The French Cosegregation Variant (COVAR) study, a collaboration by cancer genetics clinics and laboratories led by geneticists at the Curie Institute in Paris, has demonstrated that cosegregation analysis represents a powerful tool for classifying variants in BRCA1 and BRCA2 breast-ovarian cancer predisposition genes.
Reported in the September 30, 2021, edition of the American Journal of Human Genetics, the study findings have important implications for the future management of breast and ovarian cancer patients, including avoidance of unnecessary prophylactic procedures.
"The COVAR study was initiated in 2011 in order to increase the proportion of classified variants by using cosegregation data within families," said study director Sandrine Caputo, a researcher in the Department of Genetics at the Curie Institute.
"The study was designed to focus on sampling relatives of index cases (ICs) and testing whether or not they carried the variant found in ICs with reference to their cancer phenotype," said Caputo.
"ICs comprise the first case to be tested in their families and were predominantly women with a personal history of breast and/or ovarian cancer," she explained.
Pathogenic BRCA1/2 variants are mainly associated with a high risk of breast and ovarian cancer, with predictive testing having become standard practice since the initial identification of BRCA1/2 genes approximately 25 years ago.
However, "the model used here included the absence/presence and age at diagnosis of BRCA-associated cancers of the breast, ovary and pancreas for BRCA1 and BRCA2, and prostate cancer for BRCA2 only [in men]," Caputo told BioWorld Science.
"The [cosegregation] model compares the probability of observing pedigree phenotypes and variant genotypes if the variant is thought to be pathogenic, with when the variant is hypothesized to be benign with respect to risk," she said.
"If this likelihood ratio (LR) is greater than one, this indicates evidence in favor of a pathogenic effect of the variant; conversely, if the LR is less than one, this suggests the variant is benign."
Moreover, "for a given variant, the combined cosegregation likelihood of pathogenicity is calculated by multiplying the LR from families sharing the same variant, or different variants when the same impact at the mRNA and/or protein level has been demonstrated for each variant," said Caputo.
Variants are classified as pathogenic, if they have a loss-of-function effect, but many identified variants are hard to classify without further analyses, so often remain unclassified.
Moreover, numbers of affected patients and detected variants are increasing, due to next-generation sequencing (NGS) technology increasing testing capacity and the advent of poly (ADP ribose) polymerase (PARP) inhibitors for treating breast and ovarian tumors driven by BRCA1/BRCA2 inactivation.
For example, as of April 2021, about 40,000 and 25,000 different BRCA1/2 variants had been reported worldwide in the BRCA exchange and ClinVar databases, of which nearly 80% and 50%, respectively, had an unclassified pathogenic effect.
Given the positive impact of PARP inhibitors and prophylactic mastectomy or oophorectomy on survival, reliable classification of variants as pathogenic or nonpathogenic has become imperative.
Nevertheless, in a survey of 3,672 women undergoing BRCA1/BRCA2 testing in 2014-15, 51% with a variant of uncertain significance (VUS) reportedly underwent bilateral prophylactic mastectomy, despite having no familial cancer history.
The large size of BRCA1/2 proteins, their functional complexity, and lack of reliable surrogate activity markers have necessitated a multifactorial VUS approach to BRCA1/2 variant classification.
Up to 80% of BRCA1 and BRCA2 variants are classified as VUSs, but only those classified as pathogenic or probably pathogenic can reliably guide breast and ovarian cancer prevention measures and treatment with PARP inhibitors, which provided the rationale for COVAR study.
Established by the French Unicancer Genetics Group (UGG), the initial results of the COVAR study demonstrated the value of cosegregation analyses of BRCA1/BRCA2 variants in breast and ovarian cancer management.
The power of the COVAR findings in VUS classification was validated by comparison with variant scoring according to American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines.
"The cumulative breast cancer risks until aged 80 years was 72% for BRCA1 and 69% for BRCA2 carriers, while the cumulative ovarian cancer risks were 44% and 17% respectively," said Caputo.
"These findings will help to reduce the health and economic burden associated with potentially unnecessary prophylactic procedures," she told BioWorld Science.
This cosegregation classification method involved a multifactorial model, which combines different associations between VUSs and cancer, including cosegregation data.
Among 653 variants selected in the COVAR study, 101 (15%) distinct variants shared by 1,624 families were classified as pathogenic/likely pathogenic or benign/likely benign by the COVAR study.
Sixty-six of the 101 (65%) variants classified by COVAR would have remained VUSs without cosegregation data.
Of note, among the 34 variants classified as pathogenic by COVAR, 16 remained VUSs or likely pathogenic when following the ACMG/AMP variant classification guidelines.
"Risk classification from cosegregation data is [more reliable than that from conventional analyses] but is also more difficult to obtain, which provided the initial rationale for this national clinical research trial," noted Caputo.
Moreover, while the initiation and organization of cosegregation analyses are laborious, the growing number of available genetic tests results in an increasing number of families sharing a particular variant, thereby increasing the power of such analyses.
Together, these initial COVAR study findings demonstrate that variant cosegregation analyses are a powerful tool for classifying variants in the BRCA1/2 breast-ovarian cancer predisposition genes.
Looking forward, "we will be continuing with the BRCA1 and BRCA2 VUS classification, as many are yet to be classified and we have opened the study to all cancer genes of genetic origin," said Caputo, noting that further information on the COVAR study is available at ClinicalTrials.gov