Network expansion of genetic associations defines a pleiotropy map of human cell biology.
Nature Genetics
Barrio-Hernandez, Inigo I; Schwartzentruber, Jeremy J; Shrivastava, Anjali A; Del-Toro, Noemi N; Gonzalez, Asier A; Zhang, Qian Q; Mountjoy, Edward E; Suveges, Daniel D; Ochoa, David D; Ghoussaini, Maya M; Bradley, Glyn G; Hermjakob, Henning H; Orchard, Sandra S; Dunham, Ian I; Anderson, Carl A CA; Porras, Pablo P; Beltrao, Pedro P
ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC).
Plos Genetics
Ferrando, Lorenzo L; Vingiani, Andrea A; Garuti, Anna A; Vernieri, Claudio C; Belfiore, Antonino A; Agnelli, Luca L; Dagrada, Gianpaolo G; Ivanoiu, Diana D; Bonizzi, Giuseppina G; Munzone, Elisabetta E; Lippolis, Luana L; Dameri, Martina M; Ravera, Francesco F; Colleoni, Marco M; Viale, Giuseppe G; Magnani, Luca L; Ballestrero, Alberto A; Zoppoli, Gabriele G; Pruneri, Giancarlo G
Uterine lavage identifies cancer mutations and increased TP53 somatic mutation burden in individuals with ovarian cancer.
Cancer Research Communications
Ghezelayagh, Talayeh S TS; Kohrn, Brendan F BF; Fredrickson, Jeanne J; Manhardt, Enna E; Radke, Marc R MR; Katz, Ronit R; Gray, Heidi J HJ; Urban, Renata R RR; Pennington, Kathryn P KP; Liao, John B JB; Doll, Kemi M KM; Simons, Elise J EJ; Burzawa, Jennifer K JK; Goff, Barbara A BA; Speiser, Paul P; Swisher, Elizabeth M EM; Norquist, Barbara M BM; Risques, Rosa Ana RA
Persistence of ctDNA in Patients with Breast Cancer During Neoadjuvant Treatment Is a Significant Predictor of Poor Tumor Response.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Zhou, Qing Q; Gampenrieder, Simon P SP; Frantal, Sophie S; Rinnerthaler, Gabriel G; Singer, Christian F CF; Egle, Daniel D; Pfeiler, Georg G; Bartsch, Rupert R; Wette, Viktor V; Pichler, Angelika A; Petru, Edgar E; Dubsky, Peter C PC; Bago-Horvath, Zsuzsanna Z; Fesl, Christian C; Rudas, Margaretha M; Ståhlberg, Anders A; Graf, Ricarda R; Weber, Sabrina S; Dandachi, Nadia N; Filipits, Martin M; Gnant, Michael M; Balic, Marija M; Heitzer, Ellen E
Whole-genome profiling of nasopharyngeal carcinoma reveals viral-host co-operation in inflammatory NF-κB activation and immune escape.
Nature Communications
Bruce, Jeff P JP; To, Ka-Fai KF; Lui, Vivian W Y VWY; Chung, Grace T Y GTY; Chan, Yuk-Yu YY; Tsang, Chi Man CM; Yip, Kevin Y KY; Ma, Brigette B Y BBY; Woo, John K S JKS; Hui, Edwin P EP; Mak, Michael K F MKF; Lee, Sau-Dan SD; Chow, Chit C; Velapasamy, Sharmila S; Or, Yvonne Y Y YYY; Siu, Pui Kei PK; El Ghamrasni, Samah S; Prokopec, Stephenie S; Wu, Man M; Kwan, Johnny S H JSH; Liu, Yuchen Y; Chan, Jason Y K JYK; van Hasselt, C Andrew CA; Young, Lawrence S LS; Dawson, Christopher W CW; Paterson, Ian C IC; Yap, Lee-Fah LF; Tsao, Sai-Wah SW; Liu, Fei-Fei FF; Chan, Anthony T C ATC; Pugh, Trevor J TJ; Lo, Kwok-Wai KW
Publication Date: 2021-07-07
Variant appearance in text: PTEN: 71A>G; Asp24Gly; rs797044910
Integrated genomic and transcriptomic analysis reveals unique characteristics of hepatic metastases and pro-metastatic role of complement C1q in pancreatic ductal adenocarcinoma.
Distinct genetic changes reveal evolutionary history and heterogeneous molecular grade of DLBCL with MYC/BCL2 double-hit.
