Msp ments in a variety of experimental samples, including

Clinical Chemistry 46, No. 11, 2000
of sample containing multiple components (pBR322/MspI
plasmid digest; Sigma) in even-numbered wells (chiploading protocol D). No interwell contamination was
observed during chip analysis. Thus, the improved consistency of signal quantification observed was not attributable to interwell contamination but rather to enhanced
intrawell sample mixing. Chip-loading protocol D was
used for all subsequent experiments.
To evaluate the ability of the Bioanalyzer to measure
absolute concentrations, concentrated eNOS PCR product
(⬃40 ng/␮L) was diluted in Tris-EDTA buffer to yield
solutions containing 2.6, 5.1, 13.0, and 28.4 ng/␮L. Each
sample was loaded twice on each chip, with one sample
being loaded in wells 1– 6 and a duplicate sample being
loaded into wells 7–12. Concentration values generated by
the Bioanalyzer differed from concentration values obtained spectrophotometrically by 6 –16%. Well-to-well
and chip-to-chip results differed by similar amounts.
DNA sizing results were found to be independent of the
cDNA concentration.
To evaluate the ability of the Bioanalyzer to size samples containing multiple DNA fragments, commercially
available plasmid digests were analyzed. To reduce the
concentration of DNA fragments ⬍100 bp in size, plasmid
digests were spin-purified using the QIAquick PCR purification method, and samples were eluted in 1⫻ TrisEDTA buffer and diluted to yield appropriate concentrations for analysis. pUC18/MspI digest (Sigma) samples
were loaded into wells 1, 4, 7, and 10; ␾X174 RF DNA/
HaeIII fragments (Gibco) samples were loaded into wells
2, 5, 8, and 11; ␭ DNA/EcoRI marker (Promega) samples
were loaded into wells 3, 6, 9, and 12. This experiment
was performed twice on each of 2 successive days. Table
1, D and E, shows sizing and signal quantification results,
respectively, for ␾X174 RF DNA/HaeIII. The CV for DNA
sizing of fragments was ⱕ2.1%, whereas the CV for DNA
signal quantification was ⱕ6.7%. Similar CV values were
observed for pUC18/MspI digest with respect to sizing
and quantification. CVs for DNA sizing and quantification were ⬃8% and 7%, respectively, for ␭ DNA/EcoRI
markers. Similar results were observed for unpurified
plasmid digests.
In summary, we recommend a modification to the
manufacturer’s protocol for chip loading: namely, gentle
pipetting of samples with the marker mixture after loading into the sample wells, followed by vortex-mixing for 1
min at the highest setting, which does not cause liquid
loss from the sample wells. Lower concentration DNA
fragments may not be detected if poor chip preparation
leads to weak sample staining. This is particularly crucial
with respect to the manufacturer-supplied molecular size
ladder. The Bioanalyzer cannot calculate size and concentration values for the experimental samples if it fails to
detect all bands in the ladder. In addition, improper
staining of the upper molecular size marker may lead to
poor quantification of experimental DNA fragments.
We found the Agilent 2100 Bioanalyzer to be an easyto-use, time-efficient substitute to conventional CE. It was
effective at sizing and quantifying multiple DNA frag-
1853
ments in a variety of experimental samples, including
plasmid digests and PCR samples.
This work was supported by grants from the NCI (Grant
CA78848-02 to P.W. and L.J.K.) and NIH (Grant P60HL38632 to P.F.). P.W. and L.J.K. previously were recipients of grant support from Caliper Technology Corporation and were stock holders of and consultants to this
company.
References
1. Beckman Instruments, Inc. Introduction to capillary electrophoresis. Technical Bulletin 360643. Fullerton, CA: Beckman Instruments, 1994.
2. Mitchelson KR, Cheng J, Kricka LJ. The use of capillary electrophoresis for
point-mutation screening. Trends Biotechnol 1997;15:448 –58.
3. Guttman A, Ulfelder KJ. Separation of DNA by capillary electrophoresis. Adv
Chromatogr 1998;38:301– 40.
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JM. Microchip device for cell lysis, multiplex PCR amplification, and electrophoretic sizing. Anal Chem 1998;70:158 – 62.
10. Waters LC, Jacobson SC, Kroutchinina N, Kondurina J, Foote RS, Ramsey
JM. Multiple sample PCR amplification and electrophoretic analysis on a
microchip. Anal Chem 1998;70:5172– 6.
11. Khandurina J, Jacobson SC, Waters LC, Foote RS, Ramsey JM. Microfabricated porous membrane structure for sample concentration and electrophoretic analysis. Anal Chem 1999;71:1815–9.
