Skip to main content Accessibility help
×
Home
Hostname: page-component-78dcdb465f-tqmtl Total loading time: 21.53 Render date: 2021-04-16T09:05:43.049Z Has data issue: true Feature Flags: { "shouldUseShareProductTool": true, "shouldUseHypothesis": true, "isUnsiloEnabled": true, "metricsAbstractViews": false, "figures": false, "newCiteModal": false, "newCitedByModal": true }

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

Published online by Cambridge University Press:  21 February 2012

Grant W. Montgomery
Affiliation:
Queensland Institute of Medical Research, Brisbane, Australia. Grant.Montgomery@qimr.edu.au
Megan J. Campbell
Affiliation:
Queensland Institute of Medical Research, Brisbane, Australia.
Peter Dickson
Affiliation:
Queensland Institute of Medical Research, Brisbane, Australia.
Shane Herbert
Affiliation:
Australian Genome Research Facility, Melbourne, Australia.
Kirby Siemering
Affiliation:
Australian Genome Research Facility, Melbourne, Australia.
Kelly R. Ewen-White
Affiliation:
Australian Genome Research Facility, Melbourne, Australia.
Peter M. Visscher
Affiliation:
Queensland Institute of Medical Research, Brisbane, Australia.
Nicholas G. Martin
Affiliation:
Queensland Institute of Medical Research, Brisbane, Australia.
Corresponding

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.

Type
Articles
Copyright
Copyright © Cambridge University Press 2005

Full text views

Full text views reflects PDF downloads, PDFs sent to Google Drive, Dropbox and Kindle and HTML full text views.

Total number of HTML views: 0
Total number of PDF views: 190 *
View data table for this chart

* Views captured on Cambridge Core between September 2016 - 16th April 2021. This data will be updated every 24 hours.

You have Access

Send article to Kindle

To send this article to your Kindle, first ensure no-reply@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. 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 <service> 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 <service> 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
×
×

Reply to: Submit a response


Your details


Conflicting interests

Do you have any conflicting interests? *