The Diagnostic Yield and Implications of Targeted Founder Pathogenic Variant Testing in an Israeli Cohort

Aasem Abu Shtaya*, Inbal Kedar, Samar Mattar, Ahmad Mahamid, Lina Basel-Salmon, Sarit Farage Barhom, Sofia Naftaly Nathan, Nurit Magal, Noy Azulay, Michal Levy Zalcberg, Rakefet Chen-Shtoyerman, Ori Segol, Mor Seri, Gili Reznick Levi, Shiri Shkedi-Rafid, Chana Vinkler, Iris Netzer, Ofir Hagari Bechar, Liat Chamma, Sari LibermanYael Goldberg

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Founder pathogenic variants (PVs) are prevalent in Israel. This study investigated the current practice of offering cancer patients two-step genetic testing, starting with targeted testing for recurring founder PVs, followed, if negative, by next-generation sequencing. A total of 2128 subjects with cancer or a positive family history underwent oncogenetic testing with a panel of 51 recurring PVs at a tertiary medical center in March 2020–January 2023. Those with a known familial PV (n = 370) were excluded from the analysis. Among the remainder, 128/1758 (7%) were heterozygous for at least one variant, and 44 (34%) carried a PV of medium-high penetrance (MHPV). Cancer was diagnosed in 1519/1758 patients (86%). The diagnostic yield of founder MHPV testing was 2% in cancer patients and 4% in healthy individuals with a positive family history. It was higher in Ashkenazi Jews than non-Ashkenazi Jews and Arabs, but not over 10% for any type of cancer, and it was significantly higher in younger (<40 years) than older (>50 years) individuals (7% vs. 1%). Eighty-four of the heterozygotes (66%), mostly Ashkenazi Jews, harbored a low-penetrance variant (LPV) not associated with the diagnosed cancer, usually APC c.3902T>A. These findings question the advantage of two-step testing. LPVs should not be included in targeted testing because this can lead to an overestimation of the yield, and their detection does not preclude further comprehensive testing.

Original languageEnglish
Article number94
JournalCancers
Volume16
Issue number1
DOIs
StatePublished - Jan 2024

Keywords

  • APC
  • BRCA1
  • BRCA2
  • Israel
  • Lynch
  • cancer
  • founder
  • yield

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