A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes.
Npj Precision Oncology
Ritch, Elie J EJ; Herberts, Cameron C; Warner, Evan W EW; Ng, Sarah W S SWS; Kwan, Edmond M EM; Bacon, Jack V W JVW; Bernales, Cecily Q CQ; Schönlau, Elena E; Fonseca, Nicolette M NM; Giri, Veda N VN; Maurice-Dror, Corinne C; Vandekerkhove, Gillian G; Jones, Steven J M SJM; Chi, Kim N KN; Wyatt, Alexander W AW
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: 2446C>T; Arg816Ter
The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations.
Nature Cancer
Villani, Anita A; Davidson, Scott S; Kanwar, Nisha N; Lo, Winnie W WW; Li, Yisu Y; Cohen-Gogo, Sarah S; Fuligni, Fabio F; Edward, Lisa-Monique LM; Light, Nicholas N; Layeghifard, Mehdi M; Harripaul, Ricardo R; Waldman, Larissa L; Gallinger, Bailey B; Comitani, Federico F; Brunga, Ledia L; Hayes, Reid R; Anderson, Nathaniel D ND; Ramani, Arun K AK; Yuki, Kyoko E KE; Blay, Sasha S; Johnstone, Brittney B; Inglese, Cara C; Hammad, Rawan R; Goudie, Catherine C; Shuen, Andrew A; Wasserman, Jonathan D JD; Venier, Rosemarie E RE; Eliou, Marianne M; Lorenti, Miranda M; Ryan, Carol Ann CA; Braga, Michael M; Gloven-Brown, Meagan M; Han, Jianan J; Montero, Maria M; Spatare, Famida F; Whitlock, James A JA; Scherer, Stephen W SW; Chun, Kathy K; Somerville, Martin J MJ; Hawkins, Cynthia C; Abdelhaleem, Mohamed M; Ramaswamy, Vijay V; Somers, Gino R GR; Kyriakopoulou, Lianna L; Hitzler, Johann J; Shago, Mary M; Morgenstern, Daniel A DA; Tabori, Uri U; Meyn, Stephen S; Irwin, Meredith S MS; Malkin, David D; Shlien, Adam A
Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1.
Acta Neuropathologica
Lucas, Calixto-Hope G CG; Sloan, Emily A EA; Gupta, Rohit R; Wu, Jasper J; Pratt, Drew D; Vasudevan, Harish N HN; Ravindranathan, Ajay A; Barreto, Jairo J; Williams, Erik A EA; Shai, Anny A; Whipple, Nicholas S NS; Bruggers, Carol S CS; Maher, Ossama O; Nabors, Burt B; Rodriguez, Michael M; Samuel, David D; Brown, Melandee M; Carmichael, Jason J; Lu, Rufei R; Mirchia, Kanish K; Sullivan, Daniel V DV; Pekmezci, Melike M; Tihan, Tarik T; Bollen, Andrew W AW; Perry, Arie A; Banerjee, Anuradha A; Mueller, Sabine S; Gupta, Nalin N; Hervey-Jumper, Shawn L SL; Oberheim Bush, Nancy Ann NA; Daras, Mariza M; Taylor, Jennie W JW; Butowski, Nicholas A NA; de Groot, John J; Clarke, Jennifer L JL; Raleigh, David R DR; Costello, Joseph F JF; Phillips, Joanna J JJ; Reddy, Alyssa T AT; Chang, Susan M SM; Berger, Mitchel S MS; Solomon, David A DA
Genotype-Phenotype Correlations in Neurofibromatosis Type 1: Identification of Novel and Recurrent NF1 Gene Variants and Correlations with Neurocognitive Phenotype.
Genes
Napolitano, Filomena F; Dell'Aquila, Milena M; Terracciano, Chiara C; Franzese, Giuseppina G; Gentile, Maria Teresa MT; Piluso, Giulio G; Santoro, Claudia C; Colavito, Davide D; Patanè, Anna A; De Blasiis, Paolo P; Sampaolo, Simone S; Paladino, Simona S; Melone, Mariarosa Anna Beatrice MAB
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
Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers.
Nature Communications
Shukla, N N; Levine, M F MF; Gundem, G G; Domenico, D D; Spitzer, B B; Bouvier, N N; Arango-Ossa, J E JE; Glodzik, D D; Medina-Martínez, J S JS; Bhanot, U U; Gutiérrez-Abril, J J; Zhou, Y Y; Fiala, E E; Stockfisch, E E; Li, S S; Rodriguez-Sanchez, M I MI; O'Donohue, T T; Cobbs, C C; Roehrl, M H A MHA; Benhamida, J J; Iglesias Cardenas, F F; Ortiz, M M; Kinnaman, M M; Roberts, S S; Ladanyi, M M; Modak, S S; Farouk-Sait, S S; Slotkin, E E; Karajannis, M A MA; Dela Cruz, F F; Glade Bender, J J; Zehir, A A; Viale, A A; Walsh, M F MF; Kung, A L AL; Papaemmanuil, E E
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
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort.
