NEW YORK – An international team led by investigators from Oslo University Hospital in Norway and the Normandy Centre for Genomic and Personalized Medicine in France has demonstrated that multigene panel testing can pick up informative risk variants in a significant proportion of familial cancer cases.
The researchers used panel sequencing to profile 44 cancer-related genes in 191 individuals with familial breast cancer, colorectal cancer, or other forms of early-onset cancer, focusing on cases in which pathogenic variants in highly penetrant cancer risk genes had not been detected. Their findings, published online today in Scientific Reports, uncovered pathogenic or likely pathogenic variants in nearly 5 percent of cases and variants of uncertain significance in dozens more.
"Our study contributes to understanding and interpreting variants in moderate- or low-penetrance genes which are not routinely tested in the clinical genetic settings and may have a direct impact on providing an appropriate genetic counseling and clinical management for individuals and their relatives who carry these variants," corresponding and co-lead author Mev Dominguez-Valentin, a postdoctoral researcher in tumor biology at Oslo University Hospital, and her colleagues wrote.
Using the TruSeq amplicon assay and Illumina MiSeq instrument, the researchers sequenced 44 cancer-related genes in peripheral blood samples from 138 individuals with familial breast cancer, 34 familial colorectal cancer cases, and 19 other cases of early-onset cancer, drawn from the Norwegian Radium Hospital's Hereditary Cancer Biobank or the University of Manchester's genomic medicine department. The patients included in the study did not have known variants in high-profile risk genes related to their cancer type, they noted.
"Because multiple cancer gene panel testing is rapidly replacing sequential single-gene testing," the authors explained, "we need to know how to improve in the way we interpret the findings from panel testing patients in cancer kindreds who have been previously tested for BRCA1/2, PTEN, TP53, and [DNA mismatch repair] genes without detection of pathogenic variants."
When the team sifted through these sequences, classifying variants in the context of guidelines established by the American College of Medical Genetics and Genomics, it tracked down nine pathogenic or likely pathogenic variants in the familial patients, including two pathogenic variants falling in high-penetrance genes such as BRCA2 and MSH6.
The search also led to a heterozygous variant in MUTYH, which is implicated in recessive cancer risk, the researchers reported, and perhaps more surprisingly, half a dozen pathogenic variants turned up in ATM and other genes typically thought of as being moderately penetrant for cancer risk.
"Our study confirms the presence of pathogenic or likely pathogenic variants in genes that are not routinely tested in the context of the above-mentioned clinical phenotypes," the authors reported, noting that "more than half of the pathogenic germline variants were found in the moderately penetrant ATM and CHEK2 genes, where only truncating variants from these genes are recommended to be reported in clinical genetic testing practice."
Along with initial efforts to look at how pathogenic or likely pathogenic variants found by panel sequencing lined up with clinical features in the familial cancer cases, the team went on to delve into the potential functions of 87 variants of unknown significance identified in the study with a combination of in silico splicing predictions, minigene splicing assay experiments, and other approaches.
In an analysis of 11 variants of uncertain significance, for example, the investigators uncovered four variants influencing the splicing of genes such as ATM and BUB1.
"There is a need to understand and quantify the cancer risk of pathogenic and currently uncertain variants found in moderate- or low-penetrance genes," the authors wrote, noting that "there is still a high number of novel variants with an unknown significance of pathogenicity identified in cancer patients with family history awaiting classification."