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1.

Next-generation characterization of the Cancer Cell Line Encyclopedia.

Ghandi, Mahmoud; Huang, Franklin W; Jané-Valbuena, Judit; Kryukov, Gregory V; Lo, Christopher C; McDonald, E Robert; Barretina, Jordi; Gelfand, Ellen T; Bielski, Craig M; Li, Haoxin; Hu, Kevin; Andreev-Drakhlin, Alexander Y; Kim, Jaegil; Hess, Julian M; Haas, Brian J; Aguet, François; Weir, Barbara A; Rothberg, Michael V; Paolella, Brenton R; Lawrence, Michael S; Akbani, Rehan; Lu, Yiling; Tiv, Hong L; Gokhale, Prafulla C; de Weck, Antoine; Mansour, Ali Amin; Oh, Coyin; Shih, Juliann; Hadi, Kevin; Rosen, Yanay; Bistline, Jonathan; Venkatesan, Kavitha; Reddy, Anupama; Sonkin, Dmitriy; Liu, Manway; Lehar, Joseph; Korn, Joshua M; Porter, Dale A; Jones, Michael D; Golji, Javad; Caponigro, Giordano; Taylor, Jordan E; Dunning, Caitlin M; Creech, Amanda L; Warren, Allison C; McFarland, James M; Zamanighomi, Mahdi; Kauffmann, Audrey; Stransky, Nicolas; Imielinski, Marcin.

Nature; 569(7757): 503-508, 2019 05.

Artículo en Inglés | MEDLINE | ID: mdl-31068700

2.

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).

Horak, Peter; Griffith, Malachi; Danos, Arpad M; Pitel, Beth A; Madhavan, Subha; Liu, Xuelu; Chow, Cynthia; Williams, Heather; Carmody, Leigh; Barrow-Laing, Lisa; Rieke, Damian; Kreutzfeldt, Simon; Stenzinger, Albrecht; Tamborero, David; Benary, Manuela; Rajagopal, Padma Sheila; Ida, Cristiane M; Lesmana, Harry; Satgunaseelan, Laveniya; Merker, Jason D; Tolstorukov, Michael Y; Campregher, Paulo Vidal; Warner, Jeremy L; Rao, Shruti; Natesan, Maya; Shen, Haolin; Venstrom, Jeffrey; Roy, Somak; Tao, Kayoko; Kanagal-Shamanna, Rashmi; Xu, Xinjie; Ritter, Deborah I; Pagel, Kym; Krysiak, Kilannin; Dubuc, Adrian; Akkari, Yassmine M; Li, Xuan Shirley; Lee, Jennifer; King, Ian; Raca, Gordana; Wagner, Alex H; Li, Marylin M; Plon, Sharon E; Kulkarni, Shashikant; Griffith, Obi L; Chakravarty, Debyani; Sonkin, Dmitriy.

Genet Med; 24(5): 986-998, 2022 05.

Artículo en Inglés | MEDLINE | ID: mdl-35101336

3.

MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing.

Palmisano, Alida; Vural, Suleyman; Zhao, Yingdong; Sonkin, Dmitriy.

Hum Mutat; 42(4): 342-345, 2021 04.

Artículo en Inglés | MEDLINE | ID: mdl-33600011

4.

Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Barretina, Jordi; Caponigro, Giordano; Stransky, Nicolas; Venkatesan, Kavitha; Margolin, Adam A; Kim, Sungjoon; Wilson, Christopher J; Lehár, Joseph; Kryukov, Gregory V; Sonkin, Dmitriy; Reddy, Anupama; Liu, Manway; Murray, Lauren; Berger, Michael F; Monahan, John E; Morais, Paula; Meltzer, Jodi; Korejwa, Adam; Jané-Valbuena, Judit; Mapa, Felipa A; Thibault, Joseph; Bric-Furlong, Eva; Raman, Pichai; Shipway, Aaron; Engels, Ingo H; Cheng, Jill; Yu, Guoying K; Yu, Jianjun; Aspesi, Peter; de Silva, Melanie; Jagtap, Kalpana; Jones, Michael D; Wang, Li; Hatton, Charles; Palescandolo, Emanuele; Gupta, Supriya; Mahan, Scott; Sougnez, Carrie; Onofrio, Robert C; Liefeld, Ted; MacConaill, Laura; Winckler, Wendy; Reich, Michael; Li, Nanxin; Mesirov, Jill P; Gabriel, Stacey B; Getz, Gad; Ardlie, Kristin; Chan, Vivien; Myer, Vic E.

Nature; 565(7738): E5-E6, 2019 01.

Artículo en Inglés | MEDLINE | ID: mdl-30559381

5.

Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes.

Walsh, Michael F; Ritter, Deborah I; Kesserwan, Chimene; Sonkin, Dmitriy; Chakravarty, Debyani; Chao, Elizabeth; Ghosh, Rajarshi; Kemel, Yelena; Wu, Gang; Lee, Kristy; Kulkarni, Shashikant; Hedges, Dale; Mandelker, Diana; Ceyhan-Birsoy, Ozge; Luo, Minjie; Drazer, Michael; Zhang, Liying; Offit, Kenneth; Plon, Sharon E.

