FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution

被引：225

作者：

Newman, Aaron M. ^{[1
,2
]}

Bratman, Scott V. ^{[1
,3
]}

Stehr, Henning ^{[4
]}

Lee, Luke J. ^{[1
,4
]}

Liu, Chih Long ^{[1
,2
]}

Diehn, Maximilian ^{[1
,3
,4
]}

Alizadeh, Ash A. ^{[1
,2
,4
]}

机构：

[1] Stanford Univ, Inst Stem Cell Biol & Regenerat Med, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Med, Div Oncol, Stanford, CA 94305 USA

[3] Stanford Univ, Dept Radiat Oncol, Stanford, CA 94305 USA

[4] Stanford Univ, Stanford Canc Inst, Stanford, CA 94305 USA

来源：

BIOINFORMATICS | 2014年 / 30卷 / 23期

基金：

美国国家卫生研究院;

关键词：

ANAPLASTIC LYMPHOMA KINASE; CELL LUNG-CANCER; STRUCTURAL VARIATION; CHROMOSOME; TUMORS;

D O I：

10.1093/bioinformatics/btu549

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment/Map file and produces easily interpretable output. We demonstrate FACTERA's ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets.

引用

页码：3390 / 3393

页数：4

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