Genotyping of Single Nucleotide Polymorphisms in DNA Isolated from Serum Using Sequenom MassARRAY Technology.
BACKGROUND
Large epidemiologic studies have the potential to make valuable contributions to the assessment of gene-environment interactions because they prospectively collected detailed exposure data. Some of these studies, however, have only serum or plasma samples as a low quantity source of DNA.


METHODS
We examined whether DNA isolated from serum can be used to reliably and accurately genotype single nucleotide polymorphisms (SNPs) using Sequenom multiplex SNP genotyping technology. We genotyped 81 SNPs using samples from 158 participants in the NYU Women's Health Study. Each participant had DNA from serum and at least one paired DNA sample isolated from a high quality source of DNA, i.e. clots and/or cell precipitates, for comparison.


RESULTS
We observed that 60 of the 81 SNPs (74%) had high call frequencies (≥95%) using DNA from serum, only slightly lower than the 85% of SNPs with high call frequencies in DNA from clots or cell precipitates. Of the 57 SNPs with high call frequencies for serum, clot, and cell precipitate DNA, 54 (95%) had highly concordant (>98%) genotype calls across all three sample types. High purity was not a critical factor to successful genotyping.


CONCLUSIONS
Our results suggest that this multiplex SNP genotyping method can be used reliably on DNA from serum in large-scale epidemiologic studies.
Department of Population Health, New York University School of Medicine, New York, New York, United States of America.
Tess V
TV
Clendenen
Department of Population Health, New York University School of Medicine, New York, New York, United States of America.
Justin
J
Rendleman
Department of Population Health, New York University School of Medicine, New York, New York, United States of America.
Wenzhen
W
Ge
Department of Population Health, New York University School of Medicine, New York, New York, United States of America.
Karen L
KL
Koenig
Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America.
Isaac
I
Wirgin
Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America.
Diane
D
Currie
Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America; Radiation Effects Research Foundation, Hiroshima Japan.
Roy E
RE
Shore
Department of Population Health, New York University School of Medicine, New York, New York, United States of America.
Tomas
T
Kirchhoff
Department of Population Health, New York University School of Medicine, New York, New York, United States of America; NYU Cancer Institute, New York University Langone Medical Center, New York, New York, United States of America.
Anne
A
Zeleniuch-Jacquotte
D000328:Adult; D000368:Aged; D004247:DNA / Q000097:blood / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies
D004247:DNA