12. Guttman A. Effect of operating variables on the separation of DNA molecules
by capillary electrophoresis. Appl Theor Electrophor 1992;3:91– 6.
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Structure and chromosomal localization of the human constitutive endothelial nitric oxide synthase gene. J Biol Chem 1993;268:17478 – 88.
Evaluation of a Nucleic Acid-based Cross-Linking Assay to Screen for Hereditary Hemochromatosis in
Healthy Blood Donors, Christiane Wylenzek,1 Martina Engelmann,1 Dirk Holten,1 Reuel Van Atta,2 Michael Wood,2 and
Birgit Gathof 1* (1 Division of Transfusion Medicine, University Hospital of Cologne, Joseph-Stelzmann Strasse 9,
50924 Cologne, Germany; 2 NAXCOR, 4600 Bohannon
Dr., Suite 220, Menlo Park, CA 94025; * author for correspondence: fax 49-0221-478-6179, e-mail Birgit.Gathof@
medizin.uni-koeln.de)
Hereditary hemochromatosis (HH) is a common autosomal recessive disorder (frequency, 1 in 300 –500 in the
Northern European population) characterized by overabsorption of iron with consequent multiorgan failure secondary to iron overload (1, 2 ). Because early diagnosis
and therapy can entirely prevent clinical complications,
HH presents a model system for presymptomatic detection at the molecular level. HFE, the disease-causing gene
of HH, encodes a 343-amino acid protein with high
1854
Technical Briefs
structural similarity to MHC class I molecules (3, 4 ). The
primary disease-causing mutation is a single G-to-A transition at position 845, encoding a protein with a
Cys282Tyr amino acid substitution (3 ).
Current HH genotyping techniques include restriction
fragment length polymorphism (RFLP) analysis (5 ) and
heteroduplex analysis (6 ), both PCR based. We evaluated
a nucleic acid-based test with cross-linkable DNA probes
to screen for the Cys282Tyr mutation in a total of 101
presumably healthy blood donors. The assay uses oligonucleotide probes modified with photo-activatable crosslinker molecules (7 ) and has been used to detect the factor
V Leiden mutation (8 ). Two sets of allele-specific crosslinkable DNA probes were prepared that detect either the
wild-type or mutant Cys282Tyr gene sequences. Samples
prepared from donor blood were assayed with each probe
set, and the genotype of each individual was determined
by comparison of the fluorescent signals obtained. All
blood samples were also assayed by a PCR-RFLP test.
Two capture probes that hybridized preferentially to
the wild-type or mutant HFE gene sequence, respectively,
were synthesized for the cross-linking assay: (5⬘-3⬘) AXATACGTGCCAGGTG and AXATACGTACCAGGTGG
(the underlined bases represent the position of the mutation site in the target). The coumarin-based cross-linking
nucleotide is denoted as X; both probes were biotinylated
at the 3⬘ end (8 ). In addition, 24 reporter probes were
synthesized, each containing two fluorescein residues at
the 5⬘ terminus and a cross-linker molecule in place of a
nucleotide one position from the 3⬘ terminus, the 5⬘
terminus, or both. The reporter probes were designed
from HFE gene sequence flanking the mutation, corresponding to the following nucleotide positions (9 ): 6443–
6462, 6472– 6493, 6495– 6518, 6574 – 6593, 6597– 6618, 6632–
6653, 6661– 6682, 6686 – 6707, 6716 – 6739, 6780 – 6799,
6801– 6822, 6838 – 6861, 6877– 6900, 6905– 6928, 6951– 6973,
6984 –7006, 7060 –7083, 7089 –7108, 7128 –7151, 7163–7186,
7208 –7231, 7235–7256, 7301–7322, and 7381–7402.
Blood specimens were obtained from 101 blood donors
with informed consent under an institutional review
board-approved protocol (University of Cologne). Leukocytes were isolated from blood samples as described (8 ),
resuspended in leukocyte lysis reagent (0.28 mol/L
NaOH), and either boiled at 100 °C for 30 min immediately before the assay or stored at ⫺20 °C for up to 14 days
before boiling.
