Abstract for presentation at 11th International Congress of Human Genetics

Utility of whole genome amplified DNA in studies using high-density oligonucleotide array-based genotyping

  • Muhammad Kibriya, Mailman School of Public Health, Columbia University, New York, USA., United States
  • Farzana Jasmine, Mailman School of Public Health, Columbia University, New York, USA., United States
  • Irene Andrulis, University of Toronto, ON, Canada
  • Esther John, Northern California Cancer Center, CA, United States
  • Jenny Chang-Claude, German Cancer Research Center, Heidelberg, Germany
  • Habibul Ahsan, Mailman School of Public Health, Columbia University, New York, USA., United States

    • Successful whole genome amplification (WGA) removes the barrier of finite quantity of genomic DNA (gDNA) for genome wide single nucleotide polymorphism (SNP) analysis. We compared the genome-wide genotype call concordance using a total of 14 gDNA samples from 3 different centers (4 samples / center and 2 reference samples) and their corresponding 14 WGA samples by genotyping using early access Affymetrix Mendel Nsp Array chip containing 224,940 SNPs. We also checked the reproducibility of genotype calls by repeating the same gDNA on two different chips. Similarly, we also checked the reproducibility of WGA samples. We used Repli-g DNA Polymerase for WGA from 25 ng gDNA. Overall, genotype call rate was 88.54% (95% CI 81.48% – 93.22%) for gDNA and 91.39% (95% CI 87.78% -93.70%) for WGA DNA (p=0.03). There was no significant difference in call rates (%±SD) within the gDNA from different centers (87.58±2.25, 85.94±4.83, 90.26±4.01, p=0.32) as well as within their corresponding WGA samples (92.02±1.69, 90.75±2.01, 92.68±1.16, p=0.29). We also did not observe any change in call rates using 60 ug or 90 ug of amplified PCR product of WGA for hybridization (92.4±0.81 vs. 91.23±2.23, p=0.25). Concordance between genotype calls from gDNA and WGA was 98.16% (95% CI 96.28% – 99.39%) without significant difference between centers. Majority of the discordant calls involved heterozygotes. Reproducibility, calculated as concordance in duplicate sample, was 99.49% for gDNA and 99.15% for WGA sample. Detailed characteristics of the small fraction of SNPs producing discordant calls for each of the comparisons will be presented in the meeting. Our study confirms that high density oligonucleotide array-based genotyping can yield reproducible data and WGA products can be effectively used for genome-wide SNP analysis.

    Conference Organiser - ICMS Pty Ltd