J.F.J. Tromp 1, J.T.Wijnen 1, H. Morreau 9, M.
Nielsen 1
1 Department of Clinical Genetics, Leiden University Medical Centre, the Netherlands.
2 Department of Pathology, Leiden University Medical Centre, the Netherlands.
3 Department of Clinical Genetics, Maastricht University Medical Centre, the Netherlands.
4 Department of Clinical Genetics, VU Amsterdam, the Netherlands
5 Department of Clinical Genetics, University Medical Centre Utrecht, the Netherlands.
6 Department of Clinical Genetics, University Medical Centre Groningen, the Netherlands.
7 Department of Clinical Genetics, Academic Medical Centre, Amsterdam, the Netherlands.
8 Department of Clinical Genetics, Radboud University Medical Centre, the Netherlands.
9 Department of Pathology, Leiden University Medical Centre, the Netherlands.
[email protected]
Background Lynch syndrome (LS) related cancers have a different genetic background and
histology compared with sporadic colorectal cancers (CRC) and show a different treatment
response and survival. Definition of the genetic landscape and common mutational targets of
these tumours might lead to better methods of detection and provide potential therapeutic
targets. Up to now most studies on Lynch related tumours focussed on MLH1, MSH2 and
MSH6 deficient tumours, but data on PMS2 related tumours is currently lacking, likely due to
the previously hampered PMS2 mutation detection which has strongly improved in recent
years. We now aim to unravel the histological and molecular hallmarks of PMS2 associated
CRC compared with other Lynch and sporadic tumours.
Methods We obtained informed consent of PMS2 mutation carriers and were able to collect
21 CRCs for histological and molecular evaluation. Histological hallmarks were scored by an
experienced pathologist. Moreover, to get an impression of the somatic tumour spectrum, we
used the Ampliseq Cancer Hotspot panel (version 2) on isolated DNA from tumour samples.
This panel covers mutation hotspots in 50 genes (~2800 COSMIC mutations) , including well
known somatically mutated genes such as KRAS, APC and TP53. The results were compared
with a control cohort of 23 sporadic CRCs that were tested in a diagnostic setting.
Results PMS2 associated CRCs showed a number of LS associated hallmarks: 81% were
right-sided, 43% had Crohn’s like infiltrate (missing: 19%) and 81% (missing: 14%) showed
microsatellite instability. However, a majority (63%, missing: 14%) hardly had any tumour
infiltrating lymphocytes, a well-known hallmark of Lynch associated tumours. The molecular
analysis showed a relatively low percentage of TP53 and APC mutations compared with
controls and a high percentage of a specific FBXW7 mutation. Notably, 5/21 of CRCs had this
c.1393C>T transition, where the controls had none. We also found a relatively rare KRAS
hotspot mutation in exon 4 (c.436G>A, p.Ala146Thr) occurring three times in the PMS2 cohort
but not in the control cohort. Lastly, we identified a possible germline SMAD4 mutation
(c.1082G>A, p.Arg361His)(high allele frequency of 70%).
Discussion To our knowledge this is the first study to examine tumour characteristics of a
cohort consisting solely of PMS2 mutation carriers. Several findings such as the specific KRAS
and FBXW7 mutations might possibly help with the identification of PMS2 associated tumours.
The finding of a less active immune response might negatively influence survival and treatment
options, but this requires further investigation.
Rib Anomalies in People with Congenital Heart Disease
D.L. Brown 1,2, I.J. Wilson 2, M.J. Wright 1, J.J. O’Sullivan 2,3, J.A. Goodship 1,2,
C. Gowdy .4
1 Northern Genetics Service, Newcastle upon Tyne, NE1 3BZ, UK.
2 Institute of Genetic Medicine, Newcastle University, NE1 3BZ, UK.
3 Department of Paediatric Cardiology, Freeman Hospital, Newcastle upon Tyne, NE1 4LP, UK.
4 Radiology Department, Royal Victoria Infirmary, Newcastle Upon Tyne, NE1 4LP, UK.
[email protected]
Background: Minor malformations are common in people with congenital heart disease
(CHD). This study sought to determine the frequency and pattern of rib anomalies in people
with congenital heart disease.
Materials and Methods: Plain chest x-rays (CXRs) taken for clinical purposes were reviewed
in 767 people with congenital heart disease and 359 SCBU graduates without congenital heart
disease. The radiologists’ reports were also reviewed. Cases with recognised syndromes
(n=14), extracardiac malformations (n=6) and known offspring of diabetic mothers (n=4) were
excluded; control CXRs with evidence of CHD (cardiomegaly, abnormal cardiac silhouette,
pulmonary venous hypertension, sternal wires) (n=11) or an extracardiac malformation (n=9)
were excluded. Rib changes secondary to thoracotomy were not considered as anomalies.
The number of thoracic ribs was counted in CXRs showing C7 to L1 vertebrae. The presence
of neonatal cervical ribs was assessed in images taken at 1000 days of age or less. A second
interpreter reviewed 11% of cases’ images and 30% of controls’ images. Differences in
interpretation were resolved by re-evaluation of CXRs by both interpreters together. Fisher’s
exact test was used to calculate p values in R.
Results: People with CHD are more likely to have the combination of 11 pairs of thoracic ribs
and other minor anomalies of ribs or vertebrae (p=0.017); and to have bilateral neonatal
cervical ribs (p=0.00035). An asymmetric thoracic rib number in cases, with 11 on the right and
12 on the left approaches statistical significance (p=0.058). However, there is no significant
difference between cases and controls having 12 thoracic ribs on the right and 11 on the left
(p=0.18). Having 11 pairs of thoracic ribs and no other rib anomalies is not more common in
cases than controls (p=0.13), nor is the presence of 13 pairs of thoracic ribs (p=0.16). Bilateral
accessory cervical ribs are more common in controls (p= 0.0014).
Conclusions: Specific patterns of minor rib anomalies are common in people with congenital
heart disease. Minor malformations are an important part of the phenotype which may provide
useful clues to the genetic aetiology.
Perlecan (HSPG2) Mutations associated with Rolland Desbuquois
Dyssegmental Dysplasia
E. Clement.1 A. Calder 2, T. Cullup 3, E. Rosser 1.
1 Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London,
WC1N 3JH, UK.
2 Department of Radiology, Great Ormond Street Hospital for Children NHS Trust Foundation, London, WC1N
3JH, UK.
3 North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Trust
Foundation, London, WC1N 3JH, UK.
[email protected]
Schwartz- Jampel syndrome is (SJS) is a rare autosomal recessive disorder characterized by
abnormalities of the skeletal muscles, including muscle weakness, myotonia, bone dysplasia,
joint contractures and short stature. Affected individuals often develop a typical ‘pinched’ facial
appearance with small features and blepharophimosis. The range and severity of symptoms
may vary from case to case. SJS is typically divided into 2 types. Type 1 is known to result
from mutations in HSPG2 which encodes perlecan, a basement membrane component. SJS
type 2 is associated with LIFR mutations.
The skeletal changes associated with type 1 SJS are usually relatively mild and fit into the
chondrodysplasia spectrum. These may include platyspondyly with kyphoscoliosis, bowing of
the long bones and hip dysplasia. HSPG2 mutations have also been described in SilvermanHandmaker dyssegmental dysplasia (DDSH), a more severe form of skeletal dysplasia
associated with vertebral segmentation abnormalities, and short thick long bones. It is usually
fatal in the neonatal period. Rolland Desbuquois dyssegmental dysplasia (DDRD) is described
as a milder but distinct form of dyssegmental dysplasia, the genetic basis of which has not
been described.
