Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels
作者： Timothy D. O’Brien , Peilin Jia , Neil E. Caporaso , Maria Teresa Landi , Zhongming Zhao
DOI: 10.1186/S13073-018-0522-9
关键词:
摘要: There are two main types of lung cancer: small cell cancer (SCLC) and non-small (NSCLC). NSCLC has many subtypes, but the most common adenocarcinoma (LUAD) squamous carcinoma (LUSC). These subtypes mainly classified by physiological pathological characteristics, although there is increasing evidence genetic molecular differences as well. Although some work been done at somatic level to explore biological among little that interrogates these germline characterize unique shared susceptibility genes for each subtype. We used single-nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) European samples interrogate similarity SNP, gene, pathway, regulatory levels. expanded genotyped SNPs include all in linkage disequilibrium (LD) using data 1000 Genomes Project. mapped several tissue expression quantitative trait loci (eQTL) enhancer datasets identify their target genes. perform pathway analysis identified 8295, 8734, 8361 with moderate signals LUAD, LUSC, SCLC, respectively. Those had p 0.8, Europeans) SNPs. 215, 320, 172 disease-associated Only five (CHRNA5, IDH3A, PSMA4, RP11-650 L12.2, TBC1D2B) overlapped subtypes. Furthermore, we observed only pathways Kyoto Encyclopedia Genes At level, three eQTL between Our results suggest do not share much signal or which differs subtype classification based upon histology. However, PSMA4) well-known may act general regardless
biomedcentral.com
springer.com
sci-hub.se 参考文章(82)
Andrew P. Feinberg, Maxwell P. Lee, Sheri Brandenburg, Timothy D. Connors, Glenn Miller, Ren Ju Hu, Michael J. Lee, Kui Su, Cynthia Reeves, Anna Schmitt, Somatic Mutation of TSSC5, a Novel Imprinted Gene from Human Chromosome 11p15.5 Cancer Research. ,vol. 58, pp. 4155- 4159 ,(1998)
GTEx Consortium, Kristin G Ardlie, David S Deluca, Ayellet V Segrè, Timothy J Sullivan, Taylor R Young, Ellen T Gelfand, Casandra A Trowbridge, Julian B Maller, Taru Tukiainen, Monkol Lek, Lucas D Ward, Pouya Kheradpour, Benjamin Iriarte, Yan Meng, Cameron D Palmer, Tõnu Esko, Wendy Winckler, Joel N Hirschhorn, Manolis Kellis, Daniel G MacArthur, Gad Getz, Andrey A Shabalin, Gen Li, Yi-Hui Zhou, Andrew B Nobel, Ivan Rusyn, Fred A Wright, Tuuli Lappalainen, Pedro G Ferreira, Halit Ongen, Manuel A Rivas, Alexis Battle, Sara Mostafavi, Jean Monlong, Michael Sammeth, Marta Mele, Ferran Reverter, Jakob M Goldmann, Daphne Koller, Roderic Guigó, Mark I McCarthy, Emmanouil T Dermitzakis, Eric R Gamazon, Hae Kyung Im, Anuar Konkashbaev, Dan L Nicolae, Nancy J Cox, Timothée Flutre, Xiaoquan Wen, Matthew Stephens, Jonathan K Pritchard, Zhidong Tu, Bin Zhang, Tao Huang, Quan Long, Luan Lin, Jialiang Yang, Jun Zhu, Jun Liu, Amanda Brown, Bernadette Mestichelli, Denee Tidwell, Edmund Lo, Mike Salvatore, Saboor Shad, Jeffrey A Thomas, John T Lonsdale, Michael T Moser, Bryan M Gillard, Ellen Karasik, Kimberly Ramsey, Christopher Choi, Barbara A Foster, John Syron, Johnell Fleming, Harold Magazine, Rick Hasz, Gary D Walters, Jason P Bridge, Mark Miklos, Susan Sullivan, Laura K Barker, Heather M Traino, Maghboeba Mosavel, Laura A Siminoff, Dana R Valley, Daniel C Rohrer, Scott D Jewell, Philip A Branton, Leslie H Sobin, Mary Barcus, Liqun Qi, Jeffrey McLean, Pushpa Hariharan, Ki Sung Um, Shenpei Wu, David Tabor, Charles Shive, Anna M Smith, Stephen A Buia, Anita H Undale, Karna L Robinson, Nancy Roche, Kimberly M Valentino, Angela Britton, Robin Burges, Debra Bradbury, Kenneth W Hambright, John Seleski, Greg E Korzeniewski, Kenyon Erickson, Yvonne Marcus, Jorge Tejada, Mehran Taherian, Chunrong Lu, Margaret Basile, Deborah C Mash, Simona Volpi, Jeffery P Struewing, Gary F Temple, Joy Boyer, Deborah Colantuoni, Roger Little, Susan Koester, Latarsha J Carithers, Helen M Moore, Ping Guan, Carolyn Compton, Sherilyn J Sawyer, Joanne P Demchok, Jimmie B Vaught, Chana A Rabiner, Nicole C Lockhart, Kristin G Ardlie, Gad Getz, Fred A Wright, Manolis Kellis, Simona Volpi, Emmanouil T Dermitzakis, None, The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans Science. ,vol. 348, pp. 648- 660 ,(2015) , 10.1126/SCIENCE.1262110
