Comparison of structural variants detected by optical mapping with long-read next-generation sequencing

• DOI: 10.1093/bioinformatics/btab359
• Publication Date: 2021-05-09T11:08:19Z
• Authors: Jakub Savara; Tomáš Novosád; Petr Gajdoš; Eva Kriegová
• Keywords: Optical mapping

Recent studies have shown the potential of using long-read whole-genome sequencing (WGS) approaches and optical mapping (OM) for detection clinically relevant structural variants (SVs) in cancer research. Three main WGS platforms are currently use: Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT) 10x Genomics. Recently, OM technology (Bionano Genomics) has been introduced into human diagnostics. Questions remain about accuracy these platforms, how comparable/interchangeable they when searching SVs to what extent can be replaced or supplemented by OM. Moreover, no tool effectively compare obtained WGS.This study compared maps breast cell line SKBR3 with AnnotSV outputs from platforms. For this purpose, a software comparative filtering features was developed. The majority up 50 kbp distance variance threshold found were confirmed all ∼99% translocations ∼80% deletions both PacBio ONT, ∼70% being Genomics combination and/or ONT. Interestingly, long (>100 kbp) detected only Regarding insertions, ∼74% but none Inversions duplications not WGS. enabled confirmation that overlapped same gene(s) applied disease-associated SVs.https://github.com/novosadt/om-annotsv-svc.