RT Journal Article
SR Electronic
T1 Impact of DNA source on genetic variant detection from human whole-genome sequencing data
JF Journal of Medical Genetics
JO J Med Genet
FD BMJ Publishing Group Ltd
SP 809
OP 817
DO 10.1136/jmedgenet-2019-106281
VO 56
IS 12
A1 Trost, Brett
A1 Walker, Susan
A1 Haider, Syed A
A1 Sung, Wilson W L
A1 Pereira, Sergio
A1 Phillips, Charly L
A1 Higginbotham, Edward J
A1 Strug, Lisa J
A1 Nguyen, Charlotte
A1 Raajkumar, Akshaya
A1 Szego, Michael J
A1 Marshall, Christian R
A1 Scherer, Stephen W
YR 2019
UL http://jmg.bmj.com/content/56/12/809.abstract
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.