We report clinical and radiological features in 2 siblings now aged 4 and 1, born to first cousin
parents who have clinical features of SJS but with skeletal changes consistent with DDRD. A
homozygous splice site mutation has been identified on exome sequencing in HSPG2.
To our knowledge this is the first report of any genetic alteration in a case of DDRD and the
first clinical report of a case of dyssegmental dysplasia associated with myotonia. HSPG2
mutations associated with DDSH are thought to be functionally null whereas those in SJS are
thought to be associated with a reduction in protein. It is possible that our patients bridge the
phenotypic spectrum of HSPG2-related disorders.
Antenatal diagnosis of Mosaic Trisomy 13: Dilemmas in
management
E. Craft.1 T. Mousa,2 A.O. Akuma,3 F. Bulock,4 P.Vasudevan1
1 Consultant Geneticist, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, England
2 Consultant Obseterian, Fetal Medicine Unit, Royal Leicester Infirmary, Leicester, LE1 5WW, England
3 Consultant Neonatalogist Neonatal Unit, Royal Leicester Infirmary, Leicester, LE1 5WW, England
4 Consultant Paedriatric Cardiology, Cardiology Department, Genfield General Hospital, Leicester.
[email protected]
Trisomy 13 is associated with severe developmental delay, failure to thrive, microcephaly and
congenital heart defects. Due to limited life expectancy, medical intervention other than
palliative care is not generally recommended. Approximately 5% of trisomy 13 cases are
reported to be ‘mosaic’.
We present a male baby in whom an anterior diaphragmatic hernia was identified prenatally.
Amniocentesis identified ‘mosaic trisomy 13’ (66% of cells showed abnormal male karyotype).
Due to limited information about the care and outcomes of mosaic trisomy the clinical outcome
harder to predict and the parents decided to continue the pregnancy after prenatal counselling.
The baby was born at term in good condition with no apparent phenotypic features of trisomy
13 and had his surgical at 2 months of age with good result. At 15 months old he was making
good developmental progress.
This case illustrates the limited predictive value of a laboratory report of mosaicism and
‘median survival time’ of Trisomy 13 in literature resulting in difficult clinical decision making
and counselling. Ultimately, the clinical features of baby after birth, the uncertainty of
chromosomal mosaicism and parental wishes were considered in management of this cases
rather that limited descriptions of ‘mosaic trisomy 13’ in the literature.
The utility of a Carrier Register to provide long term follow up for
carriers of inherited cancer syndromes
A.Dane,1 J. Wiggins, 1 C. Moss.,1 Z. Kemp1,2 A. George1,2
1
Royal Marsden NHS Foundation Trust, London, SW3 6JJ, United Kingdom
2 Institute for Cancer Research, Sutton, SM2 5NG, United Kingdom
[email protected]
The Cancer Genetics Unit at the Royal Marsden NHS Foundation Trust established a Carrier
Register in 2013 to provide long term follow up for carriers of inherited cancer syndromes. The
utility, costs, advantages and challenges of maintaining the Register will be discussed. The
main aim of the Register is to monitor cancer surveillance, arrange referrals for screening and
risk-reducing surgery, monitor cascade testing and offer follow up appointments as needed.
Currently there are 1,233 BRCA mutation carriers, 118 Lynch syndrome (LS) carriers and 88
carriers of other inherited cancer syndromes on the Register. Carriers are entered on to the
Register at point of genetic diagnosis with a future date set for notes review. BRCA carriers’
notes are reviewed at ages 30, 40 and 50. Notes for LS carriers and carriers of other inherited
cancer syndromes are reviewed annually. In addition to its main aim, the Register has been
useful for audit and research purposes including the NHS Breast Screening Programme audit,
LS screening audit, identifying eligible CAPP3 patients, arranging a mail-out to all BRCA
carriers about NICE guidelines on chemoprevention, and identifying potential patients for
clinical trials, for example with PARP inhibitors.
Are online personal health records useful for patients with genetic
conditions to share information with family members?
Selina Goodman 1, Professor Heather Skirton 1 & Professor Ray Jones 1
1 Plymouth University, Plymouth PL4 8AA UK
[email protected]
For many genetic conditions, a family can have many people at risk of the same disease.
Therefore, for some patients it may be important to share information about the diagnosis with
relatives to enable testing, better understanding and improved self-management. This could
be supported through information provided electronically to patients, but this is still not
commonly done, despite widespread use of electronic information by families to share
information in other situations. Patient organised personal health records (PHRs) can provide
this facility, allowing individuals to decide what they share and with whom. Prior to a planned
intervention study to support patients at risk of familial colorectal cancer, we undertook a
scoping exercise to determine types and current usage of PHRs. We compared how they
differed in aspects (content, security, functionality, purpose and acceptance) relevant to users
at risk of genetic conditions. We discuss key attributes of PHRs suitable for facilitating
information exchange and highlight the importance of the healthcare professional’s approach
to ensure successful adoption. These technologies have the potential to empower patients and
their relatives. Genetic services need to address the integration of this technology into patient
care, as its use has important implications for current and future clinical practice.
An unique case of a mosaic genome-wide uniparental isodisomy in
a newborn with Beckwith-Wiedemann syndrome
Saskia M.J. Hopman 1, P.F.R. Hochstenbach 1, A.A. Verrijn Stuart 2, J.C. Giltay 1, L.T. van
der Veken 1
1 Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands.
2 Department of Endocrinology, University Medical Centre Utrecht, Utrecht, the Netherlands.
[email protected]
Background
gwUPiDMosaicism for a cell line in which all chromosome pairs consists of two identical copies
derived from only one of the parents, a so called genome-wide uniparental isodisomy
(gwUPiD) is a rare phenomenon.
Beckwith-Wiedemann syndrome
Beckwith-Wiedemann syndrome (OMIM#130650) is characterized by prenatal and postnatal
overgrowth, hemihyperplasia, macroglossia and an increased frequency of embryonic tumors.
In 60-70% of the patients, an epigenetic error at either the H19DMR (imprinting control region,
ICR1) or KvDMR (ICR2), controlling the appropriate allelic expression of the paternal IGF2 and
maternal CDKN1C genes, causes the clinical phenotype. In 10-15% of cases, the cause is
presence of two paternally derived copies of chromosome region 11p15, a so called paternal
uniparental disomy (UPD) 11p15. A small percentage of cases are caused by maternal
translocations/inversions or paternal duplications (2-3%) or mutation in CDKN1C (5-7%).
Clinical history
We report on a newborn presenting with clinical characteristics of Beckwith-Wiedemann
syndrome (BWS): high birth weight (~P80), facial dysmorphisms including ear lobe creases
and nevus flammeus, umbilical hernia, diastastis recti, hepatomegaly and hypoglycemia due
to hyperinsulinism.
Molecular investigations
To confirm clinical diagnosis, a methylation test was performed which showed
hypermethylation of H19DMR, corresponding to a paternal UPD 11p. To exclude a
chromosomal rearrangement, karyotyping and SNP-array analysis (Illumina CytoSNP-850k)
were performed on DNA isolated from peripheral blood. SNP-array showed a gwUPiD in a high
percentage of cells (>95%). No additional clinically relevant copy number alterations were
observed and karyotyping showed a normal female karyotype. Since only mosaicism for
gwUPiD can be compatible with life we decided to perform additional SNP-array analysis on
saliva and urine derived DNA, which showed normal biparental contribution without any
indication for the presence of gwUPiD cells.
Conclusion
In conclusion, we present a rare case of BWS in a newborn caused by mosaic gwUPiD.
