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Ceyhan-Birsoy O, Fiala E, Rana S, Sheehan M, Kennedy J, Yelskaya Z, Rai V, Li Y, Yang C, Wong D, Rijo I, Casanova J, Somar J, Mehta N, Park H, Ostafi S, Arora K, Padunan A, Ewalt MD, Aypar U, Terraf P, Misyura M, Haque S, Behr GG, Haque T, Sulis M, Geyer MB, Forlenza C, Thompson MC, Carlo M, Latham A, Liu Y, Zehir A, Brannon R, Berger M, Diaz LA, Dogan A, Ladanyi M, Petrova-Drus K, Nafa K, Offit K, Arcila M, Stadler ZK, Walsh MF, Mandelker D. Universal germline genetic testing in patients with hematologic malignancies using DNA isolated from nail clippings. Haematologica 2024. [PMID: 38572560 DOI: 10.3324/haematol.2024.285055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Indexed: 04/05/2024] Open
Abstract
Not available.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elise Fiala
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer Kennedy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zarina Yelskaya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vikas Rai
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yirong Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donna Wong
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua Somar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyeonjin Park
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Silvana Ostafi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kanika Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angelika Padunan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Umut Aypar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Panieh Terraf
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maksym Misyura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gerald G Behr
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tamanna Haque
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Sulis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark B Geyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher Forlenza
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meghan C Thompson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Michael F Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
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2
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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3
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Mandelker D, Marra A, Zheng-Lin B, Selenica P, Blanco-Heredia J, Zhu Y, Gazzo A, Wong D, Yelskaya Z, Rai V, Somar J, Ostafi S, Mehta N, Yang C, Li Y, Brown DN, da Silva EM, Pei X, Linkov I, Terraf P, Misyura M, Ceyhan-Birsoy O, Ladanyi M, Berger M, Pareja F, Stadler Z, Offit K, Riaz N, Park W, Chou J, Capanu M, Koehler M, Rosen E, O'Reilly EM, Reis-Filho JS. Genomic Profiling Reveals Germline Predisposition and Homologous Recombination Deficiency in Pancreatic Acinar Cell Carcinoma. J Clin Oncol 2023; 41:5151-5162. [PMID: 37607324 PMCID: PMC10667000 DOI: 10.1200/jco.23.00561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023] Open
Abstract
PURPOSE To determine the genetic predisposition underlying pancreatic acinar cell carcinoma (PACC) and characterize its genomic features. METHODS Both somatic and germline analyses were performed using an Food and Drug Administration-authorized matched tumor/normal sequencing assay on a clinical cohort of 28,780 patients with cancer, 49 of whom were diagnosed with PACC. For a subset of PACCs, whole-genome sequencing (WGS; n = 12) and RNA sequencing (n = 6) were performed. RESULTS Eighteen of 49 (36.7%) PACCs harbored germline pathogenic variants in homologous recombination (HR) and DNA damage response (DDR) genes, including BRCA1 (n = 1), BRCA2 (n = 12), PALB2 (n = 2), ATM (n = 2), and CHEK2 (n = 1). Thirty-one PACCs displayed pure, and 18 PACCs harbored mixed acinar cell histology. Fifteen of 31 (48%) pure PACCs harbored a germline pathogenic variant affecting HR-/DDR-related genes. BRCA2 germline pathogenic variants (11 of 31, 35%) were significantly more frequent in pure PACCs than in pancreatic adenocarcinoma (86 of 2,739, 3.1%; P < .001), high-grade serous ovarian carcinoma (67 of 1,318, 5.1%; P < .001), prostate cancer (116 of 3,401, 3.4%; P < .001), and breast cancer (79 of 3,196, 2.5%; P < .001). Genomic features of HR deficiency (HRD) were detected in 7 of 12 PACCs undergoing WGS, including 100% (n = 6) of PACCs with germline HR-related pathogenic mutations and 1 of 6 PACCs lacking known pathogenic alterations in HR-related genes. Exploratory analyses revealed that in PACCs, the repertoire of somatic driver genetic alterations and the load of neoantigens with high binding affinity varied according to the presence of germline pathogenic alterations affecting HR-/DDR-related genes and/or HRD. CONCLUSION In a large pan-cancer cohort, PACC was identified as the cancer type with the highest prevalence of both BRCA2 germline pathogenic variants and genomic features of HRD, suggesting that PACC should be considered as part of the spectrum of BRCA-related malignancies.