Leukemia
Cucco, Francesco F; Barrans, Sharon S; Sha, Chulin C; Clipson, Alexandra A; Crouch, Simon S; Dobson, Rachel R; Chen, Zi Z; Thompson, Joe Sneath JS; Care, Matthew A MA; Cummin, Thomas T; Caddy, Josh J; Liu, Hongxiang H; Robinson, Anne A; Schuh, Anna A; Fitzgibbon, Jude J; Painter, Daniel D; Smith, Alexandra A; Roman, Eve E; Tooze, Reuben R; Burton, Catherine C; Davies, Andrew J AJ; Westhead, David R DR; Johnson, Peter W M PWM; Du, Ming-Qing MQ
Development and validation of a targeted gene sequencing panel for application to disparate cancers.
Scientific Reports
McCabe, Mark J MJ; Gauthier, Marie-Emilie A MA; Chan, Chia-Ling CL; Thompson, Tanya J TJ; De Sousa, Sunita M C SMC; Puttick, Clare C; Grady, John P JP; Gayevskiy, Velimir V; Tao, Jiang J; Ying, Kevin K; Cipponi, Arcadi A; Deng, Niantao N; Swarbrick, Alex A; Thomas, Melissa L ML; Lord, Reginald V RV; Johns, Amber L AL; Kohonen-Corish, Maija M; O'Toole, Sandra A SA; Clark, Jonathan J; Mueller, Simon A SA; Gupta, Ruta R; McCormack, Ann I AI; Dinger, Marcel E ME; Cowley, Mark J MJ; ,
REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.
Scientific Reports
Tian, Yuan Y; Pesaran, Tina T; Chamberlin, Adam A; Fenwick, R Bryn RB; Li, Shuwei S; Gau, Chia-Ling CL; Chao, Elizabeth C EC; Lu, Hsiao-Mei HM; Black, Mary Helen MH; Qian, Dajun D
Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer.
American Journal Of Human Genetics
Smith, Iris Nira IN; Thacker, Stetson S; Seyfi, Marilyn M; Cheng, Feixiong F; Eng, Charis C
A Bayesian framework for efficient and accurate variant prediction.
Plos One
Qian, Dajun D; Li, Shuwei S; Tian, Yuan Y; Clifford, Jacob W JW; Sarver, Brice A J BAJ; Pesaran, Tina T; Gau, Chia-Ling CL; Elliott, Aaron M AM; Lu, Hsiao-Mei HM; Black, Mary Helen MH
The prognostic effects of somatic mutations in ER-positive breast cancer.
Nature Communications
Griffith, Obi L OL; Spies, Nicholas C NC; Anurag, Meenakshi M; Griffith, Malachi M; Luo, Jingqin J; Tu, Dongsheng D; Yeo, Belinda B; Kunisaki, Jason J; Miller, Christopher A CA; Krysiak, Kilannin K; Hundal, Jasreet J; Ainscough, Benjamin J BJ; Skidmore, Zachary L ZL; Campbell, Katie K; Kumar, Runjun R; Fronick, Catrina C; Cook, Lisa L; Snider, Jacqueline E JE; Davies, Sherri S; Kavuri, Shyam M SM; Chang, Eric C EC; Magrini, Vincent V; Larson, David E DE; Fulton, Robert S RS; Liu, Shuzhen S; Leung, Samuel S; Voduc, David D; Bose, Ron R; Dowsett, Mitch M; Wilson, Richard K RK; Nielsen, Torsten O TO; Mardis, Elaine R ER; Ellis, Matthew J MJ
Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board.
Jco Precision Oncology
Dalton, W Brian WB; Forde, Patrick M PM; Kang, Hyunseok H; Connolly, Roisin M RM; Stearns, Vered V; Gocke, Christopher D CD; Eshleman, James R JR; Axilbund, Jennifer J; Petry, Dana D; Geoghegan, Cindy C; Wolff, Antonio C AC; Loeb, David M DM; Pratilas, Christine A CA; Meyer, Christian F CF; Christenson, Eric S ES; Slater, Shannon A SA; Ensminger, Jennifer J; Parsons, Heather A HA; Park, Ben H BH; Lauring, Josh J
Prevalence of Clonal Hematopoiesis Mutations in Tumor-Only Clinical Genomic Profiling of Solid Tumors.
Jama Oncology
Ptashkin, Ryan N RN; Mandelker, Diana L DL; Coombs, Catherine C CC; Bolton, Kelly K; Yelskaya, Zarina Z; Hyman, David M DM; Solit, David B DB; Baselga, José J; Arcila, Maria E ME; Ladanyi, Marc M; Zhang, Liying L; Levine, Ross L RL; Berger, Michael F MF; Zehir, Ahmet A
Multiplex assessment of protein variant abundance by massively parallel sequencing.
