PT  - JOURNAL ARTICLE
AU  - Trost, Brett
AU  - Walker, Susan
AU  - Haider, Syed A
AU  - Sung, Wilson W L
AU  - Pereira, Sergio
AU  - Phillips, Charly L
AU  - Higginbotham, Edward J
AU  - Strug, Lisa J
AU  - Nguyen, Charlotte
AU  - Raajkumar, Akshaya
AU  - Szego, Michael J
AU  - Marshall, Christian R
AU  - Scherer, Stephen W
TI  - Impact of DNA source on genetic variant detection from human whole-genome sequencing data
AID  - 10.1136/jmedgenet-2019-106281
DP  - 2019 Dec 01
TA  - Journal of Medical Genetics
PG  - 809--817
VI  - 56
IP  - 12
4099  - http://jmg.bmj.com/content/56/12/809.short
4100  - http://jmg.bmj.com/content/56/12/809.full
SO  - J Med Genet2019 Dec 01; 56
AB  - 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.