Processed samples were placed into two wells each of a
96-well polypropylene microtiter plate. Each assay plate
also contained four negative controls (leukocyte lysis
reagent that had not been boiled) and two positive
controls (50 amol/well of a PCR amplicon covering the
assay locus amplified from a Cys282Tyr and wild-type
heterozygote in leukocyte lysis reagent that had not been
boiled). Two different probe solutions were prepared,
each containing the same set of 24 reporter probes and 1
of the 2 allele-specific capture probes. Aliquots of each
probe solution were added to one of each pair of sample
wells, as well as two negative and one positive control
wells. Neutralization of the solutions, photo cross-linking,
and addition of the streptavidin-coated magnetic beads
have been described (8 ). The beads were then washed
twice with wash reagent (0.15 mol/L NaCl, 0.015 mol/L
sodium citrate, 1 mL/L Tween-20). The beads were incubated in the presence of anti-fluorescein antibody-alkaline
phosphatase conjugate (Dako), washed four times, and
resuspended in AttophosTM (Promega) as described (8 ).
The fluorescence signal was determined by reading the
plate in a microplate fluorometer (Packard Instrument).
Genomic DNA was extracted from whole blood by
the QIAquick Blood reagent set (QIAGEN). A sequence
flanking the variant codon 282 was amplified by PCR
(DyNAzyme PCR reagent set; Biometra), and the amplicons were digested with RsaI (Roche), size-fractionated by
agarose gel electrophoresis, and genotyped as described
(5 ).
Determination of the genotype of an individual with
the cross-linking assay was based on the relative signals
obtained with the two allele-specific capture probe preparations. The net sample signal (NSS) was derived for
each sample and each probe set by subtracting the mean
of the negative control values from the sample signal. The
NSS ratio was defined for each sample as the NSS for the
mutation divided by the NSS for the wild type. The NSS
ratio intervals that define a particular genotype were set
before the donor samples were tested by assaying PCR
amplicons derived from individuals who were wild type,
heterozygous, or mutant homozygous for the Cys282Tyr
allele (20 determinations for each genotype). These experiments yielded the following mean NSS ratios: wild type,
0.05 (range, 0.01– 0.45); heterozygous, 1.22 (range, 0.95–
2.15); and mutant homozygous, 6.13 (range, 2.95–15.00).
On the basis of these results, the following NSS ratio
intervals were used to assign a sample genotype: wild
type, NSS ratio ⫽ 0 – 0.75; heterozygous, NSS ratio ⫽
0.76 –2.5; and homozygous mutant, NSS ratio ⬎2.5.
The sample data fell into two groups (Fig. 1). The first
group of 93 samples had NSS ratios of 0.12– 0.66 (mean ⫽
0.36; SD ⫽ 0.11) and was assigned a wild-type genotype.
The second group (eight samples) had NSS ratios of
Fig. 1. Frequency distribution of NSS ratios obtained by testing 101
blood donor samples with the cross-linking assay.
The dotted line represents the cutoff between Cys282Tyr heterozygous and
wild-type samples.
Clinical Chemistry 46, No. 11, 2000
1855
1.02–1.55 (mean ⫽ 1.30; SD ⫽ 0.18), compatible with
heterozygosity. No individuals homozygous for the
Cys282Tyr mutation were identified. To validate the
method for detection of the homozygous mutant genotype, the assay was performed on a blood sample from a
known homozygote. The NSS ratios for this individual, in
two evaluations, were 9.1 and 7.4, within the predicted
range.
The results of PCR-RFLP testing were in complete
agreement with those obtained with the cross-linking
assay for all 101 samples.
The cross-linking assay has several advantages. It allows detection of the Cys282Tyr mutation without the
laborious steps of DNA purification, PCR, and RFLP
analysis, and it eliminates problems of sample inhibition
of polymerases and sample contamination by amplicons.
An additional advantage is the large-scale simultaneous
processing of DNA samples, using the microtiter plate
format. With automated detection, the cross-linking assay
can be finished within 4 h.
Further work is needed to fully define the set of NSS
ratio ranges that determine the three genotypes. Data
from the blood sample assays showed wider variation
among samples of the same genotype than was seen with
the PCR samples. Presumably, this indicates that signal
intensity is influenced by factors such as the efficiency of
the overall sample preparation procedure and variation in
blood volume and leukocyte concentration. Further sample data will allow us to set finer intervals for genotype
assignment and to set “gray zone” values for repeat
testing.
Large-scale, presymptomatic screening of blood donors
for the Cys282Tyr mutation could identify individuals at
risk for HH, who are then candidates for prophylactic
phlebotomy, which increases the life expectancy to that of
the general population. If such a screening regimen was to
be implemented, the tests needed to perform genotype
analysis will have to be accurate, inexpensive, and automatable. The cross-linking assay used here is an efficient,
simple, and rapid method of genotyping HFE mutations
that, with automation, would be suitable for routine
genetic analysis in a large-scale manner.
hybridization assay for direct detection of factor V Leiden mutation. Clin Chem
1997;43:1703– 8.