Nature Genetics
Matreyek, Kenneth A KA; Starita, Lea M LM; Stephany, Jason J JJ; Martin, Beth B; Chiasson, Melissa A MA; Gray, Vanessa E VE; Kircher, Martin M; Khechaduri, Arineh A; Dines, Jennifer N JN; Hause, Ronald J RJ; Bhatia, Smita S; Evans, William E WE; Relling, Mary V MV; Yang, Wenjian W; Shendure, Jay J; Fowler, Douglas M DM
Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.
The Journal Of Pathology
Temko, Daniel D; Van Gool, Inge C IC; Rayner, Emily E; Glaire, Mark M; Makino, Seiko S; Brown, Matthew M; Chegwidden, Laura L; Palles, Claire C; Depreeuw, Jeroen J; Beggs, Andrew A; Stathopoulou, Chaido C; Mason, John J; Baker, Ann-Marie AM; Williams, Marc M; Cerundolo, Vincenzo V; Rei, Margarida M; Taylor, Jenny C JC; Schuh, Anna A; Ahmed, Ahmed A; Amant, Frédéric F; Lambrechts, Diether D; Smit, Vincent Thbm VT; Bosse, Tjalling T; Graham, Trevor A TA; Church, David N DN; Tomlinson, Ian I
Exome and genome sequencing of nasopharynx cancer identifies NF-κB pathway activating mutations.
Nature Communications
Li, Yvonne Y YY; Chung, Grace T Y GT; Lui, Vivian W Y VW; To, Ka-Fai KF; Ma, Brigette B Y BB; Chow, Chit C; Woo, John K S JK; Yip, Kevin Y KY; Seo, Jeongsun J; Hui, Edwin P EP; Mak, Michael K F MK; Rusan, Maria M; Chau, Nicole G NG; Or, Yvonne Y Y YY; Law, Marcus H N MH; Law, Peggy P Y PP; Liu, Zoey W Y ZW; Ngan, Hoi-Lam HL; Hau, Pok-Man PM; Verhoeft, Krista R KR; Poon, Peony H Y PH; Yoo, Seong-Keun SK; Shin, Jong-Yeon JY; Lee, Sau-Dan SD; Lun, Samantha W M SW; Jia, Lin L; Chan, Anthony W H AW; Chan, Jason Y K JY; Lai, Paul B S PB; Fung, Choi-Yi CY; Hung, Suet-Ting ST; Wang, Lin L; Chang, Ann Margaret V AM; Chiosea, Simion I SI; Hedberg, Matthew L ML; Tsao, Sai-Wah SW; van Hasselt, Andrew C AC; Chan, Anthony T C AT; Grandis, Jennifer R JR; Hammerman, Peter S PS; Lo, Kwok-Wai KW
A Landscape of Pharmacogenomic Interactions in Cancer.
Cell
Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ
Age-related mutations associated with clonal hematopoietic expansion and malignancies.
Nature Medicine
Xie, Mingchao M; Lu, Charles C; Wang, Jiayin J; McLellan, Michael D MD; Johnson, Kimberly J KJ; Wendl, Michael C MC; McMichael, Joshua F JF; Schmidt, Heather K HK; Yellapantula, Venkata V; Miller, Christopher A CA; Ozenberger, Bradley A BA; Welch, John S JS; Link, Daniel C DC; Walter, Matthew J MJ; Mardis, Elaine R ER; Dipersio, John F JF; Chen, Feng F; Wilson, Richard K RK; Ley, Timothy J TJ; Ding, Li L
Bleeker, Fonnet E FE; Lamba, Simona S; Zanon, Carlo C; Molenaar, Remco J RJ; Hulsebos, Theo J M TJ; Troost, Dirk D; van Tilborg, Angela A AA; Vandertop, W Peter WP; Leenstra, Sieger S; van Noorden, Cornelis J F CJ; Bardelli, Alberto A
A novel deleterious PTEN mutation in a patient with early-onset bilateral breast cancer.
Bmc Cancer
Pradella, Laura Maria LM; Evangelisti, Cecilia C; Ligorio, Claudia C; Ceccarelli, Claudio C; Neri, Iria I; Zuntini, Roberta R; Amato, Laura Benedetta LB; Ferrari, Simona S; Martelli, Alberto Maria AM; Gasparre, Giuseppe G; Turchetti, Daniela D