A genome-wide approach for detecting novel insertion-deletion variants of mid-range size

作者：Xia Li C; Sakshuwong Sukolsak; Hopmans Erik S; Bell John M; Grimes Susan M; Siegmund David O; Ji Hanlee P^*; Zhang Nancy R^*

来源：Nucleic Acids Research, 2016, 44(15): e126.

DOI：10.1093/nar/gkw481

We present SWAN, a statistical framework for robust detection of genomic structural variants in next-generation sequencing data and an analysis of mid-range size insertion and deletions (< 10 Kb) for whole genome analysis and DNA mixtures. To identify these mid-range size events, SWAN collectively uses information from read-pair, read-depth and one end mapped reads through statistical likelihoods based on Poisson field models. SWAN also uses softclip/split read remapping to supplement the likelihood analysis and determine variant boundaries. The accuracy of SWAN is demonstrated by in silico spike-ins and by identification of known variants in the NA12878 genome. We used SWAN to identify a series of novel set of mid-range insertion/ deletion detection that were confirmed by targeted deep resequencing. An R package implementation of SWAN is open source and freely available.

• 出版日期2016-9-6