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Journal Articles

Abstract 1075: Piloting NTRK fusion-specific oncogenicity guidelines - lessons learned

Free
Jason Saliba, Shivani Golem, Arpad Danos, Laura B. Corson, Elan Hahn, Morteza Seifi, Emma G. Sullivan, Jan Clement A. Santiago, Valentina Nardi, Theodore W. Laetsch, Marilyn M. Li, Obi L. Griffith, Malachi Griffith, Gordana Raca, Larissa V. Furtado, Alanna J. Church, Angshumoy Roy
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 1075.
https://doi.org/10.1158/1538-7445.AM2025-1075
Published: 21 April 2025
View articletitled, Abstract 1075: Piloting NTRK fusion-specific oncogenicity guidelines - lessons learned
Journal Articles

Abstract 3371: Gene deletions in estrogen receptor positive HER2-negative breast cancer are associated with worse outcome than predicted by diagnostic-grade gene expression assays

Free
Jonathan T. Lei, Kim Chu, Brian Li, Eugene Schuster, Zachary L. Skidmore, Shyam M. Kavuri, Vikrant Mehta, Nicholas C. Spies, Jason Kunisaki, Catrina Fronick, Robert S. Fulton, Malachi Griffith, Richard Buus, Jack Cuzick, Mitch Dowsett, Meenakshi Anurag, Obi L. Griffith, Matthew J. Ellis
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 3371.
https://doi.org/10.1158/1538-7445.AM2025-3371
Published: 21 April 2025
View articletitled, Abstract 3371: Gene deletions in estrogen receptor positive HER2-negative breast cancer are associated with worse outcome than predicted by diagnostic-grade gene expression assays
Journal Articles

Abstract 6: Comprehensive single-cell transcriptomic analysis of a mouse model of bladder cancer identifies endothelial cells as a principal target of interferon gamma during response to combined PD-1, CTLA-4 immune checkpoint inhibitor treatment

Free
Sharon L. Freshour, Bryan Fisk, Timothy Hung-Po Chen, Haolin Shen, Matthew Mosior, Catrina Fronick, Jennifer Bolzenius, Obi L. Griffith, Vivek Arora, Malachi Griffith
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6.
https://doi.org/10.1158/1538-7445.AM2023-6
Published: 04 April 2023
View articletitled, Abstract 6: Comprehensive single-cell transcriptomic analysis of a mouse model of bladder cancer identifies endothelial cells as a principal target of interferon gamma during response to combined PD-1, CTLA-4 immune checkpoint inhibitor treatment
Journal Articles

Abstract 6569: ClinGen Somatic and CIViC collaborate to comprehensively evaluate somatic variants in cancer

Free
Jason Saliba, Arpad Danos, Kilannin Krysiak, Adam Coffman, Susanna Kiwala, Joshua McMichael, Cameron J. Grisdale, Ian King, Shamini Selvarajah, Xinjie Xu, Rashmi Kanagal-Shamanna, Laveniya Satgunaseelan, David Meredith, Mark Evans, Charles G. Mullighan, Yassmine Akkari, Gordana Raca, Angshumoy Roy, Alex H. Wagner, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith, on behalf of the ClinGen Somatic Clinical Domain Working Group
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6569.
https://doi.org/10.1158/1538-7445.AM2023-6569
Published: 04 April 2023
View articletitled, Abstract 6569: ClinGen Somatic and CIViC collaborate to comprehensively evaluate somatic variants in cancer
Journal Articles

Abstract 1215: pVACsplice: Predicting neoantigens from tumor-specific alternative splicing events derived from cis-acting regulatory mutations using whole exome and RNA sequencing data

Free
Megan M. Richters, Kelsy C. Cotto, Susanna Kiwala, Huiming Xia, Beatriz M. Carreno, Gavin P. Dunn, Antoni Ribas, Obi L. Griffith, Malachi Griffith
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1215.
https://doi.org/10.1158/1538-7445.AM2022-1215
Published: 15 June 2022
View articletitled, Abstract 1215: pVACsplice: Predicting neoantigens from tumor-specific alternative splicing events derived from cis-acting regulatory mutations using whole exome and RNA sequencing data
Journal Articles

Abstract 3818: Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma

Free
Katie M. Campbell, Justin Saco, Egmidio Medina, Meelad Amouzgar, Shannon M. Pfeiffer, Cynthia R. Gonzalez, Gabriela Steiner, Ameya Champhekar, Cristina Puig Saus, Jesse Zaretsky, Gabriel Abril Rodriguez, Agustin Vega-Crespo, Ignacio Baselga Carretero, Mito Tariveranmoshabad, Anusha Kalbasi, Christine Spencer, Zachary L. Skidmore, Malachi Griffith, Obi L. Griffith, Daniel K. Wells, Antoni Ribas
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 3818.
https://doi.org/10.1158/1538-7445.AM2022-3818
Published: 15 June 2022
View articletitled, Abstract 3818: Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma
Journal Articles

Abstract 5036: pVACview: An integrative visualization tool for efficient neoantigen prioritization and selection