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort.
Landscape of somatic mutations in breast cancer: new opportunities for targeted therapies in Saudi Arabian patients.
Oncotarget
Barakeh, Duna H DH; Aljelaify, Rasha R; Bashawri, Yara Y; Almutairi, Amal A; Alqubaishi, Fatimah F; Alnamnakani, Mohammed M; Almubarak, Latifa L; Al Naeem, Abdulrahman A; Almushawah, Fatema F; Alrashed, May M; Abedalthagafi, Malak M
Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity.
Nature Communications
Newell, Felicity F; Wilmott, James S JS; Johansson, Peter A PA; Nones, Katia K; Addala, Venkateswar V; Mukhopadhyay, Pamela P; Broit, Natasa N; Amato, Carol M CM; Van Gulick, Robert R; Kazakoff, Stephen H SH; Patch, Ann-Marie AM; Koufariotis, Lambros T LT; Lakis, Vanessa V; Leonard, Conrad C; Wood, Scott S; Holmes, Oliver O; Xu, Qinying Q; Lewis, Karl K; Medina, Theresa T; Gonzalez, Rene R; Saw, Robyn P M RPM; Spillane, Andrew J AJ; Stretch, Jonathan R JR; Rawson, Robert V RV; Ferguson, Peter M PM; Dodds, Tristan J TJ; Thompson, John F JF; Long, Georgina V GV; Levesque, Mitchell P MP; Robinson, William A WA; Pearson, John V JV; Mann, Graham J GJ; Scolyer, Richard A RA; Waddell, Nicola N; Hayward, Nicholas K NK
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
A longitudinal footprint of genetic epilepsies using automated electronic medical record interpretation.
Genetics In Medicine : Official Journal Of The American College Of Medical Genetics
Ganesan, Shiva S; Galer, Peter D PD; Helbig, Katherine L KL; McKeown, Sarah E SE; O'Brien, Margaret M; Gonzalez, Alexander K AK; Felmeister, Alex S AS; Khankhanian, Pouya P; Ellis, Colin A CA; Helbig, Ingo I
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
High-sensitivity microsatellite instability assessment for the detection of mismatch repair defects in normal tissue of biallelic germline mismatch repair mutation carriers.
Journal Of Medical Genetics
González-Acosta, Maribel M; Marín, Fátima F; Puliafito, Benjamin B; Bonifaci, Nuria N; Fernández, Anna A; Navarro, Matilde M; Salvador, Hector H; Balaguer, Francesc F; Iglesias, Silvia S; Velasco, Angela A; Grau Garces, Elia E; Moreno, Victor V; Gonzalez-Granado, Luis Ignacio LI; Guerra-García, Pilar P; Ayala, Rosa R; Florkin, Benoît B; Kratz, Christian C; Ripperger, Tim T; Rosenbaum, Thorsten T; Januszkiewicz-Lewandowska, Danuta D; Azizi, Amedeo A AA; Ragab, Iman I; Nathrath, Michaela M; Pander, Hans-Jürgen HJ; Lobitz, Stephan S; Suerink, Manon M; Dahan, Karin K; Imschweiler, Thomas T; Demirsoy, Ugur U; Brunet, Joan J; Lázaro, Conxi C; Rueda, Daniel D; Wimmer, Katharina K; Capellá, Gabriel G; Pineda, Marta M
Clinical utility of custom-designed NGS panel testing in pediatric tumors.
Genome Medicine
Surrey, Lea F LF; MacFarland, Suzanne P SP; Chang, Fengqi F; Cao, Kajia K; Rathi, Komal S KS; Akgumus, Gozde T GT; Gallo, Daniel D; Lin, Fumin F; Gleason, Adam A; Raman, Pichai P; Aplenc, Richard R; Bagatell, Rochelle R; Minturn, Jane J; Mosse, Yael Y; Santi, Mariarita M; Tasian, Sarah K SK; Waanders, Angela J AJ; Sarmady, Mahdi M; Maris, John M JM; Hunger, Stephen P SP; Li, Marilyn M MM
Tracking tumour evolution in glioma through liquid biopsies of cerebrospinal fluid.
