Pitfalls in genetic testing: a case of a SNP in primer‐annealing region leading to allele dropout in BRCA1

BACKGROUND: Hereditary breast and ovarian cancer is characterized by mutations in BRCA1 or BRCA2 genes and PCR‐based screening techniques, such as capillary sequencing and next‐generation sequencing (NGS), are considered gold standard methods for detection of pathogenic mutations in these genes. Single‐nucleotide polymorphisms (SNPs) constitute a vast source of variation in the human genome and represent a risk for misdiagnosis in genetic testing, since the presence of a SNP in primer‐annealing sites may cause false negative results due to allele dropout. However, few reports are available and the frequency of this phenomenon in diagnostic assays remains unknown. METHODS AND RESULTS: In this article, we investigated the causes of a false negative capillary sequencing result in BRCA1 involving a mother‐daughter dyad. Using several molecular strategies, including different DNA polymerases, primer redesign, allele‐specific PCR and NGS, we established that the initial misdiagnosis was caused by a SNP located in the primer‐annealing region, leading to allele dropout of the mutated allele. CONCLUSION: Assuming that this problem can also occur in any PCR‐based method that are widely used in diagnostic settings, the clinical report presented here draws attention for one of the limitations of genetic testing in general, for which medical and laboratory communities need to be aware.