Compound heterozygosity for two novel mutations in NTHL1 in an
individual with adenomatous polyposis and multiple tumours
S. Kenwrick 1, O. Spasic-Boskovic 1, A. Taylor 1, K. Brugger 1, H. Rai 1, S. Abbs 1, J. Wyke 2,
M. Tischkowitz 1, E. Maher 1, J. Whitworth 3.
1 East Anglian Clinical Genetics Service. Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK.
2 Ipswich Hospital, Heath Road, Ipswich IP4 5PD, UK.
3 Cambridge University at Addenbrooke’s Hospital CB2 0QQ, UK.
[email protected]
A 62 year old male with Jewish ancestry presented with over 40 adenomatous polyps
throughout the large bowel following an abnormal result on faecal occult blood screening.
Family history was not consistent with dominant inheritance. He previously had a parotid
gland tumour, aged 60, and shortly after his polyposis was detected, he developed acute
myeloid leukaemia. APC, MutYH and GREM1 gene testing was normal. Interrogation of the
NTHL1 gene using the Illumina Trusight panel revealed that he is a compound heterozygote
for two truncating mutation, in trans, not previously described for cases of polyposis. These
are present only one and 23 times, respectively in the EXAC database and are therefore likely
pathogenic. Two previous reports describe three different NTHL1 mutations in four families
(Weren et al. 2015; Rivera et al. 2015). The eight affected individuals all had multiple tumours
but none presented with a parotid gland tumour, or AML. This report therefore extends the
mutation as well as the tumour spectrum associated with NTHL1 polyposis. Whole genome
sequencing of 96 individuals to date, from the Multiple Tumour Study, with a variety of multiple
tumours, study did not reveal any additional cases with homozygosity or compound
heterozygosity for NTHL1.
Brain-thyroid-lung syndrome in a child caused by a deletion on
chromosome 14 proximal of the NKX2.1 gene locus
Mira Kharbanda 1, Sunia Khadouma 3, Jeremy Jones 2, Malcolm Donaldson 2,
Joachim Pohlenz 3, Pia Hermanns 3.
1 West of Scotland Genetics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK.
2 Royal Hospital for Sick Children, Glasgow, G51 4TF, UK.
3 Children’s Hospital, Mainz, Germany.
[email protected]
Brain-lung-thyroid syndrome (BLTS) is a rare disorder characterized by congenital
hypothyroidism (CH), infant respiratory distress syndrome (IRDS) and benign hereditary
chorea (BHC). BLTS is caused by mutations in NKX2.1, a transcription factor involved in
thyroid, lung and central nervous system development.
In most previously published cases of BLTS, a point mutation or deletion of NKX2.1 has been
identified. Here we present a BLTS patient without a NKX2.1 mutation. Using array-CGH, we
identified a heterozygous 1 Mb deletion on chromosome 14, approximately 195,000 bp
proximal to NKX2.1. The deleted region encompasses 3 genes: MBIP, BRMS1L and
RALGAPA1. Currently, we are trying to determine whether NKX2.1 directly interacts with one
of these 3 proteins or whether one of the proteins binds to the NKX2.1 gene promoter.
Three other patients with deletion proximal to NKX2.1 and features of BLTS have been
described in the literature. The smallest common deleted region encompasses just MBIP
(MUK-binding inhibitory protein). MBIP is expressed in the thyroid, lung and forebrain. Our aim
is to clarify whether MBIP is involved in NKX2.1 gene expression or regulation. This finding will
help identify new mechanisms of NKX2.1 regulation and provide a deeper understanding of
possible causes of thyroid disorders.
Mast syndrome (SPG21), a rare but recognizable phenotype
Anneke Kievit 1, Esther Brusse 2, Margriet Collée 1, Erik-Jan Kamsteeg 3,
Rick van Minkelen 1
1 Dept. Of Clinical Genetics and 2 Dept. of Neurology, Erasmus MC, 3000CA Rotterdam, The Netherlands,
3 Dept. of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, The Netherlands.
[email protected]
Introduction:
Mast syndrome is an autosomal recessive complicated form of hereditary spastic paraplegia
with dementia. It was first described among Old Order Amish. Subtle childhood abnormalities
may be present, but the main features like spastic paraplegia, dementia develop in early
aduthood. The disease is slowly progressive and cerebellar and extrapyramidal signs are also
found in patients with advanced disease. Patients have a thin corpus callosum and whitematter abnormalities on MRI of the brain. Mutations were found in the acid-cluster protein of
33 kDa (ACP33) gene, which was designated “maspardin” (Mast syndrome, spastic
paraplegia, autosomal recessive with dementia). Five new patients with Mast syndrome, due
to mutations in the SPG21 gene, will be presented.
Patients:
Three Dutch patients (2 brothers and 1 sister) of a consanguineous sibship of 9, showed a
normal early development and followed normal education. At the age of resp.20/35/45 years
they started to have progressive motor problems, like problems with walking and frequent falls.
Also fatigue, concentration problems, depression and regression. At the age of resp 54/50/55
years they became bedridden due to spasticity, dementia, incontinency, swallowing difficulties
and were unable to speak. They had no epilepsy or vision problems. Neurological examination
at the age of 50/43/50 years showed bipyramidal syndrome, dysarthria and ataxia and
neuropsychological examination showed global cognitive impairment and deterioration. MRI
of the brain showed supratentorial generalized atrophy and a thin corpus callosum but no white
matter abnormalities. The eldest brother died at the age of 56 years.Two Saudi Arabian
patients of a consanguineous sibship were diagnosed with Mast syndrome and showed the
same phenotype.
Methods:
Clinical findings of the new Mast syndrome patients were collected and compared to those
described before. Whole exome sequencing was performed using DNA of the siblings followed
by homozygeous filtering of genes of the ROH and movement disorder panel consisting of 212
genes.
Results:
Clinical findings of all patients described and new, will be presented. Homozygous mutations
were detected in the SPG21 gene in the new patients.
Conclusions:
Mast syndorme is a rare, but recognizable phenotype: there is a normal early development or
a slight delay with progressive deterioration at adult age with pyramidal signs and cerebellar
and extrapyramidal signs at a later stage, cognitive decline with dementia and psychiatric
problems, a thin corpus callosum and supratentorial generalized atrophy of the brain leading
to a bedridden status and dependency within 10-20 years after onset. The differential
diagnostic considerations will be discussed and also the possible role of maspardin, which has
been shown to localize to intracellular endosomal/trans-Golgi transportation vesicles and
rather be involved in protein-protein interactions and in sorting and/or trafficking of molecules
in the endosomal pathway, a crucial process for maintenance of neuron health.
KBG Syndrome: an emerging cause of developmental delay
K.J. Low 1, T.Ashraf 2, N.L.E Canham 3, J. Clayton-Smith 4,5, C. Deshpande 2, A. Donaldson
R.B. Fisher 6, F.A. Flinter 2, N.C Foulds 7, K. Gibson 8, I. Hayes 9, A. Hills 10, S.E. Holder 3,
M.D. Irving 2, S. Joss 11, E.C. Kivuva 12, K. Lachlan 6, A.C. Magee 13, V.P.M. McConnell 13,
M. McEntagart 14, K. Metcalfe 4, T. Montgomery 15, R.A. Newbury-Ecob 1, F.J. Stewart 13,
P.D. Turnpenny 12, J. Vogt 16, M. Williams 9, DDD Study 17, S.F. Smithson 1.
1,
1 UHBristol NHS Trust, Bristol, BS2 8EG, UK.
2 Guy’s and St Thomas’ NHS Trust, London, SE1 9RT, UK.
3 North West Thames Regional Genetics Service, Harrow, HA1 3UJ, UK.
4 Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester, M13 9WL, UK.
5 Institute of Human Development, University of Manchester, M13 9NT, UK.
6 Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, TS4 3BW, UK.