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Affiliation(s)
- Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Binbin Zheng-Lin
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan Blanco-Heredia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donna Wong
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zarina Yelskaya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vikas Rai
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua Somar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Silvana Ostafi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yirong Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David N. Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Edaise M. da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xin Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Irina Linkov
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Panieh Terraf
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maksym Misyura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wungki Park
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joanne Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ezra Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eileen M. O'Reilly
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY
- David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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4
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Krysiak K, Danos A, Saliba J, McMichael J, Coffman A, Kiwala S, Barnell E, Sheta L, Grisdale C, Kujan L, Pema S, Lever J, Ridd S, Spies N, Andric V, Chiorean A, Rieke D, Clark K, Reisle C, Venigalla A, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter D, Zhou X, Ainscough B, Delong S, Kesserwan C, Lamping M, Shen H, Marr A, Hoang M, Singhal K, Khanfar M, Li B, Lin WH, Terraf P, Corson L, Salama Y, Campbell K, Farncombe K, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto K, Skidmore Z, Walker J, Zhang J, Milosavljevic A, Patel R, Giles R, Kim R, Schriml L, Mardis E, Jones SJM, Raca G, Rao S, Madhavan S, Wagner A, Griffith M, Griffith O. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Res 2023; 51:D1230-D1241. [PMID: 36373660 PMCID: PMC9825608 DOI: 10.1093/nar/gkac979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/15/2022] Open
Abstract
CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.
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Affiliation(s)
- Kilannin Krysiak
- To whom correspondence should be addressed. Tel: +1 314 273 4218;
| | | | | | - Joshua F McMichael
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Adam C Coffman
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Erica K Barnell
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Lana Sheta
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | | | - Lynzey Kujan
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Shahil Pema
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Jake Lever
- School of Computer Science, University of Glasgow, Glasgow, UK
| | - Sarah Ridd
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Veronica Andric
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Andreea Chiorean
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Damian T Rieke
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kaitlin A Clark
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- Bioinformatics Graduate Program, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | - Ajay C Venigalla
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | | | - Payal Jani
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Hideaki Takahashi
- Department of Experimental Therapeutics/Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Avila Suda
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Peter Horak
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Deborah I Ritter
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Ainscough
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Sean Delong
- Lassonde School of Engineering, York University, Toronto, Ontario, Canada
| | - Chimene Kesserwan
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA and Genetics Branch, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Mario Lamping
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Haolin Shen
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Alex R Marr
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - My H Hoang
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Kartik Singhal
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Mariam Khanfar
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Brian V Li
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | | | - Panieh Terraf
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura B Corson
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Yasser Salama
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Katie M Campbell
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jianling Ji
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology and Molecular Diagnostics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ian King
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network (UHN), Toronto, ON, Canada
| | - Kelsy C Cotto
- Department of Medicine, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rachel H Giles
- International Kidney Cancer Coalition, Duivendrecht-Amsterdam, the Netherlands
| | - Raymond H Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Ontario Institute for Cancer Research, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Departments of Pediatrics and Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Gordana Raca
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, WA DC, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, WA DC, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Departments of Pediatrics and Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Malachi Griffith
- Correspondence may also be addressed to Malachi Griffith. Tel: +1 314 286 1274;
| | - Obi L Griffith
- Correspondence may also be addressed to Obi L. Griffith. Tel: +1 314 747 9248;
