BRCA1 and BRCA2 germline testing in Cretan isolates reveals novel and strong founder effects

Abstract

Germline BRCA1 and BRCA2 loss-of-function variants have been linked to increased breast and ovarian cancer risk, with more than 5,000 distinct pathogenic variants being reported worldwide. Among individuals of Greek descent, the BRCA1/2 variant spectrum is heterogeneous, but characterized by strong founder effects. As patients from certain geographical regions of Greece (like Crete) were underrepresented in previous studies, we hypothesized that isolated Cretans, a southern Greece islanders' population with distinct demographic, cultural and genetic features, could harbor founder BRCA1/2 mutations. A total of 304 breast or/and ovarian cancer patients of Cretan descent, fulfilling NCCN criteria for genetic testing, were tested by NGS or Sanger sequencing, followed by MLPA. Haplotype analysis was subsequently performed to investigate potential founder effects of recurrent alleles. Overall, 16.5% (50/304) of the tested patients carried 22 different pathogenic variants; 48% in BRCA1, 52% in BRCA2. Three variants, namely two in BRCA2 (Δexons 12 and 13 and c.7806-2A>T) and one in BRCA1 (c.5492del), constituting approximately half (48%) of all detected pathogenic variants, were shown to have a founder effect, with all carriers sharing common haplotypes. Remarkably, these variants were confined to Cretans and have not been identified in other regions of Greece. The high prevalence of specific BRCA1/2 pathogenic variants among Cretans, provides the possibility of cost-and timeefficient screening of the Cretan population. Integrating this knowledge in local public health services may have a significant impact on cancer prevention, and may serve as a starting point for the implementation of testing on a population level.

MARGINAL: An Automatic Classification of Variants in BRCA1 and BRCA2 Genes Using a Machine Learning Model

“…A limitation of this study involves the selection of variants, which is based on a national database, i.e., CanVaS, which includes genomic data from Greek individuals only. As previously reported, the Greek population is influenced by strong founder effects, and therefore, many of the variants tested can be population-specific [ 36 , 37 , 38 , 39 ]. Although the variant classification per se described herein might not be applicable to genetic data deriving from multi-ethnic cohorts, the approach to automatically classify variants with unknown significance can find broad application.…”

CanVaS: Documenting the genetic variation spectrum of Greek cancer patients

“…Overall, this approach empowers subpopulation analysis, the study of Greek population isolates, and the investigation of possible founder effects. The strong founder effect observed in Greek subpopulations has been recently highlighted in a genetic analysis performed in Cretan isolates, where it was shown that three pathogenic variants in BRCA1 and BRCA2 , unique to the Cretan subpopulation, namely NM_007294.3:c.5492del in BRCA1 and NM_000059.3:c.7806‐2A>T and NM_000059.3:c.6842‐2675_7008‐5558del, both in BRCA2 , account for 48% of identified PVs in BRCA1 and BRCA2 among breast and ovarian cancer patients of Cretan descent (Apostolou et al, 2020).…”

“…To provide a first paradigm tackling the aforementioned open challenges, we established CanVaS, a national database that records germline genetic variation and associated clinical data of Greek cancer patients. With CanVaS, we manage to document the genetic heterogeneity of cancer susceptibility genes in Greeks, a population of unique genetic makeup, exhibiting not only extended genetic heterogeneity but also strong founder effects (Apostolou et al, 2017, 2020; Konstantopoulou et al, 2014; Pertesi et al, 2011). Most importantly, all the genetic data are accompanied by detailed phenotypic and clinical traits of tested individuals, whether a pathogenic variant has been identified or not, enabling genotype‐phenotype correlation analysis.…”

BRCA1/2 Mutation Types Do Not Affect Prognosis in Ovarian Cancer Patients

“…Blood samples were collected from each participant for germline DNA testing when the patients were referred to a Genetic Counseling Unit. All participants were screened for BRCA1 and BRCA2 mutations, either by Sanger sequencing using Applied Biosystems’ 3130XL Genetic Analyzer (Thermo Fisher Scientific, Carlsbad, CA, USA) or by massive parallel sequencing using the TruSight Cancer panel (Illumina, San Diego, CA, USA) on a MiSeq Analyzer, as previously described [ 40 ]. Carriers of variants of uncertain/unknown significance (VUSs) were deemed as non-carriers.…”