Junfeng Jiang, Peilin Jia, Bairong Shen, Zhongming Zhao, Top associated SNPs in prostate cancer are significantly enriched in cis -expression quantitative trait loci and at transcription factor binding sites Oncotarget. ,vol. 5, pp. 6168- 6177 ,(2014) , 10.18632/ONCOTARGET.2179
Hassan Lemjabbar-Alaoui, Omer UI Hassan, Yi-Wei Yang, Petra Buchanan, Lung cancer: Biology and treatment options Biochimica et Biophysica Acta. ,vol. 1856, pp. 189- 210 ,(2015) , 10.1016/J.BBCAN.2015.08.002
Maria Teresa Landi, Nilanjan Chatterjee, Kai Yu, Lynn R. Goldin, Alisa M. Goldstein, Melissa Rotunno, Lisa Mirabello, Kevin Jacobs, William Wheeler, Meredith Yeager, Andrew W. Bergen, Qizhai Li, Dario Consonni, Angela C. Pesatori, Sholom Wacholder, Michael Thun, Ryan Diver, Martin Oken, Jarmo Virtamo, Demetrius Albanes, Zhaoming Wang, Laurie Burdette, Kimberly F. Doheny, Elizabeth W. Pugh, Cathy Laurie, Paul Brennan, Rayjean Hung, Valerie Gaborieau, James D. McKay, Mark Lathrop, John McLaughlin, Ying Wang, Ming-Sound Tsao, Margaret R. Spitz, Yufei Wang, Hans Krokan, Lars Vatten, Frank Skorpen, Egil Arnesen, Simone Benhamou, Christine Bouchard, Andres Metsapalu, Tonu Vooder, Mari Nelis, Kristian Välk, John K. Field, Chu Chen, Gary Goodman, Patrick Sulem, Gudmar Thorleifsson, Thorunn Rafnar, Timothy Eisen, Wiebke Sauter, Albert Rosenberger, Heike Bickeböller, Angela Risch, Jenny Chang-Claude, H. Erich Wichmann, Kari Stefansson, Richard Houlston, Christopher I. Amos, Joseph F. Fraumeni, Sharon A. Savage, Pier Alberto Bertazzi, Margaret A. Tucker, Stephen Chanock, Neil E. Caporaso, A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma. American Journal of Human Genetics. ,vol. 85, pp. 679- 691 ,(2009) , 10.1016/J.AJHG.2009.09.012
Rimantas Kodzius, Miki Kojima, Hiromi Nishiyori, Mari Nakamura, Shiro Fukuda, Michihira Tagami, Daisuke Sasaki, Kengo Imamura, Chikatoshi Kai, Matthias Harbers, Yoshihide Hayashizaki, Piero Carninci, CAGE: cap analysis of gene expression Nature Methods. ,vol. 3, pp. 211- 222 ,(2006) , 10.1038/NMETH0306-211
Katherine A Hoadley, Christina Yau, Denise M Wolf, Andrew D Cherniack, David Tamborero, Sam Ng, Max DM Leiserson, Beifang Niu, Michael D McLellan, Vladislav Uzunangelov, Jiashan Zhang, Cyriac Kandoth, Rehan Akbani, Hui Shen, Larsson Omberg, Andy Chu, Adam A Margolin, Laura J Van’t Veer, Nuria Lopez-Bigas, Peter W Laird, Benjamin J Raphael, Li Ding, A Gordon Robertson, Lauren A Byers, Gordon B Mills, John N Weinstein, Carter Van Waes, Zhong Chen, Eric A Collisson, Christopher C Benz, Charles M Perou, Joshua M Stuart, None, Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin Cell. ,vol. 158, pp. 929- 944 ,(2014) , 10.1016/J.CELL.2014.06.049
Yan Liu, Pengyuan Liu, Weidong Wen, Michael A. James, Yian Wang, Joan E. Bailey-Wilson, Christopher I. Amos, Susan M. Pinney, Ping Yang, Mariza de Andrade, Gloria M. Petersen, Jonathan S. Wiest, Pamela R. Fain, Ann G. Schwartz, Adi Gazdar, Colette Gaba, Henry Rothschild, Diptasri Mandal, Elena Kupert, Juwon Lee, Daniela Seminara, John Minna, Marshall W. Anderson, Ming You, Haplotype and Cell Proliferation Analyses of Candidate Lung Cancer Susceptibility Genes on Chromosome 15q24-25.1 Cancer Research. ,vol. 69, pp. 7844- 7850 ,(2009) , 10.1158/0008-5472.CAN-09-1833
Christopher I Amos, Xifeng Wu, Peter Broderick, Ivan P Gorlov, Jian Gu, Timothy Eisen, Qiong Dong, Qing Zhang, Xiangjun Gu, Jayaram Vijayakrishnan, Kate Sullivan, Athena Matakidou, Yufei Wang, Gordon Mills, Kimberly Doheny, Ya-Yu Tsai, Wei Vivien Chen, Sanjay Shete, Margaret R Spitz, Richard S Houlston, Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1 Nature Genetics. ,vol. 40, pp. 616- 622 ,(2008) , 10.1038/NG.109
Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets. IEEE Transactions on Visualization and Computer Graphics. ,vol. 20, pp. 1983- 1992 ,(2014) , 10.1109/TVCG.2014.2346248