9. Albig W, Drabent B, Burmester N, Bode C, Doenecke D. GenBank Accession
No. Z92910. National Center for Biotechnology Information. http://www.
ncbi.nlm.nih.gov (accessed January 1999).
References
The human kallikrein gene family is important to the
discipline of clinical chemistry because it contains genes
that encode for valuable cancer biomarkers, including the
best tumor marker available today, prostate-specific antigen (PSA). Despite reports of numerous kallikrein-like
genes in the mouse (1 ), until 2–3 years ago, only three
human kallikrein genes were recognized: pancreatic/
renal kallikrein (KLK1), human glandular kallikrein 2
(KLK2), and prostate-specific antigen (KLK3) (1, 2 ). The
proteins encoded by the three kallikrein genes are now
known as hK1, hK2, and hK3 (PSA). These three genes
encode for serine proteases with either trypsin-like (hK1,
hK2) or chymotrypsin-like (hK3) activity. Traditionally,
kallikreins have been defined as enzymes that can act on
high-molecular weight substrates and release bioactive
peptides, known as kinins (3 ). Among the known kal-
1. Edwards CQ, Griffen LM, Goldgar D, Drummond C, Skolnick MH, Kushner JP.
Prevalence of hemochromatosis among 11065 presumably healthy blood
donors. N Engl J Med 1988;318:1355– 62.
2. McLaren C, Gordeuk V, Looker A, Hasselblad V, Edwards CQ, Griffin LM, et al.
Prevalence of heterozygotes for hemochromatosis in the white population of
the United States. Blood 1995;86:2021–7.
3. Feder JN, Gnirke A, Thomas W, Tsuchihashi Z, Ruddy DA, Basava A, et al. A
novel MHC class I-like gene is mutated in patients with hereditary hemochromatosis. Nat Genet 1996;13:399 – 408.
4. Camaschella C, Piperno A. Hereditary hemochromatosis: recent advances in
molecular genetics and clinical management. Haematologica 1997;82:77–
84.
5. Jouanolle AM, Fergelot P, Gandon G, Yaouanq J, Le Gall JY, David V. A
candidate gene for hemochromatosis: frequency of the C282Y and H63D
mutations. Hum Genet 1997;100:544 –7.
6. Jackson HA, Bowen DJ, Worwood M. Rapid genetic screening for haemochromatosis using heteroduplex technology. Br J Hematol 1997;98:856 –9.
7. Wood M, Albagli D, Cheng P, Huan B, Van Atta R. Nucleic acid crosslinking
probes for DNA/RNA diagnostics [Abstract]. Clin Chem 1996;42:S196.
8. Zehnder J, Van Atta R, Jones C, Sussmann H, Wood M. Cross-linking
New Nomenclature for the Human Tissue Kallikrein
Gene Family, Eleftherios P. Diamandis,1,2* George M.
Yousef,1,2 Judith Clements,3 Linda K. Ashworth,4 Shigetaka
Yoshida,5 Torbjorn Egelrud,6 Peter S. Nelson,7 Sadao
Shiosaka,5 Sheila Little,8 Hans Lilja,9 Ulf-Hakan Stenman,10
Harry G. Rittenhouse,11 and Hester Wain12 (1 Department of
Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; 2 Department of
Laboratory Medicine and Pathobiology, University of
Toronto, Ontario M5G 1L5, Canada; 3 Centre for Molecular Biotechnology, School of Life Sciences, Queensland
University of Technology, Brisbane, Australia 4001; 4 Human Genome Center, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94551; 5 Division of Structural Cell
Biology, Nara Institute of Science and Technology, 8916-5
Takayama Ikoma, Nara 630-0101, Japan; 6 Department of
Dermatology, University Hospital, S-901 85 Umeå, Sweden; 7 Department of Molecular Biotechnology, University of Washington, Seattle, WA 98105; 8 Central Nervous
System Research, Lilly Research Laboratories, Indianapolis, IN 46285; 9 Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, S-20502
Malmo¨, Sweden; 10 Department of Clinical Chemistry,
Helsinki University Central Hospital, FIN-00290 Helsinki,
Finland; 11 Hybritech Inc., PO Box 269006, San Diego,
CA 92196; 12 Human Gene Nomenclature Committee,
The Galton Laboratory, University College, London
NW1 2HE, United Kingdom, * address correspondence to
this author at: Department of Pathology and Laboratory
Medicine, Mount Sinai Hospital, 600 University Ave.,
Toronto, Ontario M5G 1X5, Canada; e-mail ediamandis@
mtsinai.on.ca)