Evaluating the evaluation of cancer driver genes
Tokheim, Collin J., Papadopoulos, Nickolas, Kinzler, Kenneth W., Vogelstein, Bert, Karchin, Rachel
Published in Proceedings of the National Academy of Sciences - PNAS (13.12.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (13.12.2016)
Get full text
Journal Article
Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria
Pejaver, Vikas, Byrne, Alicia B., Feng, Bing-Jian, Pagel, Kymberleigh A., Mooney, Sean D., Karchin, Rachel, O’Donnell-Luria, Anne, Harrison, Steven M., Tavtigian, Sean V., Greenblatt, Marc S., Biesecker, Leslie G., Radivojac, Predrag, Brenner, Steven E., Biesecker, Leslie G., Harrison, Steven M., Tayoun, Ahmad A., Berg, Jonathan S., Brenner, Steven E., Cutting, Garry R., Ellard, Sian, Greenblatt, Marc S., Kang, Peter, Karbassi, Izabela, Karchin, Rachel, Mester, Jessica, O’Donnell-Luria, Anne, Pesaran, Tina, Plon, Sharon E., Rehm, Heidi L., Strande, Natasha T., Tavtigian, Sean V., Topper, Scott
Published in American journal of human genetics (01.12.2022)
Published in American journal of human genetics (01.12.2022)
Get full text
Journal Article
High grade serous ovarian carcinomas originate in the fallopian tube
Labidi-Galy, S. Intidhar, Papp, Eniko, Hallberg, Dorothy, Niknafs, Noushin, Adleff, Vilmos, Noe, Michael, Bhattacharya, Rohit, Novak, Marian, Jones, Siân, Phallen, Jillian, Hruban, Carolyn A., Hirsch, Michelle S., Lin, Douglas I., Schwartz, Lauren, Maire, Cecile L., Tille, Jean-Christophe, Bowden, Michaela, Ayhan, Ayse, Wood, Laura D., Scharpf, Robert B., Kurman, Robert, Wang, Tian-Li, Shih, Ie-Ming, Karchin, Rachel, Drapkin, Ronny, Velculescu, Victor E.
Published in Nature communications (23.10.2017)
Published in Nature communications (23.10.2017)
Get full text
Journal Article
Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer
Anagnostou, Valsamo, Forde, Patrick M, White, James R, Niknafs, Noushin, Hruban, Carolyn, Naidoo, Jarushka, Marrone, Kristen, Sivakumar, I K Ashok, Bruhm, Daniel C, Rosner, Samuel, Phallen, Jillian, Leal, Alessandro, Adleff, Vilmos, Smith, Kellie N, Cottrell, Tricia R, Rhymee, Lamia, Palsgrove, Doreen N, Hann, Christine L, Levy, Benjamin, Feliciano, Josephine, Georgiades, Christos, Verde, Franco, Illei, Peter, Li, Qing Kay, Gabrielson, Edward, Brock, Malcolm V, Isbell, James M, Sauter, Jennifer L, Taube, Janis, Scharpf, Robert B, Karchin, Rachel, Pardoll, Drew M, Chaft, Jamie E, Hellmann, Matthew D, Brahmer, Julie R, Velculescu, Victor E
Published in Cancer research (Chicago, Ill.) (15.03.2019)
Published in Cancer research (Chicago, Ill.) (15.03.2019)
Get full text
Journal Article
Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer
Anagnostou, Valsamo, Smith, Kellie N, Forde, Patrick M, Niknafs, Noushin, Bhattacharya, Rohit, White, James, Zhang, Theresa, Adleff, Vilmos, Phallen, Jillian, Wali, Neha, Hruban, Carolyn, Guthrie, Violeta B, Rodgers, Kristen, Naidoo, Jarushka, Kang, Hyunseok, Sharfman, William, Georgiades, Christos, Verde, Franco, Illei, Peter, Li, Qing Kay, Gabrielson, Edward, Brock, Malcolm V, Zahnow, Cynthia A, Baylin, Stephen B, Scharpf, Robert B, Brahmer, Julie R, Karchin, Rachel, Pardoll, Drew M, Velculescu, Victor E