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Evans MG, Saliba J, Akkari Y, Bhojwani D, Blombury P, Danos A, Eckert PG, Ewalt MD, Gurbuxani S, Harrison CJ, Iacobucci I, Izraeli S, Jain N, Kanagal-Shamanna R, Kesserwan C, Kovach AE, Lee K, Helber H, Nardi V, Reshmi S, Robert K, Rouette A, Shukla N, Stock W, Terraf P, Xu X, Zhang L, Zhao X, Zhong Y, Raca G, Griffith OL, Griffith M, Krysiak K, Mullighan C. 72. Variant curation of BCR::ABL1-like B-lymphoblastic leukemia/lymphoma through expert panel consensus. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Saliba J, Raca G, Roy A, King I, Selvarajah S, Xu X, Kanagal-Shamanna R, Satgunaseelan L, Meredith D, Mullighan C, Krysiak K, Evans MG, Akkari Y, Terraf P, Church AJ, Kovach A, Williams H, Lin WH, Kesserwan C, Ritter DI, Danos A, Reshmi SC, Li MM, Sonkin D, Berg JS, Plon SE, Rehm HL, Wagner AH, Kulkarni S, Govindan R, Griffith OL, Griffith M, on behalf of the ClinGen Somatic Working Group. 22. Reimagining and enhancing the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Saliba J, Raca G, Roy A, King I, Selvarajah S, Xu X, Kanagal-Shamanna R, Satgunaseelan L, Meredith D, Evans M, Church A, Terraf P, Akkari Y, Williams HE, Lin WH, Kesserwan C, Ritter DI, Krysiak K, Danos A, Wagner A, Li MM, Sonkin D, Berg JS, Plon SE, Rehm HL, Kulkarni S, Govindan R, Griffith OL, Griffith M. Abstract 1192: The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Interpretation of the clinical significance of somatic gene variants in cancer remains a major challenge in cancer diagnosis, prognosis and treatment response prediction. We will report on progress and plans of the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG). The CDWG membership consists of over 150 multi-disciplinary experts in cancer biology, oncology, pathology, genetics, genomics and informatics. The mission of the ClinGen Somatic Cancer CDWG is to facilitate the development of data curation guidelines and standards to determine the clinical significance of somatic alterations in cancer, thereby enhancing the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource and other knowledgebases including CIViC, ClinVar, and the Variant Interpretation for Cancer Consortium (VICC) MetaKB. Our goal is to create high-quality assertions of the clinical significance of specific somatic variants in cancer by leveraging the CIViC curation interface, adapting the germline procedures of ClinGen to somatic variant interpretation, and implementing the interoperability standards of the Global Alliance for Genomics and Health (GA4GH). The ClinGen Somatic effort is overseen by the Somatic CDWG and reports progress to the overall ClinGen consortium. There are Somatic Cancer subdomains focused on particular clinically important domains of cancer variant interpretation including three Task Forces (covering Pediatric Cancer, Hematologic Cancer, and Solid Tumors) and a growing number of Somatic Cancer Variant Curation Expert Panels (SC-VCEPs). To improve quality and consistency of clinical interpretations, each candidate somatic cancer VCEP must complete a four step approval process adapted from ClinGen’s work in Germline disease domains. The Somatic CDWG works to ensure that each group is aware of available training materials and detailed standard operating procedures. Each SC-VCEP also coordinates with the ClinGen Cancer Variant Interpretation Committee (CVI) whose goal is to support development of granular specifications for the AMP/ASCO/CAP guidelines for somatic variant interpretation. New SC-VCEPs are anticipated to focus on specific clinically relevant genes, pathways, disease entities, variant classes or treatment modalities. Currently, three SC-VCEPs have begun to work through the four step process (focused on FGFR mutations, NTRK fusions, and FLT3 mutations respectively), and two more SC-VCEPs are in the planning stage (Histone H3 and Ph-like ALL). To date, ClinGen Somatic groups have contributed 619 evidence lines into CIViC from 353 published papers and 21 assertions of clinical significance. Input from the AACR community is critical for the establishment of new SC-VCEPs that address areas of variant interpretation with the greatest need.
Citation Format: 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. The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1192.
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Affiliation(s)
- Jason Saliba
- 1Washington University School of Medicine, St. Louis, MO
| | - Gordana Raca
- 2Children's Hospital Los Angeles, Los Angeles, CA
| | | | - Ian King
- 4University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- 4University Health Network and University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - David Meredith
- 8Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Mark Evans
- 6The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alanna Church
- 9Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Panieh Terraf
- 10Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | | | | | | | | | | | - Arpad Danos
- 1Washington University School of Medicine, St. Louis, MO
| | - Alex Wagner
- 15Nationwide Children's Hospital, Columbus, OH
| | - Marilyn M. Li
- 16Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | - Jonathan S. Berg
- 18University of North Carolina School of Medicine, Chapel Hill, NC
| | | | - Heidi L. Rehm
- 19Massachusetts General Hospital and Broad Institute of MIT and Harvard, Cambridge, MA
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Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M. A community approach to the cancer-variant-interpretation bottleneck. Nat Cancer 2022; 3:522-525. [PMID: 35624339 PMCID: PMC9872366 DOI: 10.1038/s43018-022-00379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpretation of Variants in Cancer, designed to reduce barriers to knowledge sharing and alleviate the variant interpretation bottleneck.
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Affiliation(s)
- Kilannin Krysiak
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Arpad M Danos
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam C Coffman
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Erica K Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lana Sheta
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Saliba
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Lynzey Kujan
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Shahil Pema
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jake Lever
- School of Computer Science, University of Glasgow, Glasgow, UK
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andreea Chiorean
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Damian T Rieke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kaitlin A Clark
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Payal Jani
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Hideaki Takahashi
- Department of Experimental Therapeutics/Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Peter Horak
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Deborah I Ritter
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Ainscough
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean Delong
- Lassonde School of Engineering, York University, Toronto, Ontario, Canada
| | - Mario Lamping
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alex R Marr
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Li
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Panieh Terraf
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasser Salama
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Katie M Campbell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jianling Ji
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology and Molecular Diagnostics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelsy C Cotto
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rachel H Giles
- International Kidney Cancer Coalition, Amsterdam, the Netherlands
| | - Raymond H Kim
- Fred A. Litwin Family Centre in Genetic Medicine, Familial Cancer Clinic, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Gordana Raca
