Whole-genome reconstruction and mutational signatures in gastric cancer

被引：121

作者：

Nagarajan, Niranjan ^{[1
]}

Bertrand, Denis ^{[1
]}

Hillmer, Axel M. ^{[1
]}

Zang, Zhi Jiang ^{[2
,3
]}

Yao, Fei ^{[1
,4
]}

Jacques, Pierre-Etienne ^{[1
]}

Teo, Audrey S. M. ^{[1
]}

Cutcutache, Ioana ^{[5
]}

Zhang, Zhenshui ^{[1
]}

Lee, Wah Heng ^{[1
]}

Sia, Yee Yen ^{[1
]}

Gao, Song ^{[6
]}

Ariyaratne, Pramila N. ^{[1
]}

Ho, Andrea ^{[1
]}

Woo, Xing Yi ^{[1
]}

Veeravali, Lavanya ^{[1
]}

Ong, Choon Kiat ^{[7
]}

Deng, Niantao ^{[5
]}

Desai, Kartiki V. ^{[8
]}

Khor, Chiea Chuen ^{[1
,3
]}

Hibberd, Martin L. ^{[1
,3
]}

Shahab, Atif ^{[1
]}

Rao, Jaideepraj ^{[9
]}

Wu, Mengchu ^{[10
]}

Teh, Ming ^{[11
]}

Zhu, Feng ^{[12
]}

Chin, Sze Yung ^{[11
]}

Pang, Brendan ^{[10
,11
]}

So, Jimmy B. Y. ^{[13
]}

Bourque, Guillaume ^{[14
,15
,16
]}

Soong, Richie ^{[10
,11
]}

Sung, Wing-Kin ^{[1
]}

Teh, Bin Tean ^{[7
]}

Rozen, Steven ^{[5
]}

Ruan, Xiaoan ^{[1
]}

Yeoh, Khay Guan ^{[12
]}

Tan, Patrick B. O. ^{[1
,5
,10
]}

Ruan, Yijun ^{[1
,17
]}

机构：

[1] Genome Inst Singapore, Singapore 138672, Singapore

[2] Natl Canc Ctr, Singapore 169610, Singapore

[3] Duke Natl Univ Singapore NUS, Grad Sch Med, Canc & Stem Cell Biol Program, Singapore 169857, Singapore

[4] Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Epidemiol & Publ Hlth, Singapore 119074, Singapore

[5] Duke NUS Grad Med Sch, Singapore 169857, Singapore

[6] NUS Grad Sch Integrat Sci & Engn, Ctr Life Sci, Singapore 117456, Singapore

[7] Natl Canc Ctr, NCCS VARI Translat Res Lab, Singapore 169610, Singapore

[8] Natl Inst Biomed Genom, Kalyani 741251, W Bengal, India

[9] Tan Tock Seng Hosp, Dept Surg, Singapore 308433, Singapore

[10] Natl Univ Singapore, Yong Loo Lin Sch Med, Canc Sci Inst Singapore, Singapore 119074, Singapore

[11] Natl Univ Singapore, Natl Univ Hlth Syst, Dept Pathol, Singapore 119074, Singapore

[12] Natl Univ Singapore, Natl Univ Hlth Syst, Dept Med, Singapore 119074, Singapore

[13] Natl Univ Singapore, Natl Univ Hlth Syst, Dept Surg, Singapore 119074, Singapore

[14] McGill Univ, Dept Human Genet, Montreal, PQ H3A 1B1, Canada

[15] McGill Univ, Montreal, PQ H3A 1A4, Canada

[16] Genome Quebec Innovat Ctr, Montreal, PQ H3A 1A4, Canada

[17] Natl Univ Singapore, Dept Biochem, Singapore 119074, Singapore

来源：

GENOME BIOLOGY | 2012年 / 13卷 / 12期

基金：

英国医学研究理事会;

关键词：

SOMATIC MUTATIONS; DNA; EXPRESSION; SEQUENCES; ALIGNMENT; PATTERNS; TARGETS; MEMBERS; GENE;

D O I：

10.1186/gb-2012-13-12-r115

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：

Background: Gastric cancer is the second highest cause of global cancer mortality. To explore the complete repertoire of somatic alterations in gastric cancer, we combined massively parallel short read and DNA paired-end tag sequencing to present the first whole-genome analysis of two gastric adenocarcinomas, one with chromosomal instability and the other with microsatellite instability. Results: Integrative analysis and de novo assemblies revealed the architecture of a wild-type KRAS amplification, a common driver event in gastric cancer. We discovered three distinct mutational signatures in gastric cancer - against a genome-wide backdrop of oxidative and microsatellite instability-related mutational signatures, we identified the first exome-specific mutational signature. Further characterization of the impact of these signatures by combining sequencing data from 40 complete gastric cancer exomes and targeted screening of an additional 94 independent gastric tumors uncovered ACVR2A, RPL22 and LMAN1 as recurrently mutated genes in microsatellite instability-positive gastric cancer and PAPPA as a recurrently mutated gene in TP53 wild-type gastric cancer. Conclusions: These results highlight how whole-genome cancer sequencing can uncover information relevant to tissue-specific carcinogenesis that would otherwise be missed from exome-sequencing data.

引用

页数：10

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