Background
BRCA
phenocopies are individuals with the same phenotype (i.e. cancer consistent with Hereditary Breast and Ovarian Cancer syndrome = HBOC) as their affected relatives, but not the same genotype as assessed by blood germline testing (i.e. they do not carry a germline
BRCA1
or
BRCA2
mutation). There is some evidence of increased risk for HBOC-related cancers in relatives of germline variant carriers even though they themselves test negative for the familial variant (
BRCA
non-carriers). At this time,
BRCA
phenocopies are recommended to undergo the same cancer surveillance as individuals in the general population. This raises the question of whether the increased cancer risk in
BRCA
non-carriers is due to alterations (germline, somatic or epigenetic) in other cancer-associated genes which were not analyzed during
BRCA
analysis.
Methods
To assess the nature and potential clinical significance of somatic variants in
BRCA
phenocopy tumors, DNA from
BRCA
non-carrier tumor tissue was analyzed using next generation sequencing of 572 cancer genes. Tumor diagnoses of the 11 subjects included breast, ovarian, endometrial and primary peritoneal carcinoma. Variants were called using FreeBayes genetic variant detector. Variants were annotated for effect on protein sequence, predicted function, and frequency in different populations from the 1000 genomes project, and presence in variant databases COSMIC and ClinVar using Annovar.
Results
None of the familial
BRCA1/2
mutations were found in the tumor samples tested. The most frequently occurring somatic gene variants were
ROS1
(6/11 cases) and
NUP98
(5/11 cases).
BRCA2
somatic variants were found in 2/6
BRCA1
phenocopies, but 0/5
BRCA2
phenocopies. Variants of uncertain significance were found in other DNA repair genes (
ERCC1, ERCC3, ERCC4, FANCD2, PALB2
), one mismatch repair gene (
PMS2
), a DNA demethylation enzyme (
TET2
), and two histone modifiers (
EZH2, SUZ12
).
Conclusions
Although limited by a small sample size, these results support a role of selected somatic variants and epigenetic mechanisms in the development of tumors in
BRCA
phenocopies.