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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Williams H, Krysiak K, Lin WH, Roy A, Church A, Saliba J, Rao S, Ritter D, Danos A, Corson L, Fisher K, Hiemenz M, Janeway KA, Ji J, Kesserwan C, Laetsch T, Parsons D, Schmidt R, Sund K, Terraf P, Xu X, Kanagal-Shamana R, Dyer L, Harris M, Lee K, Wagner A, Akkari Y, Satgunaseelan L, Griffith M, Griffith O, Kulkarni S, Schriml L, Jean J, Madhavan S, Raca G. eP063: Genetic variants associated with childhood cancers: Curation initiatives of the ClinGen Somatic Cancer Pediatric Taskforce. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Saliba J, Raca G, Roy A, King I, Selvarajah S, Xu X, Kanagal-Shamana R, Satgunaseelan L, Meredith D, Evans M, Church A, Terraf P, Akkari Y, Williams H, Lin WH, Kesserwan C, Ritter D, Krysiak K, Danos A, Wagner A, Li M, Sonkin D, Berg J, Plon S, Rehm H, Kulkarni S, Govindan R, Griffith O, Griffith M. eP055: The Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Terraf P, Sholl LM, Davids MS, Awad MM, Garcia EP, MacConaill LE, Dal Cin P, Kim A, Lindeman NI, Stachler M, Hwang DH, Dubuc AM. Twists and turns from "tumor in tumor" profiling: surveillance of chronic lymphocytic leukemia (CLL) leads to detection of a lung adenocarcinoma, whose genomic characterization alters the original hematologic diagnosis. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006089. [PMID: 34074652 PMCID: PMC8327883 DOI: 10.1101/mcs.a006089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/03/2021] [Indexed: 11/25/2022] Open
Abstract
Comprehensive characterization of somatic genomic alterations has led to fundamental shifts in our understanding of tumor biology. In clinical practice, these studies can lead to modifications of diagnosis and/or specific treatment implications, fulfilling the promise of personalized medicine. Herein, we describe a 78-yr-old woman under surveillance for long-standing untreated chronic lymphocytic leukemia (CLL). Molecular studies from a peripheral blood specimen revealed a TP53 p.V157F mutation, whereas karyotype and fluorescence in situ hybridization (FISH) identified a 17p deletion, trisomy 12, and no evidence of IGH-CCND1 rearrangement. Positron emission tomography-computed tomography scan identified multistation intra-abdominal lymphadenopathy and a pulmonary nodule, and subsequent pulmonary wedge resection confirmed the presence of a concurrent lung adenocarcinoma. Targeted next-generation sequencing of the lung tumor identified an EGFR in-frame exon 19 deletion, two TP53 mutations (p.P152Q, p.V157F), and, unexpectedly, a IGH-CCND1 rearrangement. Follow-up immunohistochemistry (IHC) studies demonstrated a cyclin D1–positive lymphoid aggregate within the lung adenocarcinoma. The presence of the TP53 p.V157F mutation in the lung resection, detection of an IGH-CCND1 rearrangement, and cyclin D1 positivity by IHC led to revision of the patient's hematologic diagnosis and confirmed the extranodal presence of mantle cell lymphoma within the lung mass, thus representing a “tumor in tumor.” Manual review of the sequencing data suggested the IGH-CCND1 rearrangement occurred via an insertional event, whose size precluded detection by original FISH studies. Thus, routine imaging for this patient's known hematologic malignancy led to detection of an unexpected solid tumor, whose subsequent precision medicine studies in the solid tumor redefined the original hematological diagnosis.
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Affiliation(s)
- Panieh Terraf
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Mark M Awad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Elizabeth P Garcia
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Annette Kim
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew Stachler
- Department of Pathology, University of California San Francisco, San Francisco, California 94143, USA
| | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adrian M Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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Danos A, Lin WH, Saliba J, Roy A, Church AJ, Rao S, Ritter D, Krysiak K, Wagner A, Barnell E, Sheta L, Coffman A, Kiwala S, McMichael JF, Corson L, Fisher K, Williams HE, Hiemenz M, Janeway KA, Ji J, Chimene KA, Fuqua L, Dyer L, Xu H, Jean J, Satgunaseelan L, Zhang L, Laetsch TW, Parsons DW, Schmidt R, Schriml LM, Sund KL, Kulkarni S, Madhavan S, Xu X, Kanagal-Shamana R, Harris M, Akkari Y, Yacov NP, Terraf P, Griffith M, Griffith OL, Raca G. Abstract 210: Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Childhood cancers are driven by unique profiles of somatic genetic alterations, with a significant contribution from predisposing germline variants. Understanding the genomic landscape of pediatric cancers is complicated by their rarity, the heterogeneity of variation within a given disease, and the complex forms of structural variation they contain. Variants in childhood disease may differ from those in adult versions of the same cancer type, or may have different clinical significance. Currently, pediatric variants are underrepresented in cancer variant databases, and an urgent need exists for their publicly available expert curation. To address this, the Pediatric Cancer Taskforce (PCT) was formed within the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG) (https://www.clinicalgenome.org/working-groups/somatic/). The PCT is a multi-institutional group of 39 members with broad experience in childhood cancer and variant curation, whose work consists of standardization and classification of genetic variants in pediatric cancers. The CIViC knowledgebase (www.civicdb.org) is a freely available resource for Clinical Interpretation of Variants in Cancer, which leverages public curation and expert moderation to address the problem of annotating the large volume of clinically actionable cancer variants. PCT curators work together with PCT expert members and the CIViC team on variant curation, and have submitted over 230 Evidence Items and over 10 Assertions to CIViC. To further address issues specific to pediatric curation, the PCT is working with CIViC to develop new pediatric-specific CIViC features and modifications of the data model that will aid in pediatric curation. A pediatric user interface, as well as representation of large scale structural and copy number variation are being developed for version two of CIViC, expected to be released in 1-2 years, which will enable curation of a new class of structural variants often encountered in pediatric cancer. A novel standard operating procedure for childhood cancer curation in CIViC is being developed by PCT experts, curators and the CIViC team. This SOP will cover topics including curation of structural variants, as well as pediatric-specific variant tiering guidelines which take into account the sparse nature of evidence in pediatric cases. A companion resource, CIViCmine (http://bionlp.bcgsc.ca/civicmine/), will be further developed to incorporate pediatric data. These and other joint efforts of the PCT and CIViC will significantly enhance pediatric variant representation for public use, to support the care of children with cancer.
