A community approach to the cancer-variant-interpretation bottleneck

Kilannin Krysiak; Arpad M Danos; Susanna Kiwala; Joshua F McMichael; Adam C Coffman; Erica K Barnell; Lana Sheta; Jason Saliba; Cameron J Grisdale; Lynzey Kujan; Shahil Pema; Jake Lever; Nicholas C Spies; Andreea Chiorean; Damian T Rieke; Kaitlin A Clark; Payal Jani; Hideaki Takahashi; Peter Horak; Deborah I Ritter; Xin Zhou; Benjamin J Ainscough; Sean Delong; Mario Lamping; Alex R Marr; Brian V Li; Wan-Hsin Lin; Panieh Terraf; Yasser Salama; Katie M Campbell; Kirsten M Farncombe; Jianling Ji; Xiaonan Zhao; Xinjie Xu; Rashmi Kanagal-Shamanna; Kelsy C Cotto; Zachary L Skidmore; Jason R Walker; Jinghui Zhang; Aleksandar Milosavljevic; Ronak Y Patel; Rachel H Giles; Raymond H Kim; Lynn M Schriml; Elaine R Mardis; Steven J M Jones; Gordana Raca; Shruti Rao; Subha Madhavan; Alex H Wagner; Obi L Griffith; Malachi Griffith

doi:10.1038/s43018-022-00379-w

A community approach to the cancer-variant-interpretation bottleneck

Nat Cancer. 2022 May;3(5):522-525. doi: 10.1038/s43018-022-00379-w.

Authors

Kilannin Krysiak^#^{1

2

3}, Arpad M Danos^#^{4

5}, Susanna Kiwala⁴, Joshua F McMichael⁴, Adam C Coffman⁴, Erica K Barnell^{4

5}, Lana Sheta^{4

5}, Jason Saliba^{4

5}, Cameron J Grisdale⁶, Lynzey Kujan^{4

5}, Shahil Pema^{4

5}, Jake Lever⁷, Nicholas C Spies^{4

5}, Andreea Chiorean⁸, Damian T Rieke⁹, Kaitlin A Clark^{4

5}, Payal Jani⁸, Hideaki Takahashi¹⁰, Peter Horak¹¹, Deborah I Ritter^{12

13}, Xin Zhou¹⁴, Benjamin J Ainscough⁴, Sean Delong¹⁵, Mario Lamping⁹, Alex R Marr¹⁶, Brian V Li^{4

5}, Wan-Hsin Lin¹⁷, Panieh Terraf¹⁸, Yasser Salama⁸, Katie M Campbell^{4

5}, Kirsten M Farncombe¹⁹, Jianling Ji²⁰, Xiaonan Zhao²¹, Xinjie Xu²², Rashmi Kanagal-Shamanna²³, Kelsy C Cotto^{4

5}, Zachary L Skidmore^{4

5}, Jason R Walker⁴, Jinghui Zhang¹⁴, Aleksandar Milosavljevic²¹, Ronak Y Patel²¹, Rachel H Giles²⁴, Raymond H Kim²⁵, Lynn M Schriml²⁶, Elaine R Mardis^{27

28

29}, Steven J M Jones⁶, Gordana Raca²⁰, Shruti Rao³⁰, Subha Madhavan³⁰, Alex H Wagner^{27

28

31}, Obi L Griffith^{32

33

34

35}, Malachi Griffith^{36

37

38

39}

Affiliations

¹ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
² McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³ Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
⁴ McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
⁵ Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
⁶ Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.
⁷ School of Computer Science, University of Glasgow, Glasgow, UK.
⁸ Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada.
⁹ Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
¹⁰ Department of Experimental Therapeutics/Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan.
¹¹ Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany.
¹² Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
¹³ Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA.
¹⁴ Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
¹⁵ Lassonde School of Engineering, York University, Toronto, Ontario, Canada.
¹⁶ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
¹⁷ Mayo Clinic Florida, Jacksonville, FL, USA.
¹⁸ Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
¹⁹ Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.
²⁰ Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA.
²¹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
²² Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
²³ Department of Hematopathology and Molecular Diagnostics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
²⁴ International Kidney Cancer Coalition, Amsterdam, the Netherlands.
²⁵ 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.
²⁶ University of Maryland School of Medicine, Baltimore, MD, USA.
²⁷ The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
²⁸ Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
²⁹ Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA.
³⁰ Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA.
³¹ Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA.
³² McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³³ Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³⁴ Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³⁵ Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³⁶ McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³⁷ Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³⁸ Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. [email protected].
³⁹ Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. [email protected].

^# Contributed equally.

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.

MeSH terms

Genetic Variation
Humans
Neoplasms* / diagnosis

Abstract

MeSH terms

Grants and funding