Identification of somatically acquired mutations in chordoma exomes

Identification of somatically acquired mutations in chordoma exomes

Identification of somatically acquired
mutations in chordoma exomes
Patrick Tarpey
Cancer Genome Project
Wellcome Trust Sanger Institute
Somatic Mutation Discovery
somatic
germline
Somatic Mutation Discovery
drivers
passengers
Somatic Mutation Discovery
Drivers
•
•
•
•
•
implicated in oncogenesis
reside in cancer genes
inform biology
aid diagnosis/prognosis
targets for therapy
Known cancer genes
• type of variant/gene
• variant known (COSMIC)
Novel cancer genes
• recurrent variants
• recurrently mutated genes
• seen in other cancers
Somatic Mutation Discovery
Passengers
• biologically inert
• reflect DNA exposures
Signature
• spectrum of variants
• sequence context
Exomes good first analysis for drivers
(Cancer Genes)
Frequently mutated cancer genes
PBRM1 (renal cancer)
SF3B1 (myelodysplasia)
4/7 tumours truncating
4/9 tumours missense (K700E)
Infrequently mutated cancer genes
Infrequently mutated cancer genes
Passengers
(mutational signatures)
PD4595a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
20
40
60
80
100
Number of substitutions
700
600
500
400
300
200
100
0
ER +ve
ER -ve
PD4106a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
20
40
60
80
100
Number of substitutions
700
600
500
400
300
200
100
0
ER +ve
ER -ve
PD4100a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
20
40
60
80
Number of substitutions
700
600
500
400
300
200
100
0
ER +ve
ER -ve
100
PD4200a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
20
40
60
80
100
Number of substitutions
700
600
500
400
300
200
100
0
ER +ve
ER -ve
PD4120a
PD4937a
PD4203a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
100
200
300
400
0
50
100
150
200
250
0
300
50
100
150
200
0
50
100
150
Number of substitutions
Number of substitutions
Number of substitutions
PD4119a
PD4123a
PD4137a
PD4125a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
20
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
Number of substitutions
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
PD4127a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
40
60
Number of substitutions
80
100
0
20
40
60
80
Number of substitutions
100
200
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
20
40
60
80
100
0
20
Number of substitutions
40
60
80
100
80
100
Number of substitutions
PD4601a
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
0
20
40
60
Number of substitutions
700
600
500
400
300
200
100
0
ER +ve
ER -ve
7000
T
6000
5000
G
4000
3000
C
2000
A
1000
0
-10 -9
PD4120a
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
0
1
2
3
4
5
6
7
8
9
10
600
500
T>G/A>C
T>C/A>G
T>A/A>T
C>T/G>A
C>G/G>C
C>A/G>T
400
T
300
200
0
100
200
300
Number of substitutions
400
100
0
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
400
600
500
250
350
500
300
400
400
200
250
300
150
200
200
150
200
300
100
100
100
100
0
0
50
50
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
0
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
0
-10 -9
10
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
140
140
120
120
120
100
100
100
100
80
80
80
60
60
40
40
20
20
0
0
180
160
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
140
120
80
60
40
60
40
20
0
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
20
0
-10 -9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
180
160
140
120
100
80
60
40
20
0
700
600
500
400
300
200
100
0
ER +ve
ER -ve
Study design
23 Chordoma exomes
Drivers
Contribution of known cancer genes
Evidence for novel cancer genes
Passengers
Mutation burden
Mutation spectrum
Strategy
Sample collection and
review
Variant discovery
(validation)
Extension study
(validation)
Data analysis
Sureselect
Hiseq
PD3905a_2
PD3905b_2
PD3904a_2
PD3904b_2
PD3890a_2
PD3890b_2
PD4116a_2
PD4116b_2
PD4113a_3
PD4113b_3
PD4112a_2
PD4112b_2
PD4110a_2
PD4110b_2
Subs (Caveman)
PD4108a_2
PD4108b_2
PD4107a_3
PD4107b_3
PD4106a_2
PD4106b_2
PD4105a_2
PD4105b_2
PD4104a_2
PD4104b_2
PD4103a_2
PD4103b_2
Variant Detection
22.5
90%
20
80%
17.5
70%
15
60%
12.5
50%
10
40%
7.5
30%
5
20%
2.5
10%
Indels (Pindel)
0%
Post-Processing Filters
‘Exomes’ do not cover all coding sequence
Coverage (%)
25
PD4102a_2
PD4102b_2
PD4100a_2
PD4100b_2
PD4099a_2
PD4099b_2
PD4098a_3
PD4098b_3
0
PD4094a_2
PD4094b_2
Sequencing
PD4093a_2
PD4093b_2
Exome
PD4092a_2
PD4092b_2
Gb
Variant discovery
100%
Variant discovery
Exome
Sequencing
Sureselect
Hiseq
Variant Detection
Subs (Caveman)
Indels (Pindel)
Post-Processing Filters
Variant detection is imprecise
Validation
Validation
Tumour
Normal
Validation
Advantages
PCR
Orthogonal
Disad
mononuc
dedicated
454
quick
analysis pipelines
non-ortho
no-pcr
performance
all variants
capacity
analysis pipelines
lead time
non-ortho
Sequence capture
miseq
miseq
Data analysis
Somatic mutations
Known cancer genes
Chordoma
Known cancer genes
Known cancer genes
Inactivating mutations in tumour supressor genes
Known cancer genes
Previously identified variants (COSMIC)
Known cancer genes
PTEN
PIK3CA
Known cancer genes
Driver (35%)
No Driver (65%)
Clinically actionable?
Novel cancer genes
Recurrently mutated genes
Missense: non-recurrent, not-clustered
Recurrently mutated genes
Missense: non-recurrent, not-clustered
LYST
Tumour
Normal
Tumour
Normal
Lysosomal trafficking regulator
•transport protein associated
proper lysosome function.
•Chédiak-Higashi syndrome.
•enlarged lysosomes
•recurrent infections
•albinism
•Neuropathy
Recurrently mutated genes
Missense: non-recurrent, not-clustered
ITGA10
Tumour
Normal
Tumour
Normal
Integrin:
transmembrane glycoprotein
receptors that mediate cell-matrix
and cell-cell interactions..
Recurrently mutated genes
Follow up investigation…?
Summary
• Known cancer genes
PI3K signalling (13%):
PIK3CA (2), PTEN (1)
Chromatin remodelling (9%)
ARID1A (1), PBRM1 (1)
PTPRD (1), CDKN2A (40%)
• Most tumours we failed to identify a driver
• No frequently mutated cancer gene
Summary
• Variant/s not called
•
•
•
not recognised (missense)
coverage
algorithm
• Variant/s not targeted
•
•
•
•
rearrangements
copy number changes
non-coding variants
epigenetic variants
• 5 whole genomes in pipeline (5 pending)
Acknowledgements
Sam Behjati,
Peter Campbell
Adrienne Flanagan Susanna Cooke
Mike Stratton
Josh Sommer
Peter Van Loo
David C Wedge
Nischalan Pilay
John Marshall
Sarah O’Meara
Helen Davies
Serena Nik-Zainal
David Beare
Adam Butler
John Gamble
Claire Hardy
Jonathon Hinton
Ming Ming Jia
Alagu Jayakumar
David Jones
Calli Latimer
Mark Maddison
Sancha Martin
Stuart McLaren
Andrew Menzies
Laura Mudie
Keiran Raine
Jon Teague
Jose Tubio
Dina Halai