Quantitative criteria for improving performance of buccal DNA for high-throughput genetic analysis

BMC Genetics

Daniel Woo²  Ranjan Deka²  Hong Cheng²  Subba R Indugula²  Guangyun Sun²  Mary Haverbusch²  Charles J Moomaw²  Carl D Langefeld³  Timothy D Howard³  W Mark Brown³  Lili Ding¹  Lisa J Martin²  Jessica G Woo² 

[1] Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229–3039, USA;University of Cincinnati College of Medicine, P.O. Box 670525, Cincinnati, OH, 45267–0525, USA;Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC, 27157, USA

关键词: Genetic;    Minor allele frequency (MAF);    Quality;    DNA;    Blood;    Buccal;   

Others  :  1121373
DOI  :  10.1186/1471-2156-13-75

 received in 2012-05-01, accepted in 2012-08-15,  发布年份 2012

【 摘 要 】

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 webcite).

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 < 0.0001). The ratio of double-stranded to total DNA (ds/total ratio) in the buccal samples was the only laboratory characteristic predicting sample success (p < 0.0001). A threshold of at least 34% ds/total DNA provided specificity of 98.7% with a 90.5% negative predictive value for eliminating probable failures. After genotyping, median sample call rates (99.1% vs. 99.4%, p < 0.0001) and heterozygosity rates (25.6% vs. 25.7%, p = 0.006) were lower for buccal versus blood DNA samples, respectively, but absolute differences were small. Minor allele frequency differences from HapMap were smaller for buccal than blood samples, and both sample types demonstrated tight genotyping clusters, even for rare alleles.

Conclusions

We identified a buccal sample characteristic, a ratio of ds/total DNA <34%, which distinguished buccal DNA samples likely to fail high-throughput genotyping. Applying this threshold, the quality of final genotyping resulting from buccal samples is somewhat lower, but compares favorably to blood. Caution is warranted if cases and controls have different sample types, but buccal samples provide comparable results to blood samples in large-scale genotyping analyses.

【 授权许可】

   
2012 Woo et al.; licensee BioMed Central Ltd.

【 图 表 】

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