Genotyping of Inversions and Tandem Duplications
2016
Motivation: Next Generation Sequencing (NGS) has enabled studying structural genomic variants
(SVs) such as duplications and inversions in large cohorts. SVs have been shown to play important
roles in multiple diseases, including cancer. As costs for NGS continue to decline and variant databases
become ever more complete, the relevance of genotyping also SVs from NGS data increases steadily,
which is in stark contrast to the lack of tools to do so.
Results: We introduce a novel statistical approach, called DIGTYPER (Duplication and Inversion
GenoTYPER), which computes genotype likelihoods for a given inversion or duplication and reports
the maximum likelihood genotype. In contrast to purely coverage-based approaches, DIGTYPER
uses breakpoint-spanning read pairs as well as split alignments for genotyping, enabling typing also
of small events. We tested our approach on simulated and on real data and compared the genotype
predictions to those made by DELLY, which discovers SVs and computes genotypes. DIGTYPER
compares favorable especially for duplications (of all lengths) and for shorter inversions (up to 300 bp).
In contrast to DELLY, our approach can genotype SVs from data bases without having to rediscover
them.
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