Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing.
Although many quality control (QC) methods have been developed to improve the quality of single-nucleotide variants (SNVs) in SNV-calling, QC methods for use subsequent to single-nucleotide polymorphism-calling have not been reported. We developed five QC metrics to improve the quality of SNVs using the whole-genome-sequencing data of a monozygotic twin pair from the Korean Personal Genome Project. The QC metrics improved both repeatability between the monozygotic twin pair and reproducibility between SNV-calling pipelines. We demonstrated the QC metrics improve reproducibility of SNVs derived from not only whole-genome-sequencing data but also whole-exome-sequencing data. The QC metrics are calculated based on the reference genome used in the alignment without accessing the raw and intermediate data or knowing the SNV-calling details. Therefore, the QC metrics can be easily adopted in downstream association analysis.
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
W
W
Zhang
Office of The Center Director, Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, MD, USA.
V
V
Soika
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
J
J
Meehan
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
Z
Z
Su
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
W
W
Ge
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
H W
HW
Ng
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
R
R
Perkins
Office of The Center Director, Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, MD, USA.
V
V
Simonyan
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
W
W
Tong
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
H
H
Hong
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000592:standards*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011786:Quality Control; D015203:Reproducibility of Results; D056910:Republic of Korea; D014430:Twins, Monozygotic