Published in Cancer discovery (01.03.2017)
Published in Cancer discovery (01.03.2017)
Get full text
Journal Article
Minimal functional driver gene heterogeneity among untreated metastases
Reiter, Johannes G, Makohon-Moore, Alvin P, Gerold, Jeffrey M, Heyde, Alexander, Attiyeh, Marc A, Kohutek, Zachary A, Tokheim, Collin J, Brown, Alexia, DeBlasio, Rayne M, Niyazov, Juliana, Zucker, Amanda, Karchin, Rachel, Kinzler, Kenneth W, Iacobuzio-Donahue, Christine A, Vogelstein, Bert, Nowak, Martin A
Published in Science (American Association for the Advancement of Science) (07.09.2018)
Published in Science (American Association for the Advancement of Science) (07.09.2018)
Get full text
Journal Article
Accumulation of driver and passenger mutations during tumor progression
Bozic, Ivana, Antal, Tibor, Ohtsuki, Hisashi, Carter, Hannah, Kim, Dewey, Chen, Sining, Karchin, Rachel, Kinzler, Kenneth W., Vogelstein, Bert, Nowak, Martin A.
Published in Proceedings of the National Academy of Sciences - PNAS (26.10.2010)
Published in Proceedings of the National Academy of Sciences - PNAS (26.10.2010)
Get full text
Journal Article
The genomic landscape of response to EGFR blockade in colorectal cancer
Bertotti, Andrea, Papp, Eniko, Jones, Siân, Adleff, Vilmos, Anagnostou, Valsamo, Lupo, Barbara, Sausen, Mark, Phallen, Jillian, Hruban, Carolyn A., Tokheim, Collin, Niknafs, Noushin, Nesselbush, Monica, Lytle, Karli, Sassi, Francesco, Cottino, Francesca, Migliardi, Giorgia, Zanella, Eugenia R., Ribero, Dario, Russolillo, Nadia, Mellano, Alfredo, Muratore, Andrea, Paraluppi, Gianluca, Salizzoni, Mauro, Marsoni, Silvia, Kragh, Michael, Lantto, Johan, Cassingena, Andrea, Li, Qing Kay, Karchin, Rachel, Scharpf, Robert, Sartore-Bianchi, Andrea, Siena, Salvatore, Diaz, Luis A., Trusolino, Livio, Velculescu, Victor E.
Published in Nature (London) (08.10.2015)
Published in Nature (London) (08.10.2015)
Get full text
Journal Article
Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene
Sosnay, Patrick R, Siklosi, Karen R, Van Goor, Fredrick, Kaniecki, Kyle, Yu, Haihui, Sharma, Neeraj, Ramalho, Anabela S, Amaral, Margarida D, Dorfman, Ruslan, Zielenski, Julian, Masica, David L, Karchin, Rachel, Millen, Linda, Thomas, Philip J, Patrinos, George P, Corey, Mary, Lewis, Michelle H, Rommens, Johanna M, Castellani, Carlo, Penland, Christopher M, Cutting, Garry R
Published in Nature genetics (01.10.2013)
Published in Nature genetics (01.10.2013)
Get full text
Journal Article
Systematic Functional Annotation of Somatic Mutations in Cancer
Ng, Patrick Kwok-Shing, Li, Jun, Jeong, Kang Jin, Shao, Shan, Chen, Hu, Tsang, Yiu Huen, Sengupta, Sohini, Wang, Zixing, Bhavana, Venkata Hemanjani, Tran, Richard, Soewito, Stephanie, Minussi, Darlan Conterno, Moreno, Daniela, Kong, Kathleen, Dogruluk, Turgut, Lu, Hengyu, Gao, Jianjiong, Tokheim, Collin, Zhou, Daniel Cui, Johnson, Amber M., Zeng, Jia, Ip, Carman Ka Man, Ju, Zhenlin, Wester, Matthew, Yu, Shuangxing, Li, Yongsheng, Vellano, Christopher P., Schultz, Nikolaus, Karchin, Rachel, Ding, Li, Lu, Yiling, Cheung, Lydia Wai Ting, Chen, Ken, Shaw, Kenna R., Meric-Bernstam, Funda, Scott, Kenneth L., Yi, Song, Sahni, Nidhi, Liang, Han, Mills, Gordon B.
