GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing

被引：97

作者：

Cameron, Daniel L. ^{[1
,2
,3
]}

Baber, Jonathan ^{[3
,4
]}

Shale, Charles ^{[3
,4
]}

Valle-Inclan, Jose Espejo ^{[5
,6
]}

Besselink, Nicolle ^{[5
,6
]}

van Hoeck, Arne ^{[5
,6
]}

Janssen, Roel ^{[5
,6
]}

Cuppen, Edwin ^{[4
,5
,6
]}

Priestley, Peter ^{[3
,4
]}

Papenfuss, Anthony T. ^{[1
,2
,7
,8
]}

机构：

[1] Walter & Eliza Hall Inst Med Res, Bioinformat Div, Parkville, Vic, Australia

[2] Univ Melbourne, Dept Med Biol, Melbourne, Vic, Australia

[3] Hartwig Med Fdn Australia, Sydney, NSW, Australia

[4] Hartwig Med Fdn, Sci Pk 408, Amsterdam, Netherlands

[5] Univ Med Ctr Utrecht, Ctr Mol Med, Heidelberglaan 100, Utrecht, Netherlands

[6] Univ Med Ctr Utrecht, Oncode Inst, Heidelberglaan 100, Utrecht, Netherlands

[7] Peter MacCallum Canc Ctr, Melbourne, Vic, Australia

[8] Univ Melbourne, Sir Peter MacCallum Dept Oncol, Melbourne, Vic, Australia

来源：

GENOME BIOLOGY | 2021年 / 22卷 / 01期

基金：

英国医学研究理事会; 澳大利亚国家健康与医学研究理事会;

关键词：

PAIRED-END; CANCER; ALIGNMENT; GENOMES; FORMAT;

D O I：

10.1186/s13059-021-02423-x

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：

GRIDSS2 is the first structural variant caller to explicitly report single breakendsbreakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromere copy number changes using single breakends to non-centromere sequence. On a cohort of 3782 deeply sequenced metastatic cancers, GRIDSS2 achieves an unprecedented 3.1% false negative rate and 3.3% false discovery rate and identifies a novel 32-100 bp duplication signature. GRIDSS2 simplifies complex rearrangement interpretation through phasing of structural variants with 16% of somatic calls phasable using paired-end sequencing.

引用

页数：25

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