Identifying viral integration sites using SeqMap 2.0

被引：28

作者：

Hawkins, Troy B. ^{[1
]}

Dantzer, Jessica ^{[2
]}

Peters, Brandon ^{[2
]}

Dinauer, Mary ^{[1
,3
]}

Mockaitis, Keithanne ^{[4
]}

Mooney, Sean ^{[5
]}

Cornetta, Kenneth ^{[1
]}

机构：

[1] Indiana Univ, Sch Med, Dept Med & Mol Genet, Indianapolis, IN 46202 USA

[2] Indiana Univ, Sch Med, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA

[3] Indiana Univ, Sch Med, Dept Pediat, Herman B Wells Ctr Pediat Res, Indianapolis, IN 46202 USA

[4] Indiana Univ, Ctr Genom & Bioinformat, Bloomington, IN 47405 USA

[5] Buck Inst Age Res, Novato, CA 94945 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 05期

基金：

美国国家卫生研究院;

关键词：

GENE-THERAPY; VECTOR INTEGRATION; HIGH-ACCURACY; ALIGNMENT; INSERTION; SCID-X1; CELLS;

D O I：

10.1093/bioinformatics/btq722

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.

引用

页码：720 / 722

页数：3

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