7 Wessex Clinical Genetics Service, Southampton, SO16 5YA, UK.
8 Genetic Health Service NZ, Christchurch Hospital, Christchurch, New Zealand.
9 Genetic Health Service NZ, Auckland Hospital, New Zealand,
10 Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, BS10 5NB, UK.
11 West of Scotland Department of Clinical Genetics, Glasgow G51 4TF, UK.
12 Royal Devon and Exeter Hospital, Exeter, EX1 2ED.
13 Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, BT9 7AB.
14 South West Thames Clinical Genetics Service, St George’s Hospital, London, SW17 0QT, UK.
15 Northern Genetics Service, Newcastle Upon Tyne, NE1 3BZ, UK.
16 West Midlands Regional Genetics Service, Birmingham, B15 2TG, UK.
17 Wellcome Trust Sanger Institute, Cambridgeshire, CB10 1SA, UK.
[email protected] k
We describe 32 KBG patients from 27 families ascertained from both targeted gene
sequencing and from exome sequencing (DDD study). The former involved ANKRD11
sequencing in patients who had a clinical diagnosis of KBG syndrome whilst the latter utilized
whole exome sequencing in a group of children with developmental delay without a diagnosis.
Our patients ranged from infancy to middle age enabling insight into the prognosis of KBG. In
this cohort speech delay and learning difficulties were highly frequent but varied. Behavioural
problems were also common. Macrodontia of permanent upper central incisors was the most
common, but not universal, physical feature. Other clinical features included short stature,
conductive hearing loss, severe and recurrent middle ear infection, subtle palatal
abnormalities, infantile or persistent feeding difficulties. We identified a wide anterior fontanelle
with delayed closure, a new feature to be described, in a fifth of the cohort. Previously
described facial features of KBG syndrome were clearly recognisable in half the patients.
Sanger sequencing of ANKRD11 confirmed mutations in all patients and we did not find any
phenotype-genotype correlations. This study demonstrates that KBG syndrome is a significant
Mendelian cause of developmental delay. By comparing the two diagnostic groups of patients
we show that the clinical features can be subtle and non-specific making the diagnosis elusive.
We therefore propose that ANKRD11 should be included on ‘developmental delay’ gene
panels. We propose updated diagnostic criteria for KBG and a new summary of care
recommendations for patients with the condition.
Retrospective analysis of the prevalence of Beckwith-Wiedermann
Syndrome in Northern Ireland
R. Moore 1, D.Donnelly 2
1,2 Clinical Genetics Department, A Floor, Belfast City Hospital, 51 Lisburn Road, Belfast, BT9 7AB, Northern
Ireland.
[email protected]
Background and Aims
Genomic imprinting is the phenomenon whereby there is exclusive monoalleleic parent-oforigin specific gene expression. One of the most commonly recognised imprinted disorders
(IDs) is Beckwith-Wiedemann syndrome (BWS). Epidemiological data on IDs is sparse. BWS
is an overgrowth disorder characterised by abdominal wall defects, macroglossia, Wilm’s
tumour, hemihypertrophy and neonatal hypoglycaemia.
BWS is caused by disruption to a number of imprinted genes at 11p15. The aim of this study
was to retrospectively analyse the prevalence of BWS within Northern Ireland. Within the study
we looked at some of the features of BWS in relation to the molecular diagnosis.
Methods
We used a search tool within our information management system to identify all patients in
Northern Ireland with a molecular or clinical diagnosis of BWS between the period of January
1987 and February 2015.
Results
37 patients in total had a diagnosis of BWS. 26 patients had molecular confirmation. Of these
26 patients, 18 had hypomethylation of ICR2, 6 had paternal uniparental disomy (UPD), 1 had
a duplication of ICR1 and 1 had a CDKN1C mutation.
The live-birth prevalence of BWS was calculated to be 5.408 x 10-5 which equates to ~ 1 in
18,500.
The majority of our patients were referred to the genetics service at birth. 17 patients had an
omphalocoele. 17 patients had neonatal hypoglycaemia. 8 patients had hemihypertrophy, 4
of whom had UPD as the molecular diagnosis. 1 patient developed a Wilm’s tumour and 1
patient developed hepatoblastoma. Both of these patients also had UPD. 1 patient had an
angiomyolipoma and maternal hypomethylation of ICR2 as the underlying molecular diagnosis.
Conclusions
The live-birth prevalence of Beckwith-Wiedemann syndrome in Northern Ireland is ~ 1 in
18,500. This is lower than the few reported prevalence statistics. The 2 characteristic tumours
of Wilm’s tumour and hepatoblastoma in our cohort of patients occurred in children with
uniparental disomy which is in keeping with the risk reported in the literature. Hemihypertrophy
was also seen more frequently in those with UPD.
Three generation family with atypical interstitial deletion within
chromosome 22q11.21
R. Moore 1, V. McConnell 1
1
Clinical Genetics Department, A Floor, Belfast City Hospital, Belfast Health & Social Care Trust, 51 Lisburn
Road, Belfast, BT9 7AB, Northern Ireland
[email protected]
We present a three generation family affected by an atypical interstitial deletion within
chromosome 22q11.21 with a minimum size of approximately 686kb. The deletion
interval involves only the distal part of the 22q11.2 deletion syndrome critical region
(which includes Di George and velocardiofacial syndrome) and therefore does not
contain the gene TBX1. To our knowledge >18 cases have been reported in the
literature to date. The phenotype is variable and includes developmental delay, subtle
dysmorphism and cardiac defects.
The 23 year old proband first presented to the genetics service at 27 weeks gestation
with her first pregnancy after referral from rheumatology for assessment of joint
hypermobility and radiological findings of high riding right patella and a left subluxed
patella with bilateral effusions and normal echocardiogram, raising the possibility of a
connective tissue disorder. Her clinical phenotype involves unusual dysmorphism
including dysplastic ears, retrognathia, dental overcrowding, a high arched palate, long
uvula, velvety skin and some keloid scar formation. Array-CGH at a resolution level of
60K detected an atypical interstitial deletion within chromosome 22q11.21 ~686kb.
Other cardiac and genetic investigations and collagen studies which were completed
will be presented.
Subsequent testing has shown the atypical interstitial deletion within chromosome
22q11.21 to be maternally inherited and has also been shown to be present in the
proband’s daughter who had surgical repair of an umbilical hernia. Interestingly the
proband’s mother has history of joint laxity and umbilical hernia. Within the family a
number of others have been affected with umbilical hernia including; a maternal aunt,
maternal grandmother and maternal great-grandmother. Segregation analysis of the
hernia and clinical phenotype with the deletion is currently in progress within the family.
Documenting the phenotype within this family will be important in expanding the
knowledge on this unusual deletion. This case demonstrates that array CGH should
be considered in referrals for assessment of possible connective tissue disorder when
atypical phenotypic features are present.
GSK2126458, a dual PI3K/mTOR inhibitor, is less effective than
rapamycin for treatment of renal lesions in a genetically engineered
Tsc2+/- mouse model
Kalin Narov*, Paulina Samsel*, Jian Yang*, Ashley Jones, Julian Sampson, Ming Hong Shen
(* Equal Contributors)
Institute of Medical Genetics, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath
Park, Cardiff CF14 4XN, UK.
[email protected]
Tuberous sclerosis (TSC) is a genetic tumour syndrome involving multiple organs. It is caused
by mutations in the TSC1 or TSC2 gene that lead to aberrant activation of the mechanistic
target of rapamycin (mTOR) signalling pathway. The allosteric mTOR inhibitor rapamycin and
its analogues (rapalogues) have demonstrated some beneficial effects for treating TSCassociated tumours in both preclinical and clinical trials. However, some tumours have little
response to treatment probably partly due to rapamycin induced activation of Akt.