Free
Huiming Xia, Susanna Kiwala, Zachary L. Skidmore, Bryan Fisk, S. Peter Goedegebuure, Christopher A. Miller, William E. Gillanders, Obi L. Griffith, Malachi Griffith
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 5036.
https://doi.org/10.1158/1538-7445.AM2022-5036
Published: 15 June 2022
View articletitled, Abstract 5036: pVACview: An integrative visualization tool for efficient neoantigen prioritization and selection
Journal Articles

Abstract 1177: Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers

Free
Matthew Cannon, Kori Kuzma, James Stevenson, Jiachen Liu, Colin O'Sullivan, Bimal P. Chaudhari, Matthew Brush, Robert R. Freimuth, Tristan Nelson, Michael Baudis, Obi L. Griffith, Malachi Griffith, Lawrence Babb, Melissa S. Cline, Xuelu Liu, Brian Walsh, Alex H. Wagner
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1177.
https://doi.org/10.1158/1538-7445.AM2022-1177
Published: 15 June 2022
View articletitled, Abstract 1177: Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers
Journal Articles

Abstract 1194: Redesigning CIViC: Enhancing the structured curation of complex cancer variant data

Free
Kilannin C. Krysiak, Adam C. Coffman, Susanna Kiwala, Joshua F. McMichael, Arpad M. Danos, Jason Saliba, Cameron J. Grisdale, Jake Lever, Lana Sheta, Shruti Rao, Alex H. Wagner, Malachi Griffith, Obi L. Griffith
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1194.
https://doi.org/10.1158/1538-7445.AM2022-1194
Published: 15 June 2022
View articletitled, Abstract 1194: Redesigning CIViC: Enhancing the structured curation of complex cancer variant data
Journal Articles

Abstract 1193: Enhancing pediatric cancer variant curation and representation through standardized classification and automation

Free
Jason Saliba, Jake Lever, Kilannin Krysiak, Arpad Danos, Alex Wagner, Heather E. Williams, Laveniya Satgunaseelan, David Meredith, Cameron J. Grisdale, Chimene Kesserwan, Jianling Ji, Shruti Rao, Catherine Cottrell, Alanna Church, Mark Evans, Yasmina Jaufeerally-Fakim, Lynn M. Schriml, Angshumoy Roy, Gordana Raca, Malachi Griffith, Obi L. Griffith
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1193.
https://doi.org/10.1158/1538-7445.AM2022-1193
Published: 15 June 2022
View articletitled, Abstract 1193: Enhancing pediatric cancer variant curation and representation through standardized classification and automation
Journal Articles

Abstract 1192: The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group

Free
Jason Saliba, Gordana Raca, Angshumoy Roy, Ian King, Shamini Selvarajah, Xinjie Xu, Rashmi Kanagal-Shamanna, Laveniya Satgunaseelan, David Meredith, Mark Evans, Alanna Church, Panieh Terraf, Yassmine Akkari, Heather E. Williams, Wan-Hsin Lin, Chimene Kesserwan, Deborah I. Ritter, Kilannin Krysiak, Arpad Danos, Alex Wagner, Marilyn M. Li, Dmitriy Sonkin, Jonathan S. Berg, Sharon E. Plon, Heidi L. Rehm, Shashikant Kulkarni, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith, on behalf of the ClinGen Somatic CDWG
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1192.
https://doi.org/10.1158/1538-7445.AM2022-1192
Published: 15 June 2022
View articletitled, Abstract 1192: The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group
Journal Articles

Abstract 5639: Computational prediction of MHC anchor locations guide neoantigen prediction and prioritization

Free
Huiming Xia, Joshua McMichael, Michelle Becker-Hapak, Onyinyechi C. Onyeador, Rico Buchli, Ethan McClain, Patrick Pence, Suangson Supabphol, Megan M. Richters, Anamika Basu, Cody A. Ramirez, Cristina Puig-Saus, Kelsy C. Cotto, Jasreet Hundal, Susanna Kiwala, S. Peter Goedegebuure, Tanner M. Johanns, Gavin P. Dunn, Antoni Ribas, Christopher A. Miller, William Gillanders, Todd A. Fehniger, Obi L. Griffith, Malachi Griffith
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 5639.
https://doi.org/10.1158/1538-7445.AM2022-5639
Published: 15 June 2022
View articletitled, Abstract 5639: Computational prediction of MHC anchor locations guide neoantigen prediction and prioritization
Journal Articles

Abstract 210: Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration

Free
Arpad Danos, Wan-Hsin Lin, Jason Saliba, Angshumoy Roy, Alanna J. Church, Shruti Rao, Deborah Ritter, Kilannin Krysiak, Alex Wagner, Erica Barnell, Lana Sheta, Adam Coffman, Susanna Kiwala, Joshua F. McMichael, Laura Corson, Kevin Fisher, Heather E. Williams, Matthew Hiemenz, Katherine A. Janeway, Jianling Ji, Kesserwan A. Chimene, Laura Fuqua, Lisa Dyer, Huiling Xu, Jeffrey Jean, Laveniya Satgunaseelan, Liying Zhang, Ted W. Laetsch, Donald W. Parsons, Ryan Schmidt, Lynn M. Schriml, Kristen L. Sund, Shashikant Kulkarni, Subha Madhavan, Xinjie Xu, Rashmi Kanagal-Shamana, Marian Harris, Yasmine Akkari, Nurit Paz Yacov, Panieh Terraf, Malachi Griffith, Obi L. Griffith, Gordana Raca
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 210.
https://doi.org/10.1158/1538-7445.AM2021-210
Published: 01 July 2021
View articletitled, Abstract 210: Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration
Journal Articles

