BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads

Linfang Jin; Jinhuo Lai; Yang Zhang; Ying Fu; Shuhang Wang; Heng Dai; Bingding Huang

doi:10.1093/bioinformatics/bty1070

BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads

Bioinformatics. 2019 Aug 15;35(16):2859-2861. doi: 10.1093/bioinformatics/bty1070.

Authors

Linfang Jin¹, Jinhuo Lai², Yang Zhang¹, Ying Fu¹, Shuhang Wang³, Heng Dai¹, Bingding Huang¹

Affiliations

¹ Department of Research and Development, Sinotech Genomics Inc., Shanghai, China.
² Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, China.
³ Thoracic Medical Oncology Department, Peking University Cancer Hospital, Beijing, China.

PMID: 30601940
DOI: 10.1093/bioinformatics/bty1070

Abstract

Summary: Here we developed a tool called Breakpoint Identification (BreakID) to identity fusion events from targeted sequencing data. Taking discordant read pairs and split reads as supporting evidences, BreakID can identify gene fusion breakpoints at single nucleotide resolution. After validation with confirmed fusion events in cancer cell lines, we have proved that BreakID can achieve high sensitivity of 90.63% along with PPV of 100% at sequencing depth of 500× and perform better than other available fusion detection tools. We anticipate that BreakID will have an extensive popularity in the detection and analysis of fusions involved in clinical and research sequencing scenarios.

Availability and implementation: Source code is freely available at https://github.com/SinOncology/BreakID.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Gene Fusion*
Genomics*
High-Throughput Nucleotide Sequencing
Humans
Neoplasms / genetics
Sequence Analysis, DNA
Software