Twin Research and Human Genetics

Articles

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

Grant W. Montgomerya1 c1, Megan J. Campbella2, Peter Dicksona3, Shane Herberta4, Kirby Siemeringa5, Kelly R. Ewen-Whitea6, Peter M. Visschera7 and Nicholas G. Martina8

a1 Queensland Institute of Medical Research, Brisbane, Australia. Grant.Montgomery@qimr.edu.au

a2 Queensland Institute of Medical Research, Brisbane, Australia.

a3 Queensland Institute of Medical Research, Brisbane, Australia.

a4 Australian Genome Research Facility, Melbourne, Australia.

a5 Australian Genome Research Facility, Melbourne, Australia.

a6 Australian Genome Research Facility, Melbourne, Australia.

a7 Queensland Institute of Medical Research, Brisbane, Australia.

a8 Queensland Institute of Medical Research, Brisbane, Australia.

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.

(Received March 31 2005)

(Accepted May 27 2005)

Correspondence:

c1 Address for correspondence: Grant Montgomery, Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Queensland 4029, Australia.

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