Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples

DSpace/Manakin Repository

Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples

Show simple item record

dc.contributor.author Loomis, Stephanie J.
dc.contributor.author Olson, Lana M.
dc.contributor.author Mirel, Daniel
dc.contributor.author Crenshaw, Andrew
dc.contributor.author Rahhal, Brandon
dc.contributor.author Tetreault, Stephanie
dc.contributor.author Kraft, Peter
dc.contributor.author Haines, Jonathan L.
dc.contributor.author Pasquale, Louis
dc.contributor.author Wiggs, Janey Lee
dc.contributor.author Parkin, Melissa
dc.contributor.author Tworoger, Shelley Slate
dc.contributor.author Kang, Jae Hee Hee
dc.date.accessioned 2012-02-12T01:34:00Z
dc.date.issued 2010
dc.identifier.citation Loomis, Stephanie J., Lana M. Olson, Louis R. Pasquale, Janey Wiggs, Daniel Mirel, Andrew Crenshaw, Melissa Parkin, et al. 2010. Feasibility of high-throughput genome-wide genotyping using DNA from stored buccal cell samples. Biomarker Insights 5: 49-55. en_US
dc.identifier.issn 1177-2719 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:8156559
dc.description.abstract It is unclear if buccal cell samples contain sufficient human DNA with adequately sized fragments for high throughput genetic bioassays. Yet buccal cell sample collection is an attractive alternative to gathering blood samples for genetic epidemiologists engaged in large-scale genetic biomarker studies. We assessed the genotyping efficiency (GE) and genotyping concordance (GC) of buccal cell DNA samples compared to corresponding blood DNA samples, from 32 Nurses’ Health Study (NHS) participants using the Illumina Infinium 660W-Quad platform. We also assessed how GE and GC accuracy varied as a function of DNA concentration using serial dilutions of buccal DNA samples. Finally we determined the nature and genomic distribution of discordant genotypes in buccal DNA samples. The mean GE of undiluted buccal cell DNA samples was high (99.32%), as was the GC between the paired buccal and blood samples (99.29%). GC between the dilutions versus the undiluted buccal DNA was also very high (greater than 97%), though both GE and GC notably declined at DNA concentrations less than 5 ng/μl. Most (greater than 95%) genotype determinations in buccal cell samples were of the “missing call” variety (as opposed to the “alternative genotype call” variety) across the spectrum of buccal DNA concentrations studied. Finally, for buccal DNA concentration above 1.7 ng/ul, discordant genotyping calls did not cluster in any particular chromosome. Buccal cell-derived DNA represents a viable alternative to blood DNA for genotyping on a high-density platform. en_US
dc.language.iso en_US en_US
dc.publisher Libertas Academica en_US
dc.relation.isversionof doi:10.4137/BMI.S5062 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879226/pdf/ en_US
dash.license LAA
dc.subject buccal cell DNA en_US
dc.subject saliva DNA en_US
dc.subject GWAS en_US
dc.subject genotyping en_US
dc.subject low concentration DNA en_US
dc.title Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal Biomarker Insights en_US
dash.depositing.author Tworoger, Shelley Slate
dc.date.available 2012-02-12T01:34:00Z
dash.affiliation.other SPH^Epidemiology en_US
dash.affiliation.other HMS^Medicine-Brigham and Women's Hospital en_US

Files in this item

Files Size Format View
2879226.pdf 550.4Kb PDF View/Open

This item appears in the following Collection(s)

Show simple item record

 
 

Search DASH


Advanced Search
 
 

Submitters