Nature
Miller, Alexandra M AM; Shah, Ronak H RH; Pentsova, Elena I EI; Pourmaleki, Maryam M; Briggs, Samuel S; Distefano, Natalie N; Zheng, Youyun Y; Skakodub, Anna A; Mehta, Smrutiben A SA; Campos, Carl C; Hsieh, Wan-Ying WY; Selcuklu, S Duygu SD; Ling, Lilan L; Meng, Fanli F; Jing, Xiaohong X; Samoila, Aliaksandra A; Bale, Tejus A TA; Tsui, Dana W Y DWY; Grommes, Christian C; Viale, Agnes A; Souweidane, Mark M MM; Tabar, Viviane V; Brennan, Cameron W CW; Reiner, Anne S AS; Rosenblum, Marc M; Panageas, Katherine S KS; DeAngelis, Lisa M LM; Young, Robert J RJ; Berger, Michael F MF; Mellinghoff, Ingo K IK
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.
Cell Reports
Way, Gregory P GP; Sanchez-Vega, Francisco F; La, Konnor K; Armenia, Joshua J; Chatila, Walid K WK; Luna, Augustin A; Sander, Chris C; Cherniack, Andrew D AD; Mina, Marco M; Ciriello, Giovanni G; Schultz, Nikolaus N; , ; Sanchez, Yolanda Y; Greene, Casey S CS
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
The genomic landscape of pediatric myelodysplastic syndromes.
Nature Communications
Schwartz, Jason R JR; Ma, Jing J; Lamprecht, Tamara T; Walsh, Michael M; Wang, Shuoguo S; Bryant, Victoria V; Song, Guangchun G; Wu, Gang G; Easton, John J; Kesserwan, Chimene C; Nichols, Kim E KE; Mullighan, Charles G CG; Ribeiro, Raul C RC; Klco, Jeffery M JM
Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma.
Nature Communications
Nikbakht, Hamid H; Panditharatna, Eshini E; Mikael, Leonie G LG; Li, Rui R; Gayden, Tenzin T; Osmond, Matthew M; Ho, Cheng-Ying CY; Kambhampati, Madhuri M; Hwang, Eugene I EI; Faury, Damien D; Siu, Alan A; Papillon-Cavanagh, Simon S; Bechet, Denise D; Ligon, Keith L KL; Ellezam, Benjamin B; Ingram, Wendy J WJ; Stinson, Caedyn C; Moore, Andrew S AS; Warren, Katherine E KE; Karamchandani, Jason J; Packer, Roger J RJ; Jabado, Nada N; Majewski, Jacek J; Nazarian, Javad J
The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma.
Nature Genetics
Wu, Gang G; Diaz, Alexander K AK; Paugh, Barbara S BS; Rankin, Sherri L SL; Ju, Bensheng B; Li, Yongjin Y; Zhu, Xiaoyan X; Qu, Chunxu C; Chen, Xiang X; Zhang, Junyuan J; Easton, John J; Edmonson, Michael M; Ma, Xiaotu X; Lu, Charles C; Nagahawatte, Panduka P; Hedlund, Erin E; Rusch, Michael M; Pounds, Stanley S; Lin, Tong T; Onar-Thomas, Arzu A; Huether, Robert R; Kriwacki, Richard R; Parker, Matthew M; Gupta, Pankaj P; Becksfort, Jared J; Wei, Lei L; Mulder, Heather L HL; Boggs, Kristy K; Vadodaria, Bhavin B; Yergeau, Donald D; Russell, Jake C JC; Ochoa, Kerri K; Fulton, Robert S RS; Fulton, Lucinda L LL; Jones, Chris C; Boop, Frederick A FA; Broniscer, Alberto A; Wetmore, Cynthia C; Gajjar, Amar A; Ding, Li L; Mardis, Elaine R ER; Wilson, Richard K RK; Taylor, Michael R MR; Downing, James R JR; Ellison, David W DW; Zhang, Jinghui J; Baker, Suzanne J SJ
A highly sensitive genetic protocol to detect NF1 mutations.
The Journal Of Molecular Diagnostics : Jmd
Valero, María Carmen MC; Martín, Yolanda Y; Hernández-Imaz, Elisabete E; Marina Hernández, Alba A; Meleán, Germán G; Valero, Ana María AM; Javier Rodríguez-Álvarez, Francisco F; Tellería, Dolores D; Hernández-Chico, Concepción C
Double inactivation of NF1 in tibial pseudarthrosis.
American Journal Of Human Genetics
Stevenson, David A DA; Zhou, Holly H; Ashrafi, Shadi S; Messiaen, Ludwine M LM; Carey, John C JC; D'Astous, Jacques L JL; Santora, Stephen D SD; Viskochil, David H DH
Minor lesion mutational spectrum of the entire NF1 gene does not explain its high mutability but points to a functional domain upstream of the GAP-related domain.
American Journal Of Human Genetics
Fahsold, R R; Hoffmeyer, S S; Mischung, C C; Gille, C C; Ehlers, C C; Kücükceylan, N N; Abdel-Nour, M M; Gewies, A A; Peters, H H; Kaufmann, D D; Buske, A A; Tinschert, S S; Nürnberg, P P