STRetch: detecting and discovering pathogenic short tandem repeat expansions

被引：84

作者：

Dashnow, Harriet ^{[1
,2
]}

Lek, Monkol ^{[3
,4
]}

Phipson, Belinda ^{[1
]}

Halman, Andreas ^{[1
,5
]}

Sadedin, Simon ^{[1
]}

Lonsdale, Andrew ^{[1
]}

Davis, Mark ^{[6
]}

Lamont, Phillipa ^{[7
]}

Clayton, Joshua S. ^{[8
]}

Laing, Nigel G. ^{[8
]}

MacArthur, Daniel G. ^{[3
,4
]}

Oshlack, Alicia ^{[1
,2
]}

机构：

[1] Royal Childrens Hosp, Murdoch Childrens Res Inst, Parkville, Vic, Australia

[2] Univ Melbourne, Sch Biosci, Parkville, Vic, Australia

[3] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA

[4] Broad Inst MIT & Harvard, Program Med & Populat Genet, Cambridge, MA 02142 USA

[5] Univ Melbourne, Florey Inst Neurosci & Mental Hlth, Parkville, Vic, Australia

[6] QEII Med Ctr, Dept Diagnost Genom, PathWest Lab Med, Nedlands, WA, Australia

[7] Royal Perth Hosp, Neurogenet Unit, Perth, WA, Australia

[8] Univ Western Australia, Ctr Med Res, Harry Perkins Inst Med Res, Nedlands, WA, Australia

来源：

GENOME BIOLOGY | 2018年 / 19卷

基金：

澳大利亚国家健康与医学研究理事会; 英国医学研究理事会;

关键词：

STRUCTURAL VARIATION; SEQUENCE; MECHANISMS; TOOL;

D O I：

10.1186/s13059-018-1505-2

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read length and so are unable to detect the majority of pathogenic expansions. Here we present STRetch, a new genome-wide method to scan for STR expansions at all loci across the human genome. We demonstrate the use of STRetch for detecting STR expansions using short-read whole-genome sequencing data at known pathogenic loci as well as novel STR loci. STRetch is open source software, available from github.com/Oshlack/STRetch.

引用

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