Citation Format: 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. Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 210.
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Affiliation(s)
| | - Wan-Hsin Lin
- 2Department of Cancer Biology, Mayo Clinic, Jacksonville, FL
| | | | - Angshumoy Roy
- 3Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | - Alanna J. Church
- 4Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Shruti Rao
- 5Georgetown Universtiy, Washington DC, DC
| | - Deborah Ritter
- 3Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | | | - Alex Wagner
- 6Nationwide Children's Hospital , Columbus, OH
| | | | | | | | | | | | | | - Kevin Fisher
- 3Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | | | - Matthew Hiemenz
- 9Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA
| | | | - Jianling Ji
- 9Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA
| | | | | | - Lisa Dyer
- 13Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Huiling Xu
- 14Peter MacCallum Cancer Center, Victoria, Australia
| | - Jeffrey Jean
- 15Keck School of Medicine of University of Southern California, Los Angeles, CA
| | | | - Liying Zhang
- 17University of California at Los Angeles, Los Angeles, CA
| | - Ted W. Laetsch
- 18University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Ryan Schmidt
- 9Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA
| | - Lynn M. Schriml
- 20University of Maryland School of Medicine, Baltimore City, MD
| | | | | | | | | | | | - Marian Harris
- 4Boston Children's Hospital and Harvard Medical School, Boston, MA
| | | | | | - Panieh Terraf
- 27Brigham and Women's Hospital Harvard Medical School, Boston, MA
| | | | | | - Gordana Raca
- 9Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA
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Wagner AH, Vlachos IS, Sonkin D, Terraf P, Kesserwan C, Sboner A, Coard T, Reich C, Ritter DI, Horak P, Zou YS, Tanska A, Berlin AM, Lu A, Cameron D, Williams HE, Lin WH, Toruner G, Danos A, Saliba J, Xu H, Xu X, Ryland G, Ceccarelli M, Zhang L, Rapisardo S, Rehder C, Liu X, Pallavajjala A, Park N, Satgunaseelan L, Lee K, Liu J, Griffith O, Freimuth RR, Stenzinger A, Baughn LB, Baudis M, Lee J, Li M, Roy A, Raca G. Abstract 449: A standard operating procedure for the curation of gene fusions. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite the well-established role of recurrent gene fusions as oncogenic drivers, current practices for characterizing and interpreting gene fusion events in clinical testing and in biomedical literature are inconsistent. From the conceptual definition of gene fusions to the salient elements that characterize these alterations, a lack of community-driven standards for the curation of gene fusions has resulted in a disparate landscape of fusion representations and supporting tools. Consequently, the evidence-based clinical evaluation of gene fusions requires extensive expert review for accurate interpretation of observed gene fusions with respect to putative evidence from biomedical literature. Furthermore, the lack of these standards inhibits the interoperability of tools, resources, and pipelines - impeding data sharing and downstream utility.To address these challenges, a cross-consortia initiative between the Variant Interpretation for Cancer Consortium and ClinGen was formed to develop a standard operating procedure (SOP) for the curation of gene fusions. The SOP is under development by an international and diverse set of experts in the representation, detection, and clinical interpretation of gene fusions. Participating stakeholders across academic, government, and industry sectors showcased challenges and solutions, and participated in community surveys and discussions to define and develop the SOP for this diverse class of alterations.An initial result of this effort was the precise molecular definition of genomic events and features constituting gene fusions. We distinguish these from similar but distinct classes of structural alterations through clinically-relevant examples. Next, we discuss our findings on community practices around the description and evaluation of gene fusions. We provide our recommendations for characterization and representation of gene fusions from these practices, and compare these recommendations to existing variant representation standards and formats (e.g. HGVS variant nomenclature). We also discuss the concurrent application of formats for standardized human- and machine-readable representations of gene fusion events.We conclude with discussion of the salient elements to enable rapid, scalable, and consistent evaluation of fusions curated from the biomedical literature. Recommendations are provided for the standardized capture of these elements to enable both intuitive and precise characterization of this diverse class of alterations in clinical reporting and literature. In summary, we provide a clinical-practice driven framework and nomenclature for gene fusions, including recommendations for human readability, computational precision, and data integrity within the SOP. This work is a substantial advancement towards standardized communication, investigation, and sharing of gene fusion data across clinical and research domains and specialties.
