501. Quantitative criteria for improving performance of buccal DNA for high-throughput genetic analysis
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Ranjan Deka, Daniel Woo, Lisa J. Martin, Mary Haverbusch, W. Mark Brown, Jessica G. Woo, Subba Rao Indugula, Charles J Moomaw, Lili Ding, Carl D. Langefeld, Hong Cheng, Timothy D. Howard, and Guangyun Sun
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Male ,Genotyping Techniques ,Minor allele frequency (MAF) ,lcsh:QH426-470 ,Population ,Biology ,Genetic analysis ,03 medical and health sciences ,Buccal ,0302 clinical medicine ,Genetic ,stomatognathic system ,medicine ,Genetics ,Humans ,Genetics(clinical) ,International HapMap Project ,education ,Genotyping ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Mouth Mucosa ,Buccal administration ,DNA ,Cheek ,Quality ,Minor allele frequency ,lcsh:Genetics ,medicine.anatomical_structure ,Blood ,030220 oncology & carcinogenesis ,Research Article - Abstract
Background DNA from buccal brush samples is being used for high-throughput analyses in a variety of applications, but the impact of sample type on genotyping success and downstream statistical analysis remains unclear. The objective of the current study was to determine laboratory predictors of genotyping failure among buccal DNA samples, and to evaluate the successfully genotyped results with respect to analytic quality control metrics. Sample and genotyping characteristics were compared between buccal and blood samples collected in the population-based Genetic and Environmental Risk Factors for Hemorrhagic Stroke (GERFHS) study (https://gerfhs.phs.wfubmc.edu/public/index.cfm). Results Seven-hundred eight (708) buccal and 142 blood DNA samples were analyzed for laboratory-based and analysis metrics. Overall genotyping failure rates were not statistically different between buccal (11.3%) and blood (7.0%, p = 0.18) samples; however, both the Contrast Quality Control (cQC) rate and the dynamic model (DM) call rates were lower among buccal DNA samples (p Conclusions We identified a buccal sample characteristic, a ratio of ds/total DNA
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