Skip to main content
×
Home
    • Aa
    • Aa

Estimation of the Rate of SNP Genotyping Errors From DNA Extracted From Different Tissues

  • Grant W. Montgomery (a1), Megan J. Campbell (a2), Peter Dickson (a3), Shane Herbert (a4), Kirby Siemering (a5), Kelly R. Ewen-White (a6), Peter M. Visscher (a7) and Nicholas G. Martin (a8)...
Abstract
Abstract

High density single nucleotide polymorphism (SNP) genotyping panels provide an alternative to microsatellite markers for genome scans. However, genotype errors have a major impact on power to detect linkage or association and are difficult to detect for SNPs. We estimated error rates with the Affymetrix GeneChip® SNP platform in samples from a family with a mixed set of monozygotic (MZ) and dizygotic (DZ) triplets using lymphocyte, buccal DNA and samples from whole genome amplification using the multiple displacement amplification (MDA) technique. The average call rate from 58,960 SNPs for five genomic samples was 99.48%. Comparison of results for the MZ twins showed only three discordant genotypes (concordance rate 99.995%). The mean concordance rate for comparisons of samples from lymphocyte and buccal DNA was 99.97%. Mendelian inconsistencies were identified in 46 SNPs with errors in one or more family members, a rate of 0.022%. Observed genotype concordance rates between parents, between parents and children, and among siblings were consistent with previously reported allele frequencies and Hardy–Weinberg equilibrium. Using the MDA technique, results for two samples had equivalent high accuracy to results with genomic samples. However, the SNP call rate for the remaining seven samples varied from 72.5% to 99.5%, with an average of 86.11%. Quality of the DNA sample following the MDA reaction appears to be the critical factor in SNP call rate for MDA samples. Our results demonstrate highly accurate and reproducible genotyping for the Affymetrix GeneChip® Human Mapping Set in lymphocyte and buccal DNA samples.

    • Send article to Kindle

      To send this article to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Estimation of the Rate of SNP Genotyping Errors From DNA Extracted From Different Tissues
      Available formats
      ×
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your Dropbox account. Find out more about sending content to Dropbox.

      Estimation of the Rate of SNP Genotyping Errors From DNA Extracted From Different Tissues
      Available formats
      ×
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your Google Drive account. Find out more about sending content to Google Drive.

      Estimation of the Rate of SNP Genotyping Errors From DNA Extracted From Different Tissues
      Available formats
      ×
Copyright
Corresponding author
*Address for correspondence: Grant Montgomery, Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Queensland 4029, Australia.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Twin Research and Human Genetics
  • ISSN: 1832-4274
  • EISSN: 1839-2628
  • URL: /core/journals/twin-research-and-human-genetics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×