Citation Format: Alex H. Wagner, Ioannis S. Vlachos, Dmitriy Sonkin, Panieh Terraf, Chimene Kesserwan, Andrea Sboner, Thomas Coard, Christian Reich, Deborah I. Ritter, Peter Horak, Ying S. Zou, Anna Tanska, Aaron M. Berlin, Anna Lu, Daniel Cameron, Heather E. Williams, Wan-Hsin Lin, Gokce Toruner, Arpad Danos, Jason Saliba, Huiling Xu, Xinjie Xu, Georgina Ryland, Michele Ceccarelli, Liying Zhang, Sarah Rapisardo, Catherine Rehder, Xuelu Liu, Aparna Pallavajjala, Nicole Park, Laveniya Satgunaseelan, Kristy Lee, Jie Liu, Obi Griffith, Robert R. Freimuth, Albrecht Stenzinger, Linda B. Baughn, Michael Baudis, Jennifer Lee, Marilyn Li, Angshumoy Roy, Gordana Raca. A standard operating procedure for the curation of gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 449.
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Affiliation(s)
| | | | | | - Panieh Terraf
- 4Memorial Sloan kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Peter Horak
- 9NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Ying S. Zou
- 10The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anna Tanska
- 11Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Anna Lu
- 13Frederick National Laboratory of Cancer Research, Frederick, MD
| | - Daniel Cameron
- 14Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | | | | | - Arpad Danos
- 18Washington University School of Medicine, St. Louis, MO
| | - Jason Saliba
- 18Washington University School of Medicine, St. Louis, MO
| | - Huiling Xu
- 11Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Liying Zhang
- 21UCLA David Geffen School of Medicine, Los Angeles, CA
| | | | | | - Xuelu Liu
- 23Dana-Farber Cancer Institute, Boston, MA
| | | | - Nicole Park
- 24University Health Network, Toronto, Ontario, Canada
| | | | - Kristy Lee
- 1Nationwide Children's Hospital, Columbus, OH
| | - Jie Liu
- 26Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Obi Griffith
- 18Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | - Marilyn Li
- 29Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Gordana Raca
- 30Keck School of Medicine of USC, Los Angeles, CA
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Saliba J, Sheta L, Krysiak K, Danos A, Marr A, Barnell E, Pema S, Lin WH, Terraf P, McMichael JF, Grisdale CJ, Rao S, Kiwala S, Coffman A, Wagner A, Griffith OL, Griffith M. Abstract 208: Development of Evidence Statement curation algorithms to aid cancer variant interpretation. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase (civicdb.org) is an open access, centralized hub for structured, community curated and expertly moderated relationships between genomic variants and cancer. Evidence is curated from peer-reviewed, published literature and is classified into one of five Types: Predisposing, Diagnostic, Prognostic, Predictive (therapeutic), or Functional. The robustness of the Evidence is conveyed through the assignment of Levels with the first three derived from patient studies (Validated, Clinical, Case Study), Preclinical, generated from in vivo or in vitro data, and Inferential, which describes indirect associations.
Each Evidence Item requires an Evidence Statement written in the curator's own words summarizing the source's results regarding the variant's clinical impact. Collaborations with groups like ClinGen have generated a significant influx of new curators, increasing the demand for detailed principles regarding data prioritization in the Evidence Statement in order to streamline the curation process. The curation community would benefit from simpler, visual guides through the complex decisions needed to appropriately and consistently curate Evidence Items. We are devoting significant effort to continue the development of straightforward Evidence curation algorithms (decision trees) similar to those used in clinical molecular testing labs to aid CIViC curators.
Previously published guidelines on development of these statements are the basis of our Evidence algorithms. Obvious inflection points for curators are clearly identified with specific details noted for each to optimize decision efficiency. As the predominant Evidence Type comprising 57% of all CIViC submissions, 58% of referenced patient trials, and 92% of Preclinical submissions, Predictive Evidence is the initial focus of our pilot guidelines with Diagnostic and Prognostic to follow. Within the Predictive Evidence Type, clinical trials, case studies, and preclinical Levels each require vastly different Evidence Statement details and ultimately the creation of three separate, uniquely modeled algorithms.