Abstract 208: Development of Evidence Statement curation algorithms to aid cancer variant interpretation

Free
Jason Saliba, Lana Sheta, Kilannin Krysiak, Arpad Danos, Alex Marr, Erica Barnell, Shahil Pema, Wan-Hsin Lin, Panieh Terraf, Joshua F. McMichael, Cameron J. Grisdale, Shruti Rao, Susanna Kiwala, Adam Coffman, Alex Wagner, Obi L. Griffith, Malachi Griffith
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 208.
https://doi.org/10.1158/1538-7445.AM2021-208
Published: 01 July 2021
View articletitled, Abstract 208: Development of Evidence Statement curation algorithms to aid cancer variant interpretation
Journal Articles

Abstract 206: CIViC knowledgebase adapts to field experts and community input

Free
Lana M. Sheta, Arpad M. Danos, Jason Saliba, Kilannin Krysiak, Alex H. Wagner, Erica K. Barnell, Susanna Kiwala, Joshua F. McMichael, Adam Coffman, Shahil Pema, Lynzey Kujan, Kelsy C. Cotto, Cody Ramirez, Zachary L. Skidmore, Cameron J. Grisdale, Shruti Rao, Subha Madhaven, Malachi Griffith, Obi L. Griffith
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 206.
https://doi.org/10.1158/1538-7445.AM2021-206
Published: 01 July 2021
View articletitled, Abstract 206: CIViC knowledgebase adapts to field experts and community input
Journal Articles

Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium

Free
Alex H. Wagner, Reece K. Hart, Larry Babb, Robert R. Freimuth, Adam Coffman, Yonghao Liang, Beth Pitel, Angshumoy Roy, Matthew Brush, Jennifer Lee, Anna Lu, Thomas Coard, Shruti Rao, Deborah Ritter, Brian Walsh, Susan Mockus, Peter Horak, Ian King, Dmitriy Sonkin, Subha Madhavan, Gordana Raca, Debyani Chakravarty, Malachi Griffith, Obi L. Griffith
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 1096.
https://doi.org/10.1158/1538-7445.AM2020-1096
Published: 15 August 2020
View articletitled, Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium
Journal Articles

Abstract 2136: RegTools: Integrative analysis of genomic and transcriptomic data to identify splice altering mutations across 35 cancer types

Free
Kelsy C. Cotto, Yang-Yang Feng, Zachary L. Skidmore, Avinash Ramu, Jason Kunisaki, Donald F. Conrad, Yiing Lin, William Chapman, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 2136.
https://doi.org/10.1158/1538-7445.AM2020-2136
Published: 15 August 2020
View articletitled, Abstract 2136: RegTools: Integrative analysis of genomic and transcriptomic data to identify splice altering mutations across 35 cancer types
Journal Articles

Abstract 4413: Accurate neoantigen prediction depends on mutation position relative to patient-specific MHC anchor location

Free
Huiming Xia, Megan M. Richters, Cody A. Ramirez, Cristina Puig-Saus, Kelsy C. Cotto, Gavin P. Dunn, Todd Fehniger, Antoni Ribas, William E. Gillanders, Obi L. Griffith, Malachi Griffith
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 4413.
https://doi.org/10.1158/1538-7445.AM2020-4413
Published: 15 August 2020
View articletitled, Abstract 4413: Accurate neoantigen prediction depends on mutation position relative to patient-specific MHC anchor location
Journal Articles

Abstract 4727: Molecular heterogeneity in glioblastoma multiforme influences variant clonality and neoantigen prediction accuracy

Free
Megan M. Richters, Maximilian Schaettler, Zach L. Skidmore, Cody A. Ramirez, Matthew C. Mosior, Obi L. Griffith, Malachi Griffith, Gavin P. Dunn
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 4727.
https://doi.org/10.1158/1538-7445.AM2020-4727
Published: 15 August 2020
View articletitled, Abstract 4727: Molecular heterogeneity in glioblastoma multiforme influences variant clonality and neoantigen prediction accuracy
Journal Articles

Abstract 5707: A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations

Free
Peter Horak, Malachi Griffith, Arpad Danos, Beth A. Pitel, Subha Madhavan, Xuelu Liu, Jennifer Lee, Gordana Raca, Shirley Li, Alex H. Wagner, Shashikant Kulkarni, Obi L. Griffith, Debyani Chakravarty, Dmitriy Sonkin
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 5707.
https://doi.org/10.1158/1538-7445.AM2020-5707
Published: 15 August 2020
View articletitled, Abstract 5707: A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations