title: A practical method to detect SNVs and indels from whole genome and exome sequencing data.
abstract: The recent development of massively parallel sequencing technology has allowed the creation of comprehensive catalogs of genetic variation. However, due to the relatively high sequencing error rate for short read sequence data, sophisticated analysis methods are required to obtain high-quality variant calls. Here, we developed a probabilistic multinomial method for the detection of single nucleotide variants (SNVs) as well as short insertions and deletions (indels) in whole genome sequencing (WGS) and whole exome sequencing (WES) data for single sample calling. Evaluation with DNA genotyping arrays revealed a concordance rate of 99.98% for WGS calls and 99.99% for WES calls. Sanger sequencing of the discordant calls determined the false positive and false negative rates for the WGS (0.0068% and 0.17%) and WES (0.0036% and 0.0084%) datasets. Furthermore, short indels were identified with high accuracy (WGS: 94.7%, WES: 97.3%). We believe our method can contribute to the greater understanding of human diseases.
authors.affiliation: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors.forename: Daichi
authors.initials: D
authors.lastname: Shigemizu
authors.forename: Akihiro
authors.initials: A
authors.lastname: Fujimoto
authors.forename: Shintaro
authors.initials: S
authors.lastname: Akiyama
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Abe
authors.forename: Kaoru
authors.initials: K
authors.lastname: Nakano
authors.forename: Keith A
authors.initials: KA
authors.lastname: Boroevich
authors.forename: Yujiro
authors.initials: Y
authors.lastname: Yamamoto
authors.forename: Mayuko
authors.initials: M
authors.lastname: Furuta
authors.forename: Michiaki
authors.initials: M
authors.lastname: Kubo
authors.forename: Hidewaki
authors.initials: H
authors.lastname: Nakagawa
authors.forename: Tatsuhiko
authors.initials: T
authors.lastname: Tsunoda
mesh_terms: D059472:Exome; D015894:Genome, Human; D006801:Humans; D020641:Polymorphism, Single Nucleotide