Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex™ whole genome amplified DNA generated from multiple DNA sources

Authors

  • Andrew W. Bergen,

    Corresponding author
    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
    • Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 6120 Executive Boulevard, Bethesda, MD. 20892-7236
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  • Kashif A. Haque,

    1. Core Genotyping Facility, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland
    2. Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC, Frederick, Maryland
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  • Ying Qi,

    1. Core Genotyping Facility, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland
    2. Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC, Frederick, Maryland
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  • Michael B. Beerman,

    1. Core Genotyping Facility, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland
    2. Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC, Frederick, Maryland
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  • Montserrat Garcia-Closas,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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  • Nathaniel Rothman,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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  • Stephen J. Chanock

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
    2. Core Genotyping Facility, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland
    3. Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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  • Communicated by Ann-Christine Syvänen

  • The contents of this publication does not necessarily reflect the views of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsed by the U.S. Government. The publisher or recipient acknowledges the right of the U.S. Government to retain a nonexclusive, royalty-free license in and to any copyright covering the article.

Abstract

The promise of whole genome amplification (WGA) is that genomic DNA (gDNA) quantity will not limit molecular genetic analyses. Multiple displacement amplification (MDA) and the OmniPlex™ PCR-based WGA protocols were evaluated using 4 and 5 ng of input gDNA from 60 gDNA samples from three tissue sources (mouthwash, buffy coat, and lymphoblast). WGA DNA (wgaDNA) yield and genotyping performance were evaluated using genotypes determined from gDNA and wgaDNA using the AmpFlSTR® Identifiler® assay and N=49 TaqMan® SNP assays. Short tandem repeat (STR) and SNP genotyping completion and concordance rates were significantly reduced with wgaDNA from all WGA methods compared with gDNA. OmniPlex wgaDNA exhibited a greater reduction in genotyping performance than MDA wgaDNA. Reduced wgaDNA genotyping performance was due to allelic (all protocols) and locus (OmniPlex) amplification bias leading to heterozygote and locus dropout, respectively, and %GC sequence content (%GC) was significantly correlated with TaqMan assay performance. Lymphoblast wgaDNA exhibited higher yield (OmniPlex), buffy coat wgaDNA exhibited higher STR genotyping completion (MDA), whereas mouthwash wgaDNA exhibited higher SNP genotyping discordance (MDA). Genotyping of wgaDNA generated from ≤5 ng gDNA, e.g., from archaeological, forensic, prenatal diagnostic, or pathology samples, may require additional genotyping validation with gDNA and/or more sophisticated analysis of genotypes incorporating observed reductions in genotyping performance. Hum Mutat 26(3), 262–270, 2005. © 2005 Wiley-Liss, Inc.

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