Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

被引：174

作者：

Carrot-Zhang, Jian ^{[1
,2
,3
]}

Chambwe, Nyasha ^{[4
]}

Damrauer, Jeffrey S. ^{[5
]}

Knijnenburg, Theo A. ^{[4
]}

Robertson, A. Gordon ^{[6
]}

Yau, Christina ^{[7
,8
]}

Zhou, Wanding ^{[9
]}

Berger, Ashton C. ^{[1
,2
]}

Huang, Kuan-Iin ^{[10
]}

Newberg, Justin Y. ^{[11
]}

Mashl, R. Jay ^{[12
]}

Romanel, Alessandro ^{[13
]}

Sayaman, Rosalyn W. ^{[14
,15
]}

Demichelis, Francesca ^{[13
]}

Felau, Ina ^{[16
]}

Frampton, Garrett M. ^{[11
]}

Han, Seunghun ^{[2
,3
]}

Hoadley, Katherine A. ^{[5
]}

Kemal, Anab ^{[16
]}

Laird, Peter W. ^{[9
]}

Lazar, Alexander J. ^{[17
,18
,19
]}

Le, Xiuning ^{[20
]}

Oak, Ninad ^{[21
,22
]}

Shen, Hui ^{[9
]}

Wong, Christopher K. ^{[23
]}

Zenklusen, Jean C. ^{[16
]}

Ziv, Elad ^{[14
]}

Cherniack, Andrew D. ^{[1
,2
,3
]}

Beroukhim, Rameen ^{[1
,2
,3
,24
,25
]}

机构：

[1] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

[2] Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA

[3] Harvard Med Sch, Boston, MA 02115 USA

[4] Inst Syst Biol, Seattle, WA 98109 USA

[5] Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA

[6] British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada

[7] Buck Inst Res Aging, Novato, CA 94945 USA

[8] Univ Calif San Francisco, Dept Surg, San Francisco, CA 94115 USA

[9] Van Andel Res Inst, Grand Rapids, MI 49503 USA

[10] Icahn Sch Med Mt Sinai, Dept Genet & Genom, New York, NY 10029 USA

[11] Fdn Med, Cambridge, MA 02141 USA

[12] Washington Univ, Dept Med, St Louis, MO 63110 USA

[13] Univ Trento, Dept Cellular Computat & Integrat Biol CIBIO, Via Sommar 9, I-38123 Povo, Trento, Italy

[14] Univ Calif San Francisco, Helen Diller Family Comprehens Canc Ctr, Dept Lab Med, San Francisco, CA 94143 USA

[15] City Hope Natl Med Ctr, Beckman Res Inst, Dept Populat Sci, Duarte, CA 91010 USA

[16] NCI, Bethesda, MD 20892 USA

[17] Univ Texas MD Anderson Canc Ctr, Dept Pathol, Houston, TX 77030 USA

[18] Univ Texas MD Anderson Canc Ctr, Dept Genom Med, Houston, TX 77030 USA

[19] Univ Texas MD Anderson Canc Ctr, Dept Translat Mol Pathol, Houston, TX 77030 USA

[20] Univ Texas MD Anderson Canc Ctr, Dept Thorac & Head & Neck Med Oncol, Houston, TX 77030 USA

[21] St Jude Childrens Res Hosp, Dept Computat Biol, Memphis, TN 38105 USA

[22] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[23] Univ Calif Santa Cruz, UC Santa Cruz Genom Inst, Santa Cruz, CA 95064 USA

[24] Brigham & Womens Hosp, Dept Med, 75 Francis St, Boston, MA 02115 USA

[25] Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02215 USA

来源：

CANCER CELL | 2020年 / 37卷 / 05期

关键词：

GLUTATHIONE-S-TRANSFERASE; PROSTATE-CANCER; RISK; POLYMORPHISMS; ASSOCIATION; PATTERNS; ENVIRONMENT; LANDSCAPE; CARCINOMA; GENOTYPE;

D O I：

10.1016/j.ccell.2020.04.012

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer Genome Atlas. We demonstrated that cancer subtypes and ancestry-related technical artifacts are important confounders that have been insufficiently accounted for. Once accounted for, ancestry-associated differences spanned all molecular features and hundreds of genes. Biologically significant differences were usually tissue specific but not specific to cancer. However, admixture and pathway analyses suggested some of these differences are causally related to cancer. Specific findings included increased FBXW7 mutations in patients of African origin, decreased VHL and PBRM1 mutations in renal cancer patients of African origin, and decreased immune activity in bladder cancer patients of East Asian origin.

