Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology.
Nature Medicine
Sturm, Dominik D; Capper, David D; Andreiuolo, Felipe F; Gessi, Marco M; Kölsche, Christian C; Reinhardt, Annekathrin A; Sievers, Philipp P; Wefers, Annika K AK; Ebrahimi, Azadeh A; Suwala, Abigail K AK; Gielen, Gerrit H GH; Sill, Martin M; Schrimpf, Daniel D; Stichel, Damian D; Hovestadt, Volker V; Daenekas, Bjarne B; Rode, Agata A; Hamelmann, Stefan S; Previti, Christopher C; Jäger, Natalie N; Buchhalter, Ivo I; Blattner-Johnson, Mirjam M; Jones, Barbara C BC; Warmuth-Metz, Monika M; Bison, Brigitte B; Grund, Kerstin K; Sutter, Christian C; Hirsch, Steffen S; Dikow, Nicola N; Hasselblatt, Martin M; Schüller, Ulrich U; Gerber, Nicolas U NU; White, Christine L CL; Buntine, Molly K MK; Kinross, Kathryn K; Algar, Elizabeth M EM; Hansford, Jordan R JR; Gottardo, Nicholas G NG; Hernáiz Driever, Pablo P; Gnekow, Astrid A; Witt, Olaf O; Müller, Hermann L HL; Calaminus, Gabriele G; Fleischhack, Gudrun G; Kordes, Uwe U; Mynarek, Martin M; Rutkowski, Stefan S; Frühwald, Michael C MC; Kramm, Christof M CM; von Deimling, Andreas A; Pietsch, Torsten T; Sahm, Felix F; Pfister, Stefan M SM; Jones, David T W DTW
APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP.
Medrxiv : The Preprint Server For Health Sciences
Walker, Logan C LC; de la Hoya, Miguel M; Wiggins, George Ar GA; Lindy, Amanda A; Vincent, Lisa M LM; Parsons, Michael M; Canson, Daffodil M DM; Bis-Brewer, Dana D; Cass, Ashley A; Tchourbanov, Alexander A; Zimmermann, Heather H; Byrne, Alicia B AB; Pesaran, Tina T; Karam, Rachid R; Harrison, Steven M SM; , ; Spurdle, Amanda B AB
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
Publication Date: 2023-02-23
Variant appearance in text: NF1: 4084C>T; Arg1362Ter
Efficacy and clinicogenomic correlates of response to immune checkpoint inhibitors alone or with chemotherapy in non-small cell lung cancer.
Nature Communications
Hong, Lingzhi L; Aminu, Muhammad M; Li, Shenduo S; Lu, Xuetao X; Petranovic, Milena M; Saad, Maliazurina B MB; Chen, Pingjun P; Qin, Kang K; Varghese, Susan S; Rinsurongkawong, Waree W; Rinsurongkawong, Vadeerat V; Spelman, Amy A; Elamin, Yasir Y YY; Negrao, Marcelo V MV; Skoulidis, Ferdinandos F; Gay, Carl M CM; Cascone, Tina T; Gandhi, Saumil J SJ; Lin, Steven H SH; Lee, Percy P PP; Carter, Brett W BW; Wu, Carol C CC; Antonoff, Mara B MB; Sepesi, Boris B; Lewis, Jeff J; Gibbons, Don L DL; Vaporciyan, Ara A AA; Le, Xiuning X; Jack Lee, J J; Roy-Chowdhuri, Sinchita S; Routbort, Mark J MJ; Gainor, Justin F JF; Heymach, John V JV; Lou, Yanyan Y; Wu, Jia J; Zhang, Jianjun J; Vokes, Natalie I NI
Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.
Proceedings Of The National Academy Of Sciences Of The United States Of America
Wang, Tianyun T; Kim, Chang N CN; Bakken, Trygve E TE; Gillentine, Madelyn A MA; Henning, Barbara B; Mao, Yafei Y; Gilissen, Christian C; , ; Nowakowski, Tomasz J TJ; Eichler, Evan E EE
Publication Date: 2022-11-15
Variant appearance in text: NF1: 4084C>T; Arg1362*
Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma.