The implementation of these algorithms will assist in streamlining both curation and the expert review process. Notably, a template is not being created, as the preservation of curator style and voice is important to maintain the community feel of the database. To ensure the highest level of clarity, our team is utilizing specific novice and experienced curators to assist with the development process. As these algorithms pass the pilot phase, they are being tested as curator training tools. Ultimately, these guidelines will be used to encourage independence in curators and to enhance the Evidence already contained in CIViC.
Citation Format: 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. Development of Evidence Statement curation algorithms to aid cancer variant interpretation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 208.
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Affiliation(s)
- Jason Saliba
- 1Washington University in St. Louis, St. Louis, MO
| | - Lana Sheta
- 1Washington University in St. Louis, St. Louis, MO
| | | | - Arpad Danos
- 1Washington University in St. Louis, St. Louis, MO
| | - Alex Marr
- 1Washington University in St. Louis, St. Louis, MO
| | | | | | | | - Panieh Terraf
- 4Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Shruti Rao
- 6Georgetown University, Washington D.C., DC
| | | | - Adam Coffman
- 1Washington University in St. Louis, St. Louis, MO
| | - Alex Wagner
- 7Nationwide Children's Hospital, Columbus, OH
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Lin WH, Roy A, Church A, Rao S, Ritter D, Danos A, Krysiak K, Corson L, Fisher K, Williams H, Hiemenz M, Janeway K, Ji J, Kesserwan C, Laetsch T, Parsons D, Schmidt R, Sund K, Griffith M, Griffith O, Kulkarni S, Madhavan S, Xu X, Kanagal-Shamana R, Dyer L, Harris M, Akkari Y, Paz-Yaacov N, Terraf P, Raca G. 30. Curation of genetic variants in childhood cancers within the Clinical Genome Resource (ClinGen). Cancer Genet 2020. [DOI: 10.1016/j.cancergen.2020.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Terraf P, Kim A, Hwang D, Dubuc A. 57. Personalized medicine in practice: Genomic profiling of a lung adenocarcinoma leads to re-classification of a lymphoma. Cancer Genet 2020. [DOI: 10.1016/j.cancergen.2020.04.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Balak C, Belnap N, Ramsey K, Joss S, Devriendt K, Naymik M, Jepsen W, Siniard AL, Szelinger S, Parker ME, Richholt R, Izatt T, LaFleur M, Terraf P, Llaci L, De Both M, Piras IS, Rangasamy S, Schrauwen I, Craig DW, Huentelman M, Narayanan V. A novel
FBXO28
frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41‐q42 deletion phenotype. Am J Med Genet A 2018; 176:1549-1558. [DOI: 10.1002/ajmg.a.38712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Chris Balak
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Newell Belnap
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Keri Ramsey
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Shelagh Joss
- West of Scotland Genetics ServiceQueen Elizabeth University HospitalGlasgow United Kingdom
| | - Koen Devriendt
- Center for Human Genetics (Centrum Menselijke Erfelijkheid)University of LeuvenLeuven Belgium
| | - Marcus Naymik
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Wayne Jepsen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ashley L. Siniard
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Szabolcs Szelinger
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- UCLA Pathology & Laboratory MedicineUCLA Center for the Health SciencesLos Angeles California
| | - Mary E. Parker
- Department of Physical TherapyTexas State UniversitySan Marcos Texas
- U.R. Our Hope, Undiagnosed and Rare Disorder OrganizationAustin Texas
| | - Ryan Richholt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Tyler Izatt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Madison LaFleur
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Panieh Terraf
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Lorida Llaci
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Matt De Both
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ignazio S. Piras
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Isabelle Schrauwen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Molecular and Human Genetics, Center for Statistical GeneticsBaylor College of MedicineHouston Texas
| | - David W. Craig
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Translational GenomicsKeck School of Medicine of USCLos Angeles California
| | - Matt Huentelman
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Vinodh Narayanan
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
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Igyártó B, Sharma R, Garcia K, David-Dirgo V, Pathak K, Kroll M, Terraf P, Van Keuren-Jensen K, Pirrotte P. Abstract P3-05-21: An integrative approach to the discovery of triple-negative breast cancer markers derived from extracellular vesicles. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p3-05-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype accounting for nearly 20% of all breast cancer (BC) cases with disproportionally poor prognosis. Treatment options are limited by the lack of expression of common BC receptors targeted by FDA-approved small molecule inhibitors, resulting in an unmet need for efficient and cost effective treatments. Immunotherapies are emerging as a powerful alternative to standard chemo- and radiation therapy. Our objectives are to generate vaccines targeting TNBC and to identify circulating biomarkers capable of monitoring their therapeutic efficacy in a human transgenic mouse model (C57BL/6) compatible with EO771.LMB, a murine cell line of TNBC with a reported basal-like phenotype.
