Skip to main content Accessibility help
×
Home
Hostname: page-component-cf9d5c678-p4zth Total loading time: 0.353 Render date: 2021-08-04T15:00:10.177Z Has data issue: true Feature Flags: { "shouldUseShareProductTool": true, "shouldUseHypothesis": true, "isUnsiloEnabled": true, "metricsAbstractViews": false, "figures": true, "newCiteModal": false, "newCitedByModal": true, "newEcommerce": true, "newUsageEvents": true }

A Comparison of DNA Pools Constructed Following Whole Genome Amplification for Two-Stage SNP Genotyping Designs

Published online by Cambridge University Press:  21 February 2012

Zhen Zhen Zhao
Affiliation:
Molecular Epidemiology and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia.
Dale R. Nyholt
Affiliation:
Molecular Epidemiology and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia.
Michael R. James
Affiliation:
Molecular Epidemiology and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia.
Renee Mayne
Affiliation:
Molecular Epidemiology and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia.
Susan A. Treloar
Affiliation:
Molecular Epidemiology and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia.
Grant W. Montgomery
Affiliation:
Molecular Epidemiology and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Australia. Grant.Montgomery@qimr.edu.au
Corresponding

Abstract

Genotyping in DNA pools reduces the cost and the time required to complete large genotyping projects. The aim of the present study was to evaluate pooling as part of a strategy for fine mapping in regions of significant linkage. Thirty-nine single nucleotide polymorphisms (SNPs) were analyzed in two genomic DNA pools of 384 individuals each and results compared with data after typing all individuals used in the pools. There were no significant differences using data from either 2 or 8 heterozygous individuals to correct frequency estimates for unequal allelic amplification. After correction, the mean difference between estimates from the genomic pool and individual allele frequencies was .033. A major limitation of the use of DNA pools is the time and effort required to carefully adjust the concentration of each individual DNA sample before mixing aliquots. Pools were also constructed by combining DNA after Multiple Displacement Amplification (MDA). The MDA pools gave similar results to pools constructed after careful DNA quantitation (mean difference from individual genotyping .040) and MDA provides a rapid method to generate pools suitable for some applications. Pools provide a rapid and cost-effective screen to eliminate SNPs that are not polymorphic in a test population and can detect minor allele frequencies as low as 1% in the pooled samples. With current levels of accuracy, pooling is best suited to an initial screen in the SNP validation process that can provide high-throughput comparisons between cases and controls to priori- tize SNPs for subsequent individual genotyping.

Type
Articles
Copyright
Copyright © Cambridge University Press 2005
You have Access
7
Cited by

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.

A Comparison of DNA Pools Constructed Following Whole Genome Amplification for Two-Stage SNP Genotyping Designs
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.

A Comparison of DNA Pools Constructed Following Whole Genome Amplification for Two-Stage SNP Genotyping Designs
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.

A Comparison of DNA Pools Constructed Following Whole Genome Amplification for Two-Stage SNP Genotyping Designs
Available formats
×
×

Reply to: Submit a response

Please enter your response.

Your details

Please enter a valid email address.

Conflicting interests

Do you have any conflicting interests? *