The Journal Of Pathology
Birkeälv, Sofia S; Harland, Mark M; Matsuyama, Larissa Satiko Alcantara Sekimoto LSAS; Rashid, Mamun M; Mehta, Ishan I; Laye, Jonathan P JP; Haase, Kerstin K; Mell, Tracey T; Iyer, Vivek V; Robles-Espinoza, Carla Daniela CD; McDermott, Ultan U; van Loo, Peter P; Kuijjer, Marieke L ML; Possik, Patricia A PA; Maria Engler, Silvya Stuchi SS; Bishop, D Timothy DT; Newton-Bishop, Julia J; Adams, David J DJ
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes.
Nature Genetics
Zhou, Xueya X; Feliciano, Pamela P; Shu, Chang C; Wang, Tianyun T; Astrovskaya, Irina I; Hall, Jacob B JB; Obiajulu, Joseph U JU; Wright, Jessica R JR; Murali, Shwetha C SC; Xu, Simon Xuming SX; Brueggeman, Leo L; Thomas, Taylor R TR; Marchenko, Olena O; Fleisch, Christopher C; Barns, Sarah D SD; Snyder, LeeAnne Green LG; Han, Bing B; Chang, Timothy S TS; Turner, Tychele N TN; Harvey, William T WT; Nishida, Andrew A; O'Roak, Brian J BJ; Geschwind, Daniel H DH; , ; Michaelson, Jacob J JJ; Volfovsky, Natalia N; Eichler, Evan E EE; Shen, Yufeng Y; Chung, Wendy K WK
Genomic landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the CALGB 10603/RATIFY trial.
Leukemia
Jahn, Nikolaus N; Jahn, Ekaterina E; Saadati, Maral M; Bullinger, Lars L; Larson, Richard A RA; Ottone, Tiziana T; Amadori, Sergio S; Prior, Thomas W TW; Brandwein, Joseph M JM; Appelbaum, Frederick R FR; Medeiros, Bruno C BC; Tallman, Martin S MS; Ehninger, Gerhard G; Heuser, Michael M; Ganser, Arnold A; Pallaud, Celine C; Gathmann, Insa I; Krzykalla, Julia J; Benner, Axel A; Bloomfield, Clara D CD; Thiede, Christian C; Stone, Richard M RM; Döhner, Hartmut H; Döhner, Konstanze K
Publication Date: 2022-09
Variant appearance in text: NF1: R1362X; rs137854560
Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma.
Nature Communications
Gounder, Mrinal M MM; Agaram, Narasimhan P NP; Trabucco, Sally E SE; Robinson, Victoria V; Ferraro, Richard A RA; Millis, Sherri Z SZ; Krishnan, Anita A; Lee, Jessica J; Attia, Steven S; Abida, Wassim W; Drilon, Alexander A; Chi, Ping P; Angelo, Sandra P D' SP; Dickson, Mark A MA; Keohan, Mary Lou ML; Kelly, Ciara M CM; Agulnik, Mark M; Chawla, Sant P SP; Choy, Edwin E; Chugh, Rashmi R; Meyer, Christian F CF; Myer, Parvathi A PA; Moore, Jessica L JL; Okimoto, Ross A RA; Pollock, Raphael E RE; Ravi, Vinod V; Singh, Arun S AS; Somaiah, Neeta N; Wagner, Andrew J AJ; Healey, John H JH; Frampton, Garrett M GM; Venstrom, Jeffrey M JM; Ross, Jeffrey S JS; Ladanyi, Marc M; Singer, Samuel S; Brennan, Murray F MF; Schwartz, Gary K GK; Lazar, Alexander J AJ; Thomas, David M DM; Maki, Robert G RG; Tap, William D WD; Ali, Siraj M SM; Jin, Dexter X DX
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants.
Nature Biotechnology
Sánchez-Rivera, Francisco J FJ; Diaz, Bianca J BJ; Kastenhuber, Edward R ER; Schmidt, Henri H; Katti, Alyna A; Kennedy, Margaret M; Tem, Vincent V; Ho, Yu-Jui YJ; Leibold, Josef J; Paffenholz, Stella V SV; Barriga, Francisco M FM; Chu, Kevan K; Goswami, Sukanya S; Wuest, Alexandra N AN; Simon, Janelle M JM; Tsanov, Kaloyan M KM; Chakravarty, Debyani D; Zhang, Hongxin H; Leslie, Christina S CS; Lowe, Scott W SW; Dow, Lukas E LE
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.
Plos One
Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.
Plos One
Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW
Germline Predisposition to Pediatric Cancer, from Next Generation Sequencing to Medical Care.