Published in Cancer cell (12.03.2018)
Published in Cancer cell (12.03.2018)
Get full text
Journal Article
Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup
Walker, Logan C., Hoya, Miguel de la, Wiggins, George A.R., Lindy, Amanda, Vincent, Lisa M., Parsons, Michael T., Canson, Daffodil M., Bis-Brewer, Dana, Cass, Ashley, Tchourbanov, Alexander, Zimmermann, Heather, Byrne, Alicia B., Pesaran, Tina, Karam, Rachid, Harrison, Steven M., Spurdle, Amanda B., Biesecker, Leslie G., Harrison, Steven M., Tayoun, Ahmad A., Berg, Jonathan S., Brenner, Steven E., Cutting, Garry R., Ellard, Sian, Greenblatt, Marc S., Kang, Peter, Karbassi, Izabela, Karchin, Rachel, Mester, Jessica, O’Donnell-Luria, Anne, Pesaran, Tina, Plon, Sharon E., Rehm, Heidi L., Strande, Natasha T., Tavtigian, Sean V., Topper, Scott
Published in American journal of human genetics (06.07.2023)
Published in American journal of human genetics (06.07.2023)
Get full text
Journal Article
SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing
Niknafs, Noushin, Beleva-Guthrie, Violeta, Naiman, Daniel Q, Karchin, Rachel
Published in PLoS computational biology (01.10.2015)
Published in PLoS computational biology (01.10.2015)
Get full text
Journal Article
Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations
CARTER, Hannah, SINING CHEN, ISIK, Leyla, TYEKUCHEVA, Svitlana, VELCULESCU, Victor E, KINZLER, Kenneth W, VOGELSTEIN, Bert, KARCHIN, Rachel
Published in Cancer research (Chicago, Ill.) (15.08.2009)
Published in Cancer research (Chicago, Ill.) (15.08.2009)
Get full text
Journal Article
Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure
Tokheim, Collin, Bhattacharya, Rohit, Niknafs, Noushin, Gygax, Derek M, Kim, Rick, Ryan, Michael, Masica, David L, Karchin, Rachel
Published in Cancer research (Chicago, Ill.) (01.07.2016)
Published in Cancer research (Chicago, Ill.) (01.07.2016)
Get full text
Journal Article
Integrated Genomic Analysis of Human Glioblastoma Multiforme
Parsons, D. Williams, Jones, Siân, Zhang, Xiaosong, Lin, Jimmy Cheng-Ho, Leary, Rebecca J, Angenendt, Philipp, Mankoo, Parminder, Carter, Hannah, Siu, I. Mei, Gallia, Gary L, Olivi, Alessandro, McLendon, Roger, Rasheed, B. Ahmed, Keir, Stephen, Nikolskaya, Tatiana, Nikolsky, Yuri, Busam, Dana A, Tekleab, Hanna, Diaz, Luis A. Jr, Hartigan, James, Smith, Doug R, Strausberg, Robert L, Marie, Suely Kazue Nagahashi, Shinjo, Sueli Mieko Oba, Yan, Hai, Riggins, Gregory J, Bigner, Darell D, Karchin, Rachel, Papadopoulos, Nick, Parmigiani, Giovanni, Vogelstein, Bert, Velculescu, Victor E, Kinzler, Kenneth W
Published in Science (American Association for the Advancement of Science) (26.09.2008)
Published in Science (American Association for the Advancement of Science) (26.09.2008)
Get full text
Journal Article