Pradhananga S
School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology,
Tomtebodavagen 23A, SE-17165 Solna
Sweden
Research Article
Comparison of Variant Calls from Whole Genome and Whole Exome Sequencing Data Using Matched Samples
Author(s): Björn N, Pradhananga S, Sigurgeirsson B, Lundeberg J, Gréen H and Sahlén PBjörn N, Pradhananga S, Sigurgeirsson B, Lundeberg J, Gréen H and Sahlén P
Whole exome sequencing (WES) has been extensively used in genomic research. As sequencing costs decline
it is being replaced by whole genome sequencing (WGS) in large-scale genomic studies, but more comparative
information on WES and WGS datasets would be valuable. Thus, we have extensively compared variant calls
obtained from WGS and WES of matched germline DNA samples from 96 lung cancer patients. WGS provided
more homogeneous coverage with higher genotyping quality, and identified more variants, than WES, regardless
of exome coverage depth. It also called more reference variants, reflecting its power to call rare variants, and
more heterozygous variants that met applied quality criteria, indicating that WGS is less prone to allelic drop outs.
However, increasing WES coverage reduced the discrepancy between the WES and WGS results. We believe that
as sequencing costs further de.. View More»