Cancers
Gargallo, Pablo P; Oltra, Silvestre S; Yáñez, Yania Y; Juan-Ribelles, Antonio A; Calabria, Inés I; Segura, Vanessa V; Lázaro, Marián M; Balaguer, Julia J; Tormo, Teresa T; Dolz, Sandra S; Fernández, José María JM; Fuentes, Carolina C; Torres, Bárbara B; Andrés, Mara M; Tasso, María M; Castel, Victoria V; Font de Mora, Jaime J; Cañete, Adela A
CDKN2A loss-of-function predicts immunotherapy resistance in non-small cell lung cancer.
Scientific Reports
Gutiontov, Stanley I SI; Turchan, William Tyler WT; Spurr, Liam F LF; Rouhani, Sherin J SJ; Chervin, Carolina Soto CS; Steinhardt, George G; Lager, Angela M AM; Wanjari, Pankhuri P; Malik, Renuka R; Connell, Philip P PP; Chmura, Steven J SJ; Juloori, Aditya A; Hoffman, Philip C PC; Ferguson, Mark K MK; Donington, Jessica S JS; Patel, Jyoti D JD; Vokes, Everett E EE; Weichselbaum, Ralph R RR; Bestvina, Christine M CM; Segal, Jeremy P JP; Pitroda, Sean P SP
A New Insight for the Identification of Oncogenic Variants in Breast and Prostate Cancers in Diverse Human Populations, With a Focus on Latinos.
Frontiers In Pharmacology
Varela, Nelson M NM; Guevara-Ramírez, Patricia P; Acevedo, Cristian C; Zambrano, Tomás T; Armendáriz-Castillo, Isaac I; Guerrero, Santiago S; Quiñones, Luis A LA; López-Cortés, Andrés A
Prevalence of germline pathogenic variants in 22 cancer susceptibility genes in Swedish pediatric cancer patients.
Scientific Reports
von Stedingk, Kristoffer K; Stjernfelt, Karl-Johan KJ; Kvist, Anders A; Wahlström, Cecilia C; Kristoffersson, Ulf U; Stenmark-Askmalm, Marie M; Wiebe, Thomas T; Hjorth, Lars L; Koster, Jan J; Olsson, Håkan H; Øra, Ingrid I
Publication Date: 2021-03-05
Variant appearance in text: NF1: 4084C>T; Arg1362Ter
Predictive Biomarkers for Immune Checkpoint Inhibitors in Metastatic Breast Cancer.
Cancer Medicine
Sivapiragasam, Abirami A; Ashok Kumar, Prashanth P; Sokol, Ethan S ES; Albacker, Lee A LA; Killian, Jonathan K JK; Ramkissoon, Shakti H SH; Huang, Richard S P RSP; Severson, Eric A EA; Brown, Charlotte A CA; Danziger, Natalie N; McGregor, Kimberly K; Ross, Jeffrey S JS
Common germline-somatic variant interactions in advanced urothelial cancer.
Nature Communications
Vosoughi, Aram A; Zhang, Tuo T; Shohdy, Kyrillus S KS; Vlachostergios, Panagiotis J PJ; Wilkes, David C DC; Bhinder, Bhavneet B; Tagawa, Scott T ST; Nanus, David M DM; Molina, Ana M AM; Beltran, Himisha H; Sternberg, Cora N CN; Motanagh, Samaneh S; Robinson, Brian D BD; Xiang, Jenny J; Fan, Xiao X; Chung, Wendy K WK; Rubin, Mark A MA; Elemento, Olivier O; Sboner, Andrea A; Mosquera, Juan Miguel JM; Faltas, Bishoy M BM
Publication Date: 2020-12-03
Variant appearance in text: NF1: 4084C>T; Arg1362*; rs137854560
Utility of a custom designed next generation DNA sequencing gene panel to molecularly classify endometrial cancers according to The Cancer Genome Atlas subgroups.
Bmc Medical Genomics
Miller, Eirwen M EM; Patterson, Nicole E NE; Gressel, Gregory M GM; Karabakhtsian, Rouzan G RG; Bejerano-Sagie, Michal M; Ravi, Nivedita N; Maslov, Alexander A; Quispe-Tintaya, Wilber W; Wang, Tao T; Lin, Juan J; Smith, Harriet O HO; Goldberg, Gary L GL; Kuo, Dennis Y S DYS; Montagna, Cristina C
Integrated molecular drivers coordinate biological and clinical states in melanoma.