GSK2126458 is a highly potent and orally bioavailable dual ATP-competitive inhibitor of PI3K
and mTOR, and may help to overcome problems caused by rapalogues. Preclinical studies
have demonstrated broad anti-tumour activity of GSK2126458 in vitro and in vivo. Preliminary
data from a phase 1 trial for advanced solid tumours suggested 2.5 mg as daily maximum
tolerated dose (MTD) while several other phase 1 trials are still under way. In this study, we
have assessed the therapeutic efficacy of GSK2126458 on renal lesions in a genetically
engineered Tsc2+/ mouse model. We first determined 2 mg/kg of GSK2126458 for males and
1 mg/kg for females as the daily MTD. We treated Tsc2+/- mice from the age of 13 months with
vehicle, rapamycin (4 mg/kg) and GSK2126458 (MTD) (n=9 per group) 5 times a week via
intraperitoneal injection for two months. Tumour burden was estimated from total whole areas
and cellular areas respectively of all lesions (cystic, papillary and solid) observed in 6 coronal
sections at a150 µm interval prepared from each kidney of a mouse. Compared to vehicle,
both rapamycin (P=0.0004 for whole areas; P=0.0006 for cellular areas) and GSK2126458
(P=0.002 for whole areas; P=0.010 for cellular areas) treated mice showed significant
reduction in overall tumour burden but GSK2126458 was less effective than rapamycin
(P=0.0643 for whole areas; P=0.0135 for cellular areas).
Feingold syndrome with no Tracheo-oesophalgeal atresia
C. Powell 1, E. Craft 2, P. Vasudevan 3.
1 Trust Grade Speciality Doctor, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, UK.
2 Consultant Geneticist, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, UK.
3 Consultant Geneticist, Clinical Genetics, Royal Leicester Infirmary, Leicester, LE1 5WW, UK.
[email protected]
Feingold syndrome is a genetic condition with autosomal dominant inheritance, characterised
by microcephaly, mild-moderate learning disability, digit anomalies and trachea-oesophageal
atresia, associated with a heterozygous mutation in the MYCN gene.
Our case is a 10 year old girl with mild learning and behavioural difficulties. Specifically, she
has delayed motor and speech development, following an uneventful pregnancy and birth and
requires educational support. No other health problems are known, including no
gastrointestinal problems. Her mother also has mild learning difficulties.
Clinically, she has relative microcephlay (<0.4th centile), with a height and weight between 25th
– 50th centiles. Bilateral 5th finger clindodactyly with a short middle phalanx. Thumb and toe
anomalies were not evident. She had unremarkable palpebral fissures and jaw shape.
Her mother similarly has relative microcephaly (<3rd centile on adult chart). Her palpebral
fissures are short and down-slanted. Her right thumb is distinctly hypoplastc and both fifth
fingers have a short middle phalanx.
Her microarray identified a maternally inherited 1.2Mb deletion within 2p24.3; encompasses
the entire MYCN gene that is associated with Feingold syndrome.
In summary we present a case of Feingold Syndrome in a mother and daughter, detected by
microarray, highlighting the phenotypic variability and absence of tracheo-oesophalgeal
atresia.
Genetic mechanisms associated with tuberous sclerosis and
tuberous sclerosis-like phenotypes
Meera Raja 1, Gemma Sharman 1, Laura Thomas 1, Angharad Walters 1, Peter Giles 1, Kevin
Ashelford 1, Matthew Mort 1, James Colley 1, Julian Sampson 1.
1 Institute of Medical Genetics, Cardiff University, UK.
[email protected]
Mutations in the TSC1 or TSC2 genes are identified in at approx. 90% of cases of tuberous
sclerosis (TSC). Their identification is important for genetic counselling and as a resource to
better understand the pathophysiology of TSC. The remaining patients are classified as no
mutation identified (NMI). It is expected that a number of different genetic mechanisms may
account for their phenotypes. They may have mutations in TSC1 or TSC2 that have escaped
detection (e.g. mutations in un-screened promoters or untranslated regions, or low level
mosaicism for conventional mutations), and/or there may be mutations in other genes that
confer similar phenotypes to TSC.
This study employs targeted ultra deep sequencing (UDS) of the genomic TSC1 and TSC2
loci and, where this is negative, whole exome sequencing (WES) to identify the genetic causes
of TSC and TSC-like phenotypes in NMI patients. Trios of samples (an affected proband and
their unaffected parents) have been analysed to aid in novel, de novo variant detection. To
date, 91 samples (29 trios and two duos) have been analysed by targeted UDS of the region
containing TSC1 and TSC2, and 15 of these samples (5 trios) have been analysed by WES.
Putative SNVs and indels were verified using a combination of PCR, COLD-PCR and Direct
Sequencing. For 28 of the patients, RNA was also available and a TSC1 and TSC2 allelic
imbalance assay is being undertaken.
UDS identified a likely pathogenic de novo TSC2 mutation (c.2590C>T; p.Q864X) in one
patient. This mutation was mosaic; present in only 1% of alleles. UDS also identified two nonmosaic de novo mutations in TSC1: c.1498C>T; p.R500X in one patient, and c.1717C>T;
p.Q573X in another patient. No imbalance of allelic expression has been detected in 3 of the
28 patients, further allelic imbalance assays are being undertaken. Additionally, further
investigation of non-TSC1/2 de novo mutations identified by WES is being undertaken.
Histiocytoid Cardiomyopathy and Microphthalmia and Linear Skin
Defects Syndrome: Phenotypes linked by truncating variants in
NDUFB11
Gillian Rea 1,2,5, James S. Ware 1,2, Tessa Homfray 3, Jan Till 3, Ferran Roses-Noguer 3,
Rachel Buchan 1,2, Sam Wilkinson 1,2, Alicja Wilk 1,2, Roddy Walsh 1,2, Shibu John 1,2, Shane
McKee 5, Fiona J. Stewart 5, Victoria Murday 6, Robert W. Taylor 7, John Baksi 3, Piers
Daubeney 3, Sanjay Prasad 1,3, Paul J.R. Barton 1,2, Stuart Cook 1,2,4.
1 NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College
London, London, SW3 6NP, UK.
2 National Heart and Lung Institute, Imperial College London, London SW3 6NP, UK.
3 Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.
4 National Heart Centre Singapore, Singapore 169609, Singapore.
5 Department of Clinical Genetics, Belfast City Hospital, Belfast, BT9 7AB, UK.
6 Department of Clinical Genetics, NHS Greater Glasgow and Clyde, Southern General Hospital, Glasgow, G51 4TF, UK.
7 Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne,
NE2 4HH, UK.
[email protected]
Background: Mutations in NDUFB11, which encodes a component of the Mitochondrial
Respiratory Chain (MRC) were recently reported to cause both Histiocytoid Cardiomyopathy
(Histiocytoid CM) and Microphthalmia with Linear Skin Defects Syndrome (MLS syndrome).
Histiocytoid CM is a rare, distinctive form of cardiomyopathy with ~ 150 cases reported
worldwide, that predominantly affects females early in life and is characterized by arrhythmias
and associated sudden death. MLS syndrome, also known as a MIDAS (microphthalmia,
dermal aplasia, and sclerocornea syndrome, is a rare X-linked disorder with male lethality in
utero, characterized by unilateral or bilateral microphthalmia and linear skin defects, along
Blaschko lines, which are classically limited to the face and neck, present from birth, and heal
with time, often leaving minimal scarring.
