44. An international landscape of cancer NGS reporting practices

Beth Pitel

Beth Pitel is a Clinical Variant Scientist and Assistant Professor in the Division of Laboratory Genetics and Genomics at Mayo Clinic. Beth is the lead of the Genomics of Oncology Annotation Team (GOAT) at Mayo Clinic, which creates interpretive resources for the laboratory based on current knowledgebase content, database content, commercial oncology NGS assays, and prevalent literature.

Beth has worked at Mayo Clinic since 2007 and completed her master’s degree in Biochemistry and Molecular biology in 2015 with foci on cancer biology and bioinformatics at the Mayo Graduate School. Her interpretation worked has led to platform presentations at the Cancer Genomics Consortium annual meeting as well as several well-attended online webinars. Beth is an active member of the Cancer Genomics Consortium (CGC), an affiliate member of the American Association for Cancer Research (AACR) and has contributed to the ClinGen Somatic Working Group in addition to her involvement in the Variant Interpretation for Cancer Consortium (VICC) as a co-director and a co-lead for the VICC virtual molecular tumor board.

Beth has co-authored over 35 peer-reviewed manuscripts and is frequently involved in clinical and translational research in the Mayo Clinic Genomics Laboratory within the Department of Laboratory Medicine and Pathology.


Beth Pitela, Manuela Benaryb, Shruti Raoc, Paulo Campregherd, Ian Kinge, Gordana Racaf, P. Sheila Rajagopalg, Jason Salibah, Dmitriy Sonking, Ioannis Vlachosi, Malachi Griffithh, Obi L. Griffithh, Debyani Chakravartyj, Alex Wagnerk

aMayo Clinic, Rochester, MN, USA; bBerlin Institute of Health at Charite, Berlin, Germany; cCedars Sinai, Los Angeles, CA, USA; dHospital Albert Einstein, Sao Paulo, Brazil; eUniversity Health Network, Toronto, Ontario, CA; fChildren’s Hospital of Los Angeles, Los Angeles, CA, USA; gNational Cancer Institute, Bethesda, MD, USA; hWashington University School of Medicine, St. Louis, MO, USA; iBeth Israel Deaconess Medical Center, Boston, MA, USA; jMemorial Sloan Kettering Cancer Center, New York City, NY, USA; kNationwide Children’s Hospital, Columbus, OH, USA

Multiple guidelines and standards have been issued globally to aid in Next Generation Sequencing (NGS) variant interpretation. The AMP/ASCO/CAP, ACMG/AMP, and ESMO published guidelines are incorporated into cancer NGS reports in different ways around the globe. The Variant Interpretation for Cancer Consortium Virtual Molecular Tumor Board (VICC-VMTB), in collaboration with the Cancer Genomics Consortium (CGC) and the ClinGen Somatic Clinical Domain Working Group (CDWG), distributed a comprehensive survey to membership of each group regarding reporting practices for cancer NGS testing worldwide. Seventy-nine survey responses representing 17 countries in 6 continents were collected. Respondents are involved in reporting cancer NGS tests in clinical laboratories (n=58), academic/research laboratories (n=30), and/or commercial laboratories (n=5). The use of reporting elements both consistently and differentially was evaluated. Consistently reported elements used globally include but are not limited to inclusion of the tissue source, diagnosis, protein-level amino acid sequence-based (p.) variant annotation, and the inclusion of relevant treatment information. Differentially reported elements include but are not limited to the usage of  genomic DNA reference sequence-based (g.) nomenclature, the combination of different variant types into a single report, and the practices around  reporting mutational signatures. This global survey helps inform communities providing guidance on reporting structure and the necessary components of cancer NGS report. This snapshot of current reporting practices helps further the discussions about differentially utilized report elements and clarify the context of their use on a global scale.