引用

页码：639 / +

页数：22

共 64 条

[1] The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes
Ai Ling Teh
Pan, Hong
Chen, Li
Ong, Mei-Lyn
Dogra, Shaillay
Wong, Johnny
MacIsaac, Julia L.
Mah, Sarah M.
McEwen, Lisa M.
Saw, Seang-Mei
Godfrey, Keith M.
Chong, Yap-Seng
Kwek, Kenneth
Kwoh, Chee-Keong
Soh, Shu-E.
Chong, Mary F. F.
Barton, Sheila
Karnani, Neerja
Cheong, Clara Y.
Buschdorf, Jan Paul
Stunkel, Walter
Kobor, Michael S.
Meaney, Michael J.
Gluckman, Peter D.
Holbrook, Joanna D.
[J]. GENOME RESEARCH, 2014, 24 (07) : 1064 - 1074
[2] Fast model-based estimation of ancestry in unrelated individuals
Alexander, David H.
Novembre, John
Lange, Kenneth
[J]. GENOME RESEARCH, 2009, 19 (09) : 1655 - 1664
[3] The repertoire of mutational signatures in human cancer
Alexandrov, Ludmil B.
Kim, Jaegil
Haradhvala, Nicholas J.
Huang, Mi Ni
Ng, Alvin Wei Tian
Wu, Yang
Boot, Arnoud
Covington, Kyle R.
Gordenin, Dmitry A.
Bergstrom, Erik N.
Islam, S. M. Ashiqul
Lopez-Bigas, Nuria
Klimczak, Leszek J.
McPherson, John R.
Morganella, Sandro
Sabarinathan, Radhakrishnan
Wheeler, David A.
Mustonen, Ville
Getz, Gad
Rozen, Steven G.
Stratton, Michael R.
[J]. NATURE, 2020, 578 (7793) : 94 - +
[4] Bailey MH, 2018, CELL, V173, P371, DOI [10.1016/j.cell.2018.02.060, 10.1016/j.cell.2018.07.034]
[5] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING
BENJAMINI, Y
HOCHBERG, Y
[J]. JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) : 289 - 300
[6] Patterns of Gene Expression and Copy-Number Alterations in von-Hippel Lindau Disease-Associated and Sporadic Clear Cell Carcinoma of the Kidney
Beroukhim, Rameen
Brunet, Jean-Philippe
Di Napoli, Arianna
Mertz, Kirsten D.
Seeley, Apryle
Pires, Maira M.
Linhart, David
Worrell, Robert A.
Moch, Holger
Rubin, Mark A.
Sellers, William R.
Meyerson, Matthew
Linehan, W. Marston
Kaelin, William G., Jr.
Signoretti, Sabina
[J]. CANCER RESEARCH, 2009, 69 (11) : 4674 - 4681
[7] Role of polymorphisms of GSTM1, GSTT1 and GSTP1 Ile105Val in Hodgkin and non-Hodgkin lymphoma risk: a Human Genome Epidemiology (HuGE) review
Bin, Qiong
Luo, Jianming
[J]. LEUKEMIA & LYMPHOMA, 2013, 54 (01) : 14 - 20
[8] Worldwide patterns of human epigenetic variation
Carja, Oana
Maclsaac, Julia L.
Mah, Sarah M.
Henn, Brenna M.
Kobor, Michael S.
Feldman, Marcus W.
Fraser, Hunter B.
[J]. NATURE ECOLOGY & EVOLUTION, 2017, 1 (10): : 1577 - 1583
[9] Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
Carmi, Shai
Hui, Ken Y.
Kochav, Ethan
Liu, Xinmin
Xue, James
Grady, Fillan
Guha, Saurav
Upadhyay, Kinnari
Ben-Avraham, Dan
Mukherjee, Semanti
Bowen, B. Monica
Thomas, Tinu
Vijai, Joseph
Cruts, Marc
Froyen, Guy
Lambrechts, Diether
Plaisance, Stephane
Van Broeckhoven, Christine
Van Damme, Philip
Van Marck, Herwig
Barzilai, Nir
Darvasi, Ariel
Offit, Kenneth
Bressman, Susan
Ozelius, Laurie J.
Peter, Inga
Cho, Judy H.
Ostrer, Harry
Atzmon, Gil
Clark, Lorraine N.
Lencz, Todd
Pe'er, Itsik
[J]. NATURE COMMUNICATIONS, 2014, 5
[10] Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations
Chang, Jiang
Tan, Wenle
Ling, Zhiqiang
Xi, Ruibin
Shao, Mingming
Chen, Mengjie
Luo, Yingying
Zhao, Yanjie
Liu, Yun
Huang, Xiancong
Xia, Yuchao
Hu, Jinlin
Parker, Joel S.
Marron, David
Cui, Qionghua
Peng, Linna
Chu, Jiahui
Li, Hongmin
Du, Zhongli
Han, Yaling
Tan, Wen
Liu, Zhihua
Zhan, Qimin
Li, Yun
Mao, Weimin
Wu, Chen
Lin, Dongxin
[J]. NATURE COMMUNICATIONS, 2017, 8

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