Nature Genetics
Conway, Jake R JR; Dietlein, Felix F; Taylor-Weiner, Amaro A; AlDubayan, Saud S; Vokes, Natalie N; Keenan, Tanya T; Reardon, Brendan B; He, Meng Xiao MX; Margolis, Claire A CA; Weirather, Jason L JL; Haq, Rizwan R; Schilling, Bastian B; Stephen Hodi, F F; Schadendorf, Dirk D; Liu, David D; Van Allen, Eliezer M EM
Pediatric Somatic Tumor Sequencing Identifies Underlying Cancer Predisposition.
Jco Precision Oncology
MacFarland, Suzanne P SP; Zelley, Kristin K; Surrey, Lea F LF; Gallo, Daniel D; Luo, Minjie M; Raman, Pichai P; Wertheim, Gerald G; Hunger, Stephen P SP; Li, Marilyn M MM; Brodeur, Garrett M GM
Publication Date: 2019
Variant appearance in text: NF1: 4084C>T; Arg1362*
A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population.
Breast Cancer Research : Bcr
Kang, Taekyu T; Yau, Christina C; Wong, Christopher K CK; Sanborn, John Z JZ; Newton, Yulia Y; Vaske, Charlie C; Benz, Stephen C SC; Krings, Gregor G; Camarda, Roman R; Henry, Jill E JE; Stuart, Josh J; Powell, Mark M; Benz, Christopher C CC
mTOR Signaling and SREBP Activity Increase FADS2 Expression and Can Activate Sapienate Biosynthesis.
Cell Reports
Triki, Mouna M; Rinaldi, Gianmarco G; Planque, Melanie M; Broekaert, Dorien D; Winkelkotte, Alina M AM; Maier, Carina R CR; Janaki Raman, Sudha S; Vandekeere, Anke A; Van Elsen, Joke J; Orth, Martin F MF; Grünewald, Thomas G P TGP; Schulze, Almut A; Fendt, Sarah-Maria SM
Genomic and signalling pathway characterization of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma.
Pigment Cell & Melanoma Research
Tran, Khanh B KB; Gimenez, Gregory G; Tsai, Peter P; Kolekar, Sharada S; Rodger, Euan J EJ; Chatterjee, Aniruddha A; Jabed, Anower A; Shih, Jen-Hsing JH; Joseph, Wayne R WR; Marshall, Elaine S ES; Wang, Qian Q; Print, Cristin G CG; Eccles, Michael R MR; Baguley, Bruce C BC; Shepherd, Peter R PR
Phase and context shape the function of composite oncogenic mutations.
Nature
Gorelick, Alexander N AN; Sánchez-Rivera, Francisco J FJ; Cai, Yanyan Y; Bielski, Craig M CM; Biederstedt, Evan E; Jonsson, Philip P; Richards, Allison L AL; Vasan, Neil N; Penson, Alexander V AV; Friedman, Noah D ND; Ho, Yu-Jui YJ; Baslan, Timour T; Bandlamudi, Chaitanya C; Scaltriti, Maurizio M; Schultz, Nikolaus N; Lowe, Scott W SW; Reznik, Ed E; Taylor, Barry S BS
Clinical spectrum of individuals with pathogenic NF1 missense variants affecting p.Met1149, p.Arg1276, and p.Lys1423: genotype-phenotype study in neurofibromatosis type 1.
