Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol

F. Meric-Bernstam, L. Brusco, M. Daniels, C. Wathoo, A. M. Bailey, L. Strong, K. Shaw, K. Lu, Y. Qi, H. Zhao, H. Lara-Guerra, J. Litton, B. Arun, A. K. Eterovic, U. Aytac, M. Routbort, V. Subbiah, F. Janku, M. A. Davies, S. KopetzJ. Mendelsohn, Gordon Mills, K. Chen

Research output: Contribution to journalArticle

58 Scopus citations

Abstract

Background: Next-generation sequencing in cancer research may reveal germline variants of clinical significance. We report patient preferences for return of results and the prevalence of incidental pathogenic germline variants (PGVs). Patients and methods: Targeted exome sequencing of 202 genes was carried out in 1000 advanced cancers using tumor and normal DNA in a research laboratory. Pathogenic variants in 18 genes, recommended for return by The American College of Medical Genetics and Genomics, as well as PALB2, were considered actionable. Patient preferences of return of incidental germline results were collected. Return of results was initiated with genetic counseling and repeat CLIA testing. Results: Of the 1000 patients who underwent sequencing, 43 had likely PGVs: APC (1), BRCA1 (11), BRCA2 (10), TP53 (10), MSH2 (1), MSH6 (4), PALB2 (2), PTEN (2), TSC2 (1), and RB1 (1). Twenty (47%) of 43 variants were previously known based on clinical genetic testing. Of the 1167 patients who consented for a germline testing protocol, 1157 (99%) desired to be informed of incidental results. Twenty-three previously unrecognized mutations identified in the research environment were confirmed with an orthogonal CLIA platform. All patients approached decided to proceed with formal genetic counseling; in all cases where formal genetic testing was carried out, the germline variant of concern validated with clinical genetic testing. Conclusions: In this series, 2.3% patients had previously unrecognized pathogenic germline mutations in 19 cancerrelated genes. Thus, genomic sequencing must be accompanied by a plan for return of germline results, in partnership with genetic counseling.

Original languageEnglish (US)
Article numbermdw018
Pages (from-to)795-800
Number of pages6
JournalAnnals of Oncology
Volume27
Issue number5
DOIs
StatePublished - May 1 2016
Externally publishedYes

Keywords

  • BRCA1
  • Genetics
  • Hereditary cancer risk
  • Incidental results
  • Next-generation sequencing
  • Personalized therapy

ASJC Scopus subject areas

  • Hematology
  • Oncology

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    Meric-Bernstam, F., Brusco, L., Daniels, M., Wathoo, C., Bailey, A. M., Strong, L., Shaw, K., Lu, K., Qi, Y., Zhao, H., Lara-Guerra, H., Litton, J., Arun, B., Eterovic, A. K., Aytac, U., Routbort, M., Subbiah, V., Janku, F., Davies, M. A., ... Chen, K. (2016). Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. Annals of Oncology, 27(5), 795-800. [mdw018]. https://doi.org/10.1093/annonc/mdw018