Our current study characterized the cancer-related proteomic and metabolic signatures derived from extracellular vesicles isolated from EO771.LMB. It has been shown that extracellular vesicles (EV) shed by tumors carry complex cargos comprised of proteins, metabolites and nucleic acids and may exhibit cancer-specific signatures with a potential as prognostic markers or predictors of therapy response. EVs released by TNBC tumors into circulation might provide non-invasive and highly actionable insight into the tumor biology of this aggressive cancer.
To further our understanding of cancer-specific EV proteomes, we used mass-spectrometry based proteomics and identified a total of 2265 unique proteins from EVs isolated from conditioned media from EO771.LMB. Our survey across the EV proteome, the expression proteome (5096) and phosphoproteome (2728) identified 6461 unique proteins overall. Within EV sub-fractions, microvesicles and apoptotic bodies were characterized by proteomic cargos different from exosomes. Over 90% of proteins identified in EVs shed by cultured EO771.LMB mapped with proteins curated in ExoCarta. Of interest, exploration of the EV proteome identified 47 GPI-anchored surface proteins. These candidate membrane proteins included Glypican-1 and CD109, previously reported as highly specific to cancer, as well as potential TNBC-specific markers. Our multipronged strategy for deep proteomic profiling of EO771.LMB enhanced identification by ˜25% compared to global whole cell proteomics alone. We also identified ˜3150 metabolites corresponding to lysophosphatidyl choline (35%), fatty-acids, -esters, -amides, -alcohols (30%), glycerophospholipids and sphingolipids (16%), sugar (1%), amino acids and biogenic amines (4%), organic acids and derivatives, cyclic alcohols, aromatic compounds and steroids (13%). Of these, 1450 metabolites were shared between cell line and EVs.
A proteogenomic approach expanded identification to onco-proteoforms and tumor-specific peptides not represented in canonical databases. Custom, cell-specific protein databases derived from whole transcriptome sequencing of EO771.LMB elucidated novel protein variants and mutations. Pan-cancer markers vs. TNBC-specific markers will be verified in other murine cell lines, across multiple cancer types and fibroblast controls. Optimal membrane markers for downstream immune-affinity purification from plasma will be proposed, and their ability to diagnose disease or monitor tumor load during treatment will be discussed.
Citation Format: Igyártó B, Sharma R, Garcia K, David-Dirgo V, Pathak K, Kroll M, Terraf P, Van Keuren-Jensen K, Pirrotte P. An integrative approach to the discovery of triple-negative breast cancer markers derived from extracellular vesicles [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-05-21.
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Affiliation(s)
- B Igyártó
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - R Sharma
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - K Garcia
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - V David-Dirgo
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - K Pathak
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - M Kroll
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - P Terraf
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - K Van Keuren-Jensen
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
| | - P Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ; Baylor Institute for Immunology Research, Dallas, TX; Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ
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Terraf P, Babaloo H, Kouhsari SM. Directed Differentiation of Dopamine-Secreting Cells from Nurr1/GPX1 Expressing Murine Embryonic Stem Cells Cultured on Matrigel-Coated PCL Scaffolds. Mol Neurobiol 2016; 54:1119-1128. [DOI: 10.1007/s12035-016-9726-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/13/2016] [Indexed: 12/01/2022]
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20
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Massumi M, Abasi M, Babaloo H, Terraf P, Safi M, Saeed M, Barzin J, Zandi M, Soleimani M. The effect of topography on differentiation fates of matrigel-coated mouse embryonic stem cells cultured on PLGA nanofibrous scaffolds. Tissue Eng Part A 2011; 18:609-20. [PMID: 21981309 DOI: 10.1089/ten.tea.2011.0368] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Due to pluripotency of embryonic stem (ES) cells, these cells are an invaluable in vitro model that investigates the influence of different physical and chemical cues on differentiation/development pathway of specialized cells. We sought the effect of roughness and alignment, as topomorpholocial properties of scaffolds on differentiation of green fluorescent protein-expressing ES (GFP-ES) cells into three germ layers derivates simultaneously. Furthermore, the effect of Matrigel as a natural extracellular matrix in combination with poly(lactic-co-glycolic acid) (PLGA) nanofibrous scaffolds on differentiation of mouse ES cells has been investigated. The PLGA nanofibrous scaffolds with different height and distribution of roughness and alignments were fabricated. Then, the different cell differentiation fats of GFP-ES cells plated on PLGA and PLGA/Matrigel scaffolds were analyzed by gene expression profiling. The findings demonstrated that distinct ranges of roughness, height, and distribution can support/promote a specific cell differentiation fate on scaffolds. Coating of scaffolds with Matrigel has a synergistic effect in differentiation of mesoderm-derived cells and germ cells from ES cells, whereas it inhibits the derivation of endodermal cell lineages. It was concluded that the topomorpholocial cues such as roughness and alignment should be considered in addition to other scaffolds properties to design an efficient electrospun scaffold for specific tissue engineering.
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Affiliation(s)
- Mohammad Massumi
- Department of Animal and Marine Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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