Human Mutation
Koczkowska, Magdalena M; Callens, Tom T; Chen, Yunjia Y; Gomes, Alicia A; Hicks, Alesha D AD; Sharp, Angela A; Johns, Eric E; Uhas, Kim Armfield KA; Armstrong, Linlea L; Bosanko, Katherine Armstrong KA; Babovic-Vuksanovic, Dusica D; Baker, Laura L; Basel, Donald G DG; Bengala, Mario M; Bennett, James T JT; Chambers, Chelsea C; Clarkson, Lola K LK; Clementi, Maurizio M; Cortés, Fanny M FM; Cunningham, Mitch M; D'Agostino, M Daniela MD; Delatycki, Martin B MB; Digilio, Maria C MC; Dosa, Laura L; Esposito, Silvia S; Fox, Stephanie S; Freckmann, Mary-Louise ML; Fauth, Christine C; Giugliano, Teresa T; Giustini, Sandra S; Goetsch, Allison A; Goldberg, Yael Y; Greenwood, Robert S RS; Griffis, Cristin C; Gripp, Karen W KW; Gupta, Punita P; Haan, Eric E; Hachen, Rachel K RK; Haygarth, Tamara L TL; Hernández-Chico, Concepción C; Hodge, Katelyn K; Hopkin, Robert J RJ; Hudgins, Louanne L; Janssens, Sandra S; Keller, Kory K; Kelly-Mancuso, Geraldine G; Kochhar, Aaina A; Korf, Bruce R BR; Lewis, Andrea M AM; Liebelt, Jan J; Lichty, Angie A; Listernick, Robert H RH; Lyons, Michael J MJ; Maystadt, Isabelle I; Martinez Ojeda, Mayra M; McDougall, Carey C; McGregor, Lesley K LK; Melis, Daniela D; Mendelsohn, Nancy N; Nowaczyk, Malgorzata J M MJM; Ortenberg, June J; Panzer, Karin K; Pappas, John G JG; Pierpont, Mary Ella ME; Piluso, Giulio G; Pinna, Valentina V; Pivnick, Eniko K EK; Pond, Dinel A DA; Powell, Cynthia M CM; Rogers, Caleb C; Ruhrman Shahar, Noa N; Rutledge, S Lane SL; Saletti, Veronica V; Sandaradura, Sarah A SA; Santoro, Claudia C; Schatz, Ulrich A UA; Schreiber, Allison A; Scott, Daryl A DA; Sellars, Elizabeth A EA; Sheffer, Ruth R; Siqveland, Elizabeth E; Slopis, John M JM; Smith, Rosemarie R; Spalice, Alberto A; Stockton, David W DW; Streff, Haley H; Theos, Amy A; Tomlinson, Gail E GE; Tran, Grace G; Trapane, Pamela L PL; Trevisson, Eva E; Ullrich, Nicole J NJ; Van den Ende, Jenneke J; Schrier Vergano, Samantha A SA; Wallace, Stephanie E SE; Wangler, Michael F MF; Weaver, David D DD; Yohay, Kaleb H KH; Zackai, Elaine E; Zonana, Jonathan J; Zurcher, Vickie V; Claes, Kathleen B M KBM; Eoli, Marica M; Martin, Yolanda Y; Wimmer, Katharina K; De Luca, Alessandro A; Legius, Eric E; Messiaen, Ludwine M LM
Publication Date: 2020-01
Variant appearance in text: NF1: 4084C>T; Arg1362*
Septal dysembryoplastic neuroepithelial tumor: a comprehensive clinical, imaging, histopathologic, and molecular analysis.
Neuro-Oncology
Chiang, Jason C H JCH; Harreld, Julie H JH; Tanaka, Ryuma R; Li, Xiaoyu X; Wen, Ji J; Zhang, Chenran C; Boué, Daniel R DR; Rauch, Tracy M TM; Boyd, J Todd JT; Chen, Jie J; Corbo, Joseph C JC; Bouldin, Thomas W TW; Elton, Scott W SW; Liu, Le-Wen L LL; Schofield, Deborah D; Lee, Sunhee C SC; Bouffard, John-Paul JP; Georgescu, Maria-Magdalena MM; Dossani, Rimal H RH; Aguiar, Maria A MA; Sances, Richard A RA; Saad, Ali G AG; Boop, Frederick A FA; Qaddoumi, Ibrahim I; Ellison, David W DW
Assessing the Pathogenicity, Penetrance, and Expressivity of Putative Disease-Causing Variants in a Population Setting.
American Journal Of Human Genetics
Wright, Caroline F CF; West, Ben B; Tuke, Marcus M; Jones, Samuel E SE; Patel, Kashyap K; Laver, Thomas W TW; Beaumont, Robin N RN; Tyrrell, Jessica J; Wood, Andrew R AR; Frayling, Timothy M TM; Hattersley, Andrew T AT; Weedon, Michael N MN
Publication Date: 2019-02-07
Variant appearance in text: NF1: R1362X; rs137854560
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
NF1 mutations are recurrent in adult acute myeloid leukemia and confer poor outcome.
Leukemia
Eisfeld, Ann-Kathrin AK; Kohlschmidt, Jessica J; Mrózek, Krzysztof K; Mims, Alice A; Walker, Christopher J CJ; Blachly, James S JS; Nicolet, Deedra D; Orwick, Shelley S; Maharry, Sophia E SE; Carroll, Andrew J AJ; Powell, Bayard L BL; Kolitz, Jonathan E JE; Wang, Eunice S ES; Stone, Richard M RM; de la Chapelle, Albert A; Byrd, John C JC; Bloomfield, Clara D CD