Methods and results: Here we report a fourth case of Histiocytoid CM with a de novo
nonsense mutation in NDUFB11 (ENST00000276062.8: c.262C>T; p.Arg88Ter), identified
using Whole Exome Sequencing (WES) of a family trio. An identical mutation has been
previously reported in association with MLS syndrome. Our case lacked the diagnostic
features of MLS syndrome but detailed clinical comparison of the two cases revealed
significant phenotypic overlap. Heterozygous mutations in HCCS and COX7B, which, like
NDUFB1, encode proteins of the MRC, have also previously been identified in MLS syndrome
including a case with features of both MLS syndrome and Histiocytoid CM.
However, a
systematic review of WES data from previously published Histiocytoid CM cases, alongside
four additional cases presented here for the first time, did not identify any mutations in these
genes.
Conclusion: We conclude that NDUFB11 is a cause of both Histiocytoid CM and MLS, and
that these disorders are allelic (genetically related). Screening for evidence of malignant
arrhythmias and cardiomyopathy would be appropriate in individuals with MLS syndrome.
Additional nuclear encoded mitochondrial or mitochondrial DNA genes are good candidates
for further causes of both Histiocytoid CM and MLS syndrome.
Audit of Tuberous Sclerosis Diagnostic assessment and
surveillance in the Northern Region.
R. Richardson1, A. Henderson2
1,2 Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne, NE1 3BZ, UK
[email protected]
Background
Tuberous Sclerosis Complex (TSC) is an autosomal dominantly inherited multisystem
disorder. (1) Birth incidence is estimated at 1:5800 (2). Consensus guidelines were first
proposed in 1999 (3) and were reviewed and an update published in 2013 (4). Level of
adherence to these guidelines in the Northern Region was unknown. This audit reviewed
management of the TSC patients in the Northern Region.
Method
Patients were identified via the Northern Genetics service (NGS) database. Additional patients
were identified from a Paediatric TSC MDT meeting. NGS notes were reviewed. Newcastle
Hospitals Trust records were reviewed where available. If no records existed in Newcastle
Trust, and care was being received in another hospital, efforts were made to review those
hospital notes. Up to 2013, the 1998 TSC consensus guidelines were used. From 2013
onwards, the 2013 guidelines were used.
Results
101 patients were identified. 58 sets of notes were retrieved. 46 of which were included. 28
were diagnosed when 1999 guidelines applied. 4 were diagnosed when the 2013 guidelines
applied. 41 had management/surveillance when the 1999 guideline applied. 45 had
management/surveillance when the 2013 guideline applied
Audit against the 1999 guidelines showed less than 50% adherence in: fundoscopy, ECG, skin
assessment, annual BP, annual U&E (if PKD), pulmonary investigations
Audit against the 2013 guidelines showed less than 50% adherence: in use of abdominal MRI
for screening for AMLs , BP, GFR, counselling about Oestrogens use, assessment of teeth,
MRI brain surveillance, TAND screening, LAM screening, skin surveillance, Cardiology and
Ophthalmology follow up.
Conclusions
There is poor adherence to the consensus guidelines for diagnostic assessment and
surveillance of TSC. It was also observed that there is no agreement as to which specialty
coordinates overall care for TSC patients.
Limitations
Efforts were made to review all notes for patients, including NGS notes, Newcastle Hospital
notes and relevant local hospital notes. General practice information was not sought and it is
possible that some patients were receiving surveillance from their GP, which was not
documented in hospital notes. In many cases, information was not documented, for example,
asking about pulmonary or cardiac symptoms. The assumption was made therefore that this
was not done.
References
1 Curatolo P ‘Tuberous sclerosis’. Lancet. 2008;372:657–668.
2 O'Callaghan ‘Prevalence of tuberous sclerosis estimated by capture-recapture analysis.’ Lancet. 1998;352:318–319.
3 Tuberous Sclerosis Consensus Conference: recommendations for diagnostic evaluation. National Tuberous Sclerosis
Association. RoachES, DiMarioFJ, Kandt RS, Northrup H. Journal Child Neurology. 1999 Jun;14(6):401-7.
4 Tuberous Sclerosis Complex Surveillance and Management. Krueger, Northrup, International Tuberous Sclerosis Complex
consensus group. Ped Neurology. Oct 2013 Volume 49, Issue 4, Pages 255–265
A Clinical Audit of a Lynch Syndrome Referral Protocol
Peter Risby 1, Dr. Verna Lavender 2,
1 Oxford Dept. of Clinical Genetics, Churchill Hospital, Oxford, OX5 1SU, UK.
2 Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0fl, UK.
[email protected]
Background
Around 14% of patients with colorectal cancer have tumours that exhibit a deficiency in
mismatch repair (MMR) genes1. Three percent of these patients have Lynch syndrome, where
the MMR gene mutations are germline in origin. Lynch syndrome is associated with significant
lifetime cancer risks2, so early diagnosis is required to optimise outcomes; however, previous
identification of individuals with Lynch syndrome has depended on the use of family
assessment-based guidelines, which fail to capture a significant proportion due to familial
heterogeneity3. Routine MMR immunohistochemistry testing of resected primary colorectal
cancers has, therefore, been practiced at a local NHS Trust since 20124.
Method
A clinical audit was conducted between 01.01.2014 and 31.12.2014 to identify compliance with
the Lynch syndrome referral protocol. The Lynch syndrome referral protocol, developed by the
local NHS Trust MMR Group, was used to develop the audit standard that all patients aged
between 18 and 70 and treated with surgical resection for primary colorectal cancer and found
to be mismatch repair deficient, should be referred to the clinical genetics service for
counselling and potential investigation of germline mutations. De-identified binomial data were
summarised using descriptive statistics to analyse the proportion of patients who were treated
according to the Lynch syndrome referral protocol. Sub-analysis by age stratification was also
conducted.
Results
256 adult patients had resection of primary colorectal cancer at the local NHS Trust during the
data collection period. Of the 256 patients, 130 (50.8 %) were aged 70 or under, 113 (87%)
had MMR testing, and 10 (3.9%) had potentially clinically significant results. Of these ten
patients, only three were referred to clinical genetics; two of which were found to have germline
mutations (both were aged 50 - 70).
Conclusions
The majority of patients who met the Lynch syndrome referral protocol inclusion criteria (based
on age, diagnosis and treatment) were referred for MMR testing and tested; however not all
eligible patients were tested. A key area of improvement to ensure both compliance with the
Lynch syndrome referral protocol and identification of all individuals with an MMR germline
mutation, is referring suitable patients to the clinical genetics service for counselling and testing
for germline mutations, as currently only 30% are referred. Although the proportion of patients
with MMR (sporadic and germline) mutations is relatively low, the results have major clinical
significance, informing decision making about both adjuvant treatments and familial screening
(where germline mutations have been detected).
References
1. Guinney, J. et al (2015) The consensus molecular subtypes of colorectal cancer. Nature medicine. Advanced online publication.
doi:10.1038/nm.3967
2. Vasen H, F, A. et al (2015) Clinical management of hereditary colorectal cancer syndromes. Nature Reviews Gastroenterology
& Hepatology. 12 p88-97
3. Serrano, M. et al (2012) Bethesda criteria for microsatellite instability testing: impact on the detection of new cases of Lynch
syndrome. Familial Cancer 11: 571-578.
4. Colling, R. et al (2015) Screening for Lynch syndrome and referral to clinical genetics by selective mismatch repair protein
immunohistochemistry testing: an audit and cost analysis. Journal of Clinical Pathology 0: p1-4
A single centre experience of tumour immunohistochemistry and
mutation analysis in the investigation of Muir Torre Syndrome
Katherine Schon 1, Ed Rytina 2, James Drummond 1, Stephen Abbs 1, Marc Tischkowitz 1,3
1 East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK.
2 Histopathology Department, Addenbrooke’s Hospital, Cambridge, CB1 0QQ, UK.
3 Department of Medical Genetics, University of Cambridge, CB2 0QQ, UK.
[email protected]
Introduction Sebaceous tumours are rare in the general population (prevalence <1%) but
occur relatively frequently in Lynch syndrome (~9%) as part of Muir Torre Syndrome (MTS).
Here we evaluate the diagnostic and genetic work up of sebaceous tumours in our region.
Methods
Patients with sebaceous tumours were ascertained from the pathology
database over a two year period (October 2012 to 2014). IHC results, clinical genetics notes
and molecular genetics results were reviewed.
Results
Of forty-five patients with sebaceous tumours, six were already diagnosed with
MTS. 20/38 IHC results were abnormal and fourteen new referrals were made to Genetics with
nine patients having genetic testing. A new MTS diagnosis was made in two patients (22%)
with sebaceous adenomas: an 81 year old female with previous duodenal and endometrial
cancer (MSH2) and a 56 year old female with a previous history of endometrial cancer (PMS2).
Discussion Making a diagnosis of MTS has significant implications for the patient and their
family. Our experience shows that offering molecular testing to individuals with a sebaceous
tumour and abnormal IHC has a good yield, detecting a pathogenic mutation in 22%. One
individual had a mutation in PMS2, which has not previously been associated with MTS.
Genetic Mechanisms in Colorectal Polyposis
Dr. E. Short, Dr. L. Thomas, Dr. P. Giles, Dr. J. Colley, Dr. K. Ashelford, Dr. M. Mort, Prof. J.
Sampson.
Institute of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XW, UK.
[email protected]
Background
Familial Adenomatous Polyposis (FAP), MUTYH-Associated Polyposis (MAP) and
Polymerase Proofreading-Associated Polyposis (PPAP) are syndromes of adenomatous
polyposis, and are due to mutations in APC, MUTYH, POLE and POLD1. Up to 90% of
patients with a phenotype of typical FAP (>100 adenomas) have a pathogenic APC germline
mutation identified through sequencing of coding exons and deletion/duplication analysis via
MLPA. Of those with a phenotype of attenuated FAP (AFAP) with 10-100 adenomas, an APC
or MUTYH germline mutation is detected in only 10-50% of cases.
The aim of this study is to identify novel constitutional mutations predisposing to multiple
colorectal polyps (>10) when no mutation is identified (NMI) in APC or MUTYH during routine
genetic diagnosis. Such currently undetected mutations may occur outside of the open reading
frame (ORF) of the known polyposis-associated genes, such as in promoters, UTRs or introns,
they may occur as conventional mutations at low frequency in mosaic cases or additional
genes may be responsible for the phenotype.
Methods
60 patients with ≥ 10 colorectal polyps have been recruited. All are negative for APC/MUTYH
mutations following sequence/dosage analysis of coding exons.
Haloplex (Agilent) is being employed for targeted sequence capture of the genomic
APC/MUTYH loci, and the ORFs of an additional 15 genes related to, or possibly related to,
colorectal neoplasia (BMPR1A, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, PMS2, PTEN,
SMAD4, STK11, TP53, POLE, POLD1, and AXIN2. This is followed by ultradeep sequencing
(UDS) on a HiSeq (Illumina). Samples are also undergoing cDNA sequencing to screen for
APC/MUTYH allelic imbalance (AI) and splicing abnormalities, and qPCR is being employed
to assess APC/MUTYH gene expression. Samples that remain NMI following these tests
undergo whole exome sequencing.
Results
 UDS and data analysis has been completed on 31 patients. Putative novel pathogenic
variants have been identified in 3 patients in APC, AXIN2 and POLE.
 AI assays are in progress. So far 6/33 patients displayed AI in APC and 5/40 patients
displayed AI in MUTYH. These findings are being confirmed with gene expression
studies using qPCR.
 cDNA sequencing has been completed on 17 patients to date and there was no
evidence of splicing abnormalities.
Conclusions
The identification of novel genetic variants or mechanisms responsible for colorectal polyposis
may provide benefits for patients and their families through improved diagnosis and clinical
genetic management.
Genetic Weight Watching
C.T.R.M Stumple 1, D.A. Schott 1,2, T. Rinne 3, M.M. van Haelst 4, M.F. Stokman 4, E.C.M
Mariman 5
1 Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastrictt UMC +
Maastricht; 2 Department of Pediatrics, Zuyderland Medical Centre, Heerlen; 3 Department of Human Genetics,
Radboud University Medical Centre, Nijmegen; 4 Department of Genetics, University Medical Centre Utrecht; 5
Department of Human Biology, NUTRIM, Masstricht University Medical Centre, Masstricht, the Netherlands
[email protected]
A teenage boy born to American-Danish parents was presented with morbid obesity since the
neonatal period. The cause of this extreme obesity was never found, despite all kinds of
investigations (eg Prader-Willi syndrome) during childhood in several countries. The parents
told that despite a diet since neonatal period and a very active life, there was no effect on his
weight control. Anamnestic there was also an anosmia and no signs of pubertal development
at age 11 years, leading to a clinical suspicion of Kallmann syndrome. Physical examination
showed morbid obesity with acanthosis nigricans (sign of insulin resistance). He had a normal
intelligence, without any dysmorphism and prepubertal Tanner stadia. Regular laboratory
investigation for obesity showed no abnormalities, including OGTT and OSAS survey.
Investigation of the Kallmann genes was normal. Recently, physical puberty started, excluding
the clinical suspicion.
Exome sequencing revealed two compound heterozygous mutations in the ADCY3 gene; a
truncating mutation and an in-frame deletion of an evolutionarily highly conserved amino acid
located in the adenylyl cyclase domain of the ADCY3 protein. Mutations in this gene have not
been associated with human genetic obesity so far, although previous GWAS studies showed
that ADCY3 is a susceptibility locus for childhood body mass index.
Differential diagnosis, especially with Bardet-Biedl syndrome (BBS) will be discussed.
Mutations in the ADCY3 gene have not been reported sofar in BBS.
Ciliopathies are a heterogeneous group of conditions due to mutations in genes coding for
proteins with a function in primary and/or sensory cilia. Obesity and impairment of the olfactory
system can be part of the symptoms. ACDY3 is used as a histological marker for cilia, because
it is relatively highly expressed in cilia, where it functions in signal transduction. Considering
the fact that the Adcy3 knockout-mouse is obese and has an impaired smell, mutations in the
human ADCY3 gene can be regarded as possibly underlying the clinical condition of the
presented patient. Causality of ADCY3 mutations will be further investigated using cilia assays
in patient-derived cells.
Exome sequencing reveals distinct molecular mechanisms of
duodenal and colorectal tumorigenesis in familial adenomatous
polyposis and MUTYH-associated polyposis
Laura E. Thomas 1, Joanna Hurley 2, Sian Jose 1, Kevin Ashelford 1, Matthew Mort 1, Shelley
Idzizazyczk 1, Julie Maynard 1, Helena Leon Brito 1, Manon Harry 1, Angharad Walters 1,
Sarah Jane Walton 3, Sunil Dolwani 1, Geraint Williams 1, Meleri Morgan 4, Susan Clark 3,
Julian R. Sampson 1.
1 Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff
University CF14 4XN, UK.
2 Dept. of Gastroenterology, Prince Charles Hospital, Merthyr Tydfil, CF47 9DT, UK.
Dept. of Surgery, St Marks Hospital, London, HA1 3UJ, UK.
