Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity.
Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity.
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DOI:
10.1186/s13059-018-1507-0
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发表时间:
2018-09-11
期刊:
影响因子:
12.3
通讯作者:
Stephanie Huang R
中科院分区:
文献类型:
--
作者:
Geeleher P;Nath A;Wang F;Zhang Z;Barbeira AN;Fessler J;Grossman RL;Seoighe C;Stephanie Huang R
Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we have demonstrated a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity. Only one third of breast cancer risk variants, identified as eQTLs from a conventional analysis, could be confidently attributed to cancer cells. The remaining variants could affect cells of the tumor microenvironment, such as immune cells and fibroblasts. Deconvolution of tumor eQTLs will help determine how inherited polymorphisms influence cancer risk, development, and treatment response. The online version of this article (10.1186/s13059-018-1507-0) contains supplementary material, which is available to authorized users.
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DOI:
10.1056/nejmp1607591
发表时间:
2016-09-22
期刊:
The New England journal of medicine
影响因子:
--
作者:
Grossman RL;Heath AP;Ferretti V;Varmus HE;Lowy DR;Kibbe WA;Staudt LM
通讯作者:
Staudt LM
影响因子:
28.2
作者:
Kar SP;Beesley J;Amin Al Olama A;Michailidou K;Tyrer J;Kote-Jarai Z;Lawrenson K;Lindstrom S;Ramus SJ;Thompson DJ;ABCTB Investigators;Kibel AS;Dansonka-Mieszkowska A;Michael A;Dieffenbach AK;Gentry-Maharaj A;Whittemore AS;Wolk A;Monteiro A;Peixoto A;Kierzek A;Cox A;Rudolph A;Gonzalez-Neira A;Wu AH;Lindblom A;Swerdlow A;AOCS Study Group & Australian Cancer Study (Ovarian Cancer);APCB BioResource;Ziogas A;Ekici AB;Burwinkel B;Karlan BY;Nordestgaard BG;Blomqvist C;Phelan C;McLean C;Pearce CL;Vachon C;Cybulski C;Slavov C;Stegmaier C;Maier C;Ambrosone CB;Høgdall CK;Teerlink CC;Kang D;Tessier DC;Schaid DJ;Stram DO;Cramer DW;Neal DE;Eccles D;Flesch-Janys D;Edwards DR;Wokozorczyk D;Levine DA;Yannoukakos D;Sawyer EJ;Bandera EV;Poole EM;Goode EL;Khusnutdinova E;Høgdall E;Song F;Bruinsma F;Heitz F;Modugno F;Hamdy FC;Wiklund F;Giles GG;Olsson H;Wildiers H;Ulmer HU;Pandha H;Risch HA;Darabi H;Salvesen HB;Nevanlinna H;Gronberg H;Brenner H;Brauch H;Anton-Culver H;Song H;Lim HY;McNeish I;Campbell I;Vergote I;Gronwald J;Lubiński J;Stanford JL;Benítez J;Doherty JA;Permuth JB;Chang-Claude J;Donovan JL;Dennis J;Schildkraut JM;Schleutker J;Hopper JL;Kupryjanczyk J;Park JY;Figueroa J;Clements JA;Knight JA;Peto J;Cunningham JM;Pow-Sang J;Batra J;Czene K;Lu KH;Herkommer K;Khaw KT;kConFab Investigators;Matsuo K;Muir K;Offitt K;Chen K;Moysich KB;Aittomäki K;Odunsi K;Kiemeney LA;Massuger LF;Fitzgerald LM;Cook LS;Cannon-Albright L;Hooning MJ;Pike MC;Bolla MK;Luedeke M;Teixeira MR;Goodman MT;Schmidt MK;Riggan M;Aly M;Rossing MA;Beckmann MW;Moisse M;Sanderson M;Southey MC;Jones M;Lush M;Hildebrandt MA;Hou MF;Schoemaker MJ;Garcia-Closas M;Bogdanova N;Rahman N;NBCS Investigators;Le ND;Orr N;Wentzensen N;Pashayan N;Peterlongo P;Guénel P;Brennan P;Paulo P;Webb PM;Broberg P;Fasching PA;Devilee P;Wang Q;Cai Q;Li Q;Kaneva R;Butzow R;Kopperud RK;Schmutzler RK;Stephenson RA;MacInnis RJ;Hoover RN;Winqvist R;Ness R;Milne RL;Travis RC;Benlloch S;Olson SH;McDonnell SK;Tworoger SS;Maia S;Berndt S;Lee SC;Teo SH;Thibodeau SN;Bojesen SE;Gapstur SM;Kjær SK;Pejovic T;Tammela TL;GENICA Network;PRACTICAL consortium;Dörk T;Brüning T;Wahlfors T;Key TJ;Edwards TL;Menon U;Hamann U;Mitev V;Kosma VM;Setiawan VW;Kristensen V;Arndt V;Vogel W;Zheng W;Sieh W;Blot WJ;Kluzniak W;Shu XO;Gao YT;Schumacher F;Freedman ML;Berchuck A;Dunning AM;Simard J;Haiman CA;Spurdle A;Sellers TA;Hunter DJ;Henderson BE;Kraft P;Chanock SJ;Couch FJ;Hall P;Gayther SA;Easton DF;Chenevix-Trench G;Eeles R;Pharoah PD;Lambrechts D
通讯作者:
Lambrechts D
影响因子:
30.8
作者:
Das, Sayantan;Forer, Lukas;Schoenherr, Sebastian;Sidore, Carlo;Locke, Adam E.;Kwong, Alan;Vrieze, Scott I.;Chew, Emily Y.;Levy, Shawn;McGue, Matt;Schlessinger, David;Stambolian, Dwight;Loh, Po-Ru;Iacono, William G.;Swaroop, Anand;Scott, Laura J.;Cucca, Francesco;Kronenberg, Florian;Boehnke, Michael;Abecasis, Goncalo R.;Fuchsberger, Christian
通讯作者:
Fuchsberger, Christian
影响因子:
4.4
作者:
LaCroix, Bonnie;Gamazon, Eric R.;Huang, Rong Stephanie
通讯作者:
Huang, Rong Stephanie
影响因子:
64.5
作者:
Boyle EA;Li YI;Pritchard JK
通讯作者:
Pritchard JK