Hum Mutat; 39(11): 1542-1552, 2018 11.

Artículo en Inglés | MEDLINE | ID: mdl-30311369

6.

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.

Danos, Arpad M; Ritter, Deborah I; Wagner, Alex H; Krysiak, Kilannin; Sonkin, Dmitriy; Micheel, Christine; McCoy, Matthew; Rao, Shruti; Raca, Gordana; Boca, Simina M; Roy, Angshumoy; Barnell, Erica K; McMichael, Joshua F; Kiwala, Susanna; Coffman, Adam C; Kujan, Lynzey; Kulkarni, Shashikant; Griffith, Malachi; Madhavan, Subha; Griffith, Obi L.

Hum Mutat; 39(11): 1721-1732, 2018 11.

Artículo en Inglés | MEDLINE | ID: mdl-30311370

7.

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Barretina, Jordi; Caponigro, Giordano; Stransky, Nicolas; Venkatesan, Kavitha; Margolin, Adam A; Kim, Sungjoon; Wilson, Christopher J; Lehár, Joseph; Kryukov, Gregory V; Sonkin, Dmitriy; Reddy, Anupama; Liu, Manway; Murray, Lauren; Berger, Michael F; Monahan, John E; Morais, Paula; Meltzer, Jodi; Korejwa, Adam; Jané-Valbuena, Judit; Mapa, Felipa A; Thibault, Joseph; Bric-Furlong, Eva; Raman, Pichai; Shipway, Aaron; Engels, Ingo H; Cheng, Jill; Yu, Guoying K; Yu, Jianjun; Aspesi, Peter; de Silva, Melanie; Jagtap, Kalpana; Jones, Michael D; Wang, Li; Hatton, Charles; Palescandolo, Emanuele; Gupta, Supriya; Mahan, Scott; Sougnez, Carrie; Onofrio, Robert C; Liefeld, Ted; MacConaill, Laura; Winckler, Wendy; Reich, Michael; Li, Nanxin; Mesirov, Jill P; Gabriel, Stacey B; Getz, Gad; Ardlie, Kristin; Chan, Vivien; Myer, Vic E.

Nature; 483(7391): 603-7, 2012 Mar 28.

Artículo en Inglés | MEDLINE | ID: mdl-22460905

8.

Detection of homozygous deletions in tumor-suppressor genes ranging from dozen to hundreds nucleotides in cancer models.

Chang, Lun-Ching; Vural, Suleyman; Sonkin, Dmitriy.

Hum Mutat; 38(11): 1449-1453, 2017 11.

Artículo en Inglés | MEDLINE | ID: mdl-28762582

9.

Response to Mehta et al.

Horak, Peter; Chakravarty, Debyani; Sonkin, Dmitriy.

Genet Med; 24(9): 1989-1990, 2022 Sep.

Artículo en Inglés | MEDLINE | ID: mdl-35796744

10.

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).

Horak, Peter; Griffith, Malachi; Danos, Arpad M; Pitel, Beth A; Madhavan, Subha; Liu, Xuelu; Chow, Cynthia; Williams, Heather; Carmody, Leigh; Barrow-Laing, Lisa; Rieke, Damian; Kreutzfeldt, Simon; Stenzinger, Albrecht; Tamborero, David; Benary, Manuela; Rajagopal, Padma Sheila; Ida, Cristiane M; Lesmana, Harry; Satgunaseelan, Laveniya; Merker, Jason D; Tolstorukov, Michael Y; Campregher, Paulo Vidal; Warner, Jeremy L; Rao, Shruti; Natesan, Maya; Shen, Haolin; Venstrom, Jeffrey; Roy, Somak; Tao, Kayoko; Kanagal-Shamanna, Rashmi; Xu, Xinjie; Ritter, Deborah I; Pagel, Kym; Krysiak, Kilannin; Dubuc, Adrian; Akkari, Yassmine M; Li, Xuan Shirley; Lee, Jennifer; King, Ian; Raca, Gordana; Wagner, Alex H; Li, Marylin M; Plon, Sharon E; Kulkarni, Shashikant; Griffith, Obi L; Chakravarty, Debyani; Sonkin, Dmitriy.

Genet Med; 24(9): 1991, 2022 Sep.

Artículo en Inglés | MEDLINE | ID: mdl-36063163

11.

TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data.

Bouaoun, Liacine; Sonkin, Dmitriy; Ardin, Maude; Hollstein, Monica; Byrnes, Graham; Zavadil, Jiri; Olivier, Magali.

Hum Mutat; 37(9): 865-76, 2016 09.

Artículo en Inglés | MEDLINE | ID: mdl-27328919

12.

Cancer treatments: Past, present, and future.

Sonkin, Dmitriy; Thomas, Anish; Teicher, Beverly A.

Cancer Genet; 286-287: 18-24, 2024 Jun 17.

Artículo en Inglés | MEDLINE | ID: mdl-38909530

13.

Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems-based Resource.

Morris, Joel; Kunkel, Mark W; White, Stephen L; Wishka, Donn G; Lopez, Omar D; Bowles, Lori; Sellers Brady, Penny; Ramsey, Patricia; Grams, Julie; Rohrer, Tiffany; Martin, Karen; Dexheimer, Thomas S; Coussens, Nathan P; Evans, David; Risbood, Prabhakar; Sonkin, Dmitriy; Williams, John D; Polley, Eric C; Collins, Jerry M; Doroshow, James H; Teicher, Beverly A.

Mol Cancer Ther; 22(11): 1270-1279, 2023 Nov 01.

Artículo en Inglés | MEDLINE | ID: mdl-37550087

14.

Genetic mechanisms in Apc-mediated mammary tumorigenesis.

Kuraguchi, Mari; Ohene-Baah, Nana Yaw; Sonkin, Dmitriy; Bronson, Roderick Terry; Kucherlapati, Raju.

PLoS Genet; 5(2): e1000367, 2009 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-19197353

15.

Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon.

Kucherlapati, Melanie H; Yang, Kan; Fan, Kunhua; Kuraguchi, Mari; Sonkin, Dmitriy; Rosulek, Andrew; Lipkin, Martin; Bronson, Roderick T; Aronow, Bruce J; Kucherlapati, Raju.

Proc Natl Acad Sci U S A; 105(40): 15493-8, 2008 Oct 07.

Artículo en Inglés | MEDLINE | ID: mdl-18832169

16.

TP53 isoform junction reads based analysis in malignant and normal contexts.

Vural, Suleyman; Chang, Lun-Ching; Yee, Laura M; Sonkin, Dmitriy.

Sci Rep; 11(1): 17275, 2021 08 26.

Artículo en Inglés | MEDLINE | ID: mdl-34446762

17.

Bioinformatics Tools and Resources for Cancer Immunotherapy Study.

Palmisano, Alida; Krushkal, Julia; Li, Ming-Chung; Fang, Jianwen; Sonkin, Dmitriy; Wright, George; Yee, Laura; Zhao, Yingdong; McShane, Lisa.

Methods Mol Biol; 2055: 649-678, 2020.

Artículo en Inglés | MEDLINE | ID: mdl-31502173

18.

Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets.

Krushkal, Julia; Silvers, Thomas; Reinhold, William C; Sonkin, Dmitriy; Vural, Suleyman; Connelly, John; Varma, Sudhir; Meltzer, Paul S; Kunkel, Mark; Rapisarda, Annamaria; Evans, David; Pommier, Yves; Teicher, Beverly A.

Clin Epigenetics; 12(1): 93, 2020 06 25.

Artículo en Inglés | MEDLINE | ID: mdl-32586373

19.

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.

Wagner, Alex H; Walsh, Brian; Mayfield, Georgia; Tamborero, David; Sonkin, Dmitriy; Krysiak, Kilannin; Deu-Pons, Jordi; Duren, Ryan P; Gao, Jianjiong; McMurry, Julie; Patterson, Sara; Del Vecchio Fitz, Catherine; Pitel, Beth A; Sezerman, Ozman U; Ellrott, Kyle; Warner, Jeremy L; Rieke, Damian T; Aittokallio, Tero; Cerami, Ethan; Ritter, Deborah I; Schriml, Lynn M; Freimuth, Robert R; Haendel, Melissa; Raca, Gordana; Madhavan, Subha; Baudis, Michael; Beckmann, Jacques S; Dienstmann, Rodrigo; Chakravarty, Debyani; Li, Xuan Shirley; Mockus, Susan; Elemento, Olivier; Schultz, Nikolaus; Lopez-Bigas, Nuria; Lawler, Mark; Goecks, Jeremy; Griffith, Malachi; Griffith, Obi L; Margolin, Adam A.

Nat Genet; 52(4): 448-457, 2020 04.

Artículo en Inglés | MEDLINE | ID: mdl-32246132

20.

Are neuroendocrine negative small cell lung cancer and large cell neuroendocrine carcinoma with WT RB1 two faces of the same entity?

Sonkin, Dmitriy; Thomas, Anish; Teicher, Beverly A.

Lung Cancer Manag; 8(2): LMT13, 2019 Aug 21.

Artículo en Inglés | MEDLINE | ID: mdl-31645891

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Next-generation characterization of the Cancer Cell Line Encyclopedia.

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).

MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing.

Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes.

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Detection of homozygous deletions in tumor-suppressor genes ranging from dozen to hundreds nucleotides in cancer models.

Response to Mehta et al.

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).

TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data.

Cancer treatments: Past, present, and future.

Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems-based Resource.

Genetic mechanisms in Apc-mediated mammary tumorigenesis.

Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon.

TP53 isoform junction reads based analysis in malignant and normal contexts.

Bioinformatics Tools and Resources for Cancer Immunotherapy Study.

Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets.

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.

Are neuroendocrine negative small cell lung cancer and large cell neuroendocrine carcinoma with WT RB1 two faces of the same entity?