TY - JOUR T1 - Impact of DNA source on genetic variant detection from human whole-genome sequencing data JF - Journal of Medical Genetics JO - J Med Genet DO - 10.1136/jmedgenet-2019-106281 SP - jmedgenet-2019-106281 AU - Brett Trost AU - Susan Walker AU - Syed A Haider AU - Wilson W L Sung AU - Sergio Pereira AU - Charly L Phillips AU - Edward J Higginbotham AU - Lisa J Strug AU - Charlotte Nguyen AU - Akshaya Raajkumar AU - Michael J Szego AU - Christian R Marshall AU - Stephen W Scherer Y1 - 2019/09/12 UR - http://jmg.bmj.com/content/early/2019/09/11/jmedgenet-2019-106281.abstract N2 - Background Whole blood is currently the most common DNA source for whole-genome sequencing (WGS), but for studies requiring non-invasive collection, self-collection, greater sample stability or additional tissue references, saliva or buccal samples may be preferred. However, the relative quality of sequencing data and accuracy of genetic variant detection from blood-derived, saliva-derived and buccal-derived DNA need to be thoroughly investigated.Methods Matched blood, saliva and buccal samples from four unrelated individuals were used to compare sequencing metrics and variant-detection accuracy among these DNA sources.Results We observed significant differences among DNA sources for sequencing quality metrics such as percentage of reads aligned and mean read depth (p<0.05). Differences were negligible in the accuracy of detecting short insertions and deletions; however, the false positive rate for single nucleotide variation detection was slightly higher in some saliva and buccal samples. The sensitivity of copy number variant (CNV) detection was up to 25% higher in blood samples, depending on CNV size and type, and appeared to be worse in saliva and buccal samples with high bacterial concentration. We also show that methylation-based enrichment for eukaryotic DNA in saliva and buccal samples increased alignment rates but also reduced read-depth uniformity, hampering CNV detection.Conclusion For WGS, we recommend using DNA extracted from blood rather than saliva or buccal swabs; if saliva or buccal samples are used, we recommend against using methylation-based eukaryotic DNA enrichment. All data used in this study are available for further open-science investigation. ER -