BreakID：使用不一致对和拆分读取进行基因组学断点识别以检测基因融合事件。

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

机构信息

Department of Research and Development, Sinotech Genomics Inc., Shanghai, China.

Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, China.

出版信息

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

DOI:10.1093/bioinformatics/bty1070

PMID:30601940

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.

摘要

在这里，我们开发了一种名为 Breakpoint Identification（BreakID）的工具，用于从靶向测序数据中识别融合事件。BreakID 以不一致的读对和拆分读作为支持证据，可以在单核苷酸分辨率处识别基因融合断点。在通过癌细胞系中确认的融合事件进行验证后，我们证明了在测序深度为 500×时，BreakID 可以实现 90.63%的高灵敏度和 100%的 PPV，并且优于其他可用的融合检测工具。我们预计 BreakID 将在临床和研究测序场景中涉及融合的检测和分析中得到广泛应用。