4 Dept. of Pathology, University of Wales Hospital, Cardiff, CF14 4XN, UK.
[email protected]
Background
With improved management of colorectal disease, duodenal cancer is becoming the leading
cause of familial adenomatous polyposis (FAP)-associated mortality. The risks of duodenal
polyposis and cancer in MUTYH-associated polyposis (MAP) are uncertain. Molecular studies
of duodenal tumorigenesis in FAP and MAP are virtually non-existent and the underlying
genetic mechanisms of adenoma development in both disease contexts remain unclear.
Methods
This study utilised exome sequencing (Agilent, 50Mb SureSelect), targeted Sanger
sequencing and array comparative genomic hybridisation (CGH) (Illumina, BlueGnome) to
characterise somatic mutational events in 74 duodenal adenomas from patients with FAP
(N=13) or MAP (N=13). The disease contexts were compared to each other and the duodenal
findings to the reported somatic landscape in colorectal adenomas in FAP and MAP.
Results and Conclusions
Significant differences in the underlying mutational spectra were identified between FAP and
MAP duodenal adenomas, including the numbers of single nucleotide variants (SNVs) and the
frequency of G>T transversions. Moreover, although both duodenal and colorectal adenomas
were characterised by somatic APC and KRAS mutations, there were significant differences
in the involvement of other driver genes, with multiple mutations in duodenal adenomas in
genes affecting the hedgehog, HER and Cadherin signalling pathways. These mutations are
largely absent from colorectal adenomas. These differences may be important in relation to
the identification of molecular biomarkers for “high risk” duodenal adenomas and for strategies
for pharmacological prevention or treatment of duodenal polyposis.
Skin lesions and arthralgias in a large pedigree with a partially
anakinra-responsive and possibly IL-18 driven NLRC4-related
autoinflammatory disease
C.M.L. Volker-Touw* 1, H.D. de Koning* 2, T. van Kempen 3, K. Oberndorff 4, J. Giltay 1,
C.G.F. de Kovel 1, M. Boes 5, M.A.M. van Steensel 6, G.T.J. van Well 7, A. Simon 8, J.
Frenkel* 9, M.E. van Gijn* 1.
1 Dept. of Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands; 2 Dept. of Dermatology,
Radboud University Medical Centre, Nijmegen, the Netherlands; 3 Dept. of Rheumatology and Clinical
Immunology Laboratory of Translational Immunology (LTI) University Medical Centre Utrecht, the Netherlands.
4 Dept. of Pediatrics, Atrium-Orbis Medicla Centre, Sittard, the Netherlands; 5 Dept. of Pediatric Immunology and
Laboratory of Translation Immunology (LTI) University Medical Centre, Utrecht, the Netherlands; 6 Dept. of
Dermatology, Maastricht University Medical Centre, Maastricht, the Netherlands.
7 Dept. of Pediatrics, Maastricht University Medical Centre, Maastricht, the Netherlands.
8 Dept. of General Internal Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands.
9 Dept. of Pediatrics, University Medical Centre Utrecht, Utrecht, the Netherlands
*These authors contributed equally.
[email protected]
Background: Autoinflammatory disorders (AID) are a heterogeneous group of diseases
characterized by chronic or recurrent systemic sterile inflammation. The best-known subset of AIDs
is mediated by IL-1β production. Recently, gain of function mutations in NLRC4 have been
described in association with autoinflammatory disease.
Methods: We performed whole exome sequencing in members of a large 6 generation pedigree
with a hitherto unknown AID. Medical data were collected retrospectively. IL-1β and IL-18
concentrations were analyzed in plasma. Skin biopsies were obtained of lesional and uninvolved
skin from three patients for routine histology and immunohistochemical staining of IL-1β and IL-17.
Results: WES revealed a novel heterozygous p.Ser445Pro variant in NLRC4, which segregated
with the 13 affected family members (LOD-score 3.58), and is located next to the recently described
p.His443Pro pathogenic mutation. Prediction software programs (Sift, Polyphen) indicated
pathogenic properties. The clinical phenotype was influenced by weather conditions, stress, and
infection. Skin lesions included painful erythematous nodes on the shins and feet, bouts of urticarial
skin rash, or a combination of both. Two patients presented with late-onset enterocolitis, one with
a fulminant polyarthritis. In a subset of the patients, the clinical symptoms resolved promptly upon
treatment with the IL-1 receptor antagonist anakinra. Plasma concentrations of IL-1β were normal,
whereas IL-18 concentrations were extremely elevated in all patients, even without an inflammatory
episode (median 4,324 pg/ml; ref. 0-34 pg/ml). Biopsies of lesional skin showed a non-specific
lymphocytic-histiocytic infiltrate in the dermis, unlike the histology of previously described
autoinflammatory skin diseases. IL-1β could not be detected, IL-17 was present in mast cells in
both lesional and uninvolved skin.
Conclusions: In this study we describe a novel variant in NLRC4 in a large pedigree with a
possibly IL-18-driven and partially anakinra-responsive AID. We present for the first time the
histopathological findings associated with mutations in NLRC4. The phenotype consisted of
erythematous skin nodes, urticaria and arthralgias, with late-onset enterocolitis in two patients.
Plasma IL-1β concentrations were normal. A lymphocytic-histiocytic infiltrate without IL-1β
expression was identified in affected skin tissue, which enables differentiation from the
phenotype observed in CAPS and Schnitzler’s syndrome.
Audit of BRCA gene testing and demand for risk reducing
mastectomy in Essex
E. Williams 1, B. Hoskins 2, V. Ramakrishnan 3, L. Side 1
1 North East Thames Regional Genetic Service, Great Ormond Street Hospital, London, WC1N 3JH, UK.
2 North East Thames Regional Genetic Service Laboratory, Great Ormond Street Hospital, London, WC1N 3JH,
UK.
3 St Andrews Centre for Plastic Surgery, Broomfield Hospital, Chelmsford, CM1 7ET, UK.
[email protected]
We established a risk-reducing mastectomy MDT (RRM MDT) in 2011, to ensure consistency
of decision-making following requests for risk-reducing mastectomies by women in Essex.
Meetings were initially held 3 times a year, but this was increased to quarterly in 2014 due to
an increase in requests for surgery. Clinicians attending this meeting noticed an increase in
numbers of patients discussed, particularly the number of BRCA1/2 gene mutation carriers.
Currently the service does not have dedicated funding, so we conducted an audit to look at
increasing demand for the service with a view to approaching commissioners for funding.
The key questions we addressed were, (1) whether the number of BRCA1/2 gene tests, and
in particular predictive tests had increased; (2) whether the number of BRCA1/2 gene mutation
carriers identified increased; (3) whether the number of women discussed at the RRM MDT
increased, and (4) whether the number of BRCA1/2 gene mutation carriers requesting RRM
increased.
As BRCA1/2 gene testing is arranged in-house, our genetics laboratory provided data about
all BRCA1/2 genetic testing arranged between January 2013 and May 2015, including results.
We undertook a notes review of all BRCA1/2 gene mutation carriers tested within this time
frame to identify those living in Essex and those who had been referred for discussion at the
Essex RRM MDT. Additionally, the RRM MDT discussion lists and patient proformas were
reviewed to provide data since the inception of this meeting.
Our data showed an approximately two-fold increase in number of BRCA1/2 genetic tests
requested over the reviewed timeframe. The number of predictive BRCA1/2 gene tests
arranged has approximately doubled since January 2013. Furthermore, the number of
BRCA1/2 gene mutation carriers identified has approximately doubled since January 2013. As
the frequency of RRM MDT meetings has increased from three to four per year, we observed
a concomitant increase in the number of women discussed. Finally, while the proportion of
women requesting RRM was found to be about constant at a third, because the numbers of
women identified as BRCA1/2 gene mutation carriers continues to increase, so does the total
number of BRCA1/2 gene mutation carriers requesting RRM.
Meeting organisation by
The Wales Gene Park