Large-Scale Sequencing Study Identifies BRIP1 as an Ovarian Cancer Risk Gene

The mining of whole genomes from 656 Icelanders with ovarian cancer and the comparison of these genomes to 41,675 control-genotyped Icelanders has led to the identification of 16 million sequence variants that were tested for their association to ovarian cancer, one of the deadliest forms of cancer among women.

A teal ribbon, which is an awareness ribbon for Ovarian cancer.

From this analysis, the BRCA1-interacting protein C-terminal helicase 1 (BRIP1, also known as BACH1 or FANCJ) has been isolated as an ovarian cancer risk gene. Rare frame-shift mutations in the BRIP1 gene were found to be associated with an eight-fold increase in ovarian cancer risk in the Icelandic population as well as a higher general risk of cancer and a lifespan reduced by 3.6 years. Thorunn Rafnar, Daniel F Gudbjartsson, and Kri Stefnsson of deCODE Genetics in Reykjavic, Iceland and colleagues have reported the result in an advanced online publication in Nature Genetics this week (doi:10.1038/ng.955). The study was in collaboration with Illumina, Inc.

Rationale and Methods

Approximately 5-15% of ovarian cancer tumors have mutations in BRCA1 or BRCA2 and 2% harbor mutations in the MMR genes. However, the known variants explain only a small fraction of the genetic risk for ovarian cancer. The authors described their motivations for the CancerNetwork: “The rationale is that ovarian cancer constitutes one of the big unmet medical needs. Ovarian cancer still has only about a 45% five-year survival because the disease is diagnosed so late. If we can find sequence variants that confer a risk of ovarian cancer that is equivalent to the risk conferred by the BRCA genes in breast cancer, we actually might be able to put together a risk assessment test that could be used to find women in ovarian cancer families that could be saved from the disease by identifying them as much higher-risk individuals. I think that the risk conferred by the gene mutations we found is sufficient to make it clinically useful.” said Kri Stefnsson.

In order to identify new variants, the single-nucleotide polymorphisms (SNPs) of 656 women with ovarian cancer were compared with control SNPs of 41,675 Icelanders. What is key is that deCODE has a nationwide Icelandic genealogical database that allows the creation of genotypes for close relatives of the individuals whose SNPs were identified in this study.

The Results

Nine highly correlated SNPs were identified that were strongly associated with ovarian cancer. The most significant association was within the BRIP1 gene. The protein encoded by the BRIP1 protein is required for homologous recombination-mediated double stranded repair, interacts with BRCA1, and is also necessary for the G2/M cell-cycle checkpoint as well as normal progression from the replication phase of the cell cycle. Mutations in BRIP1 can result in the rare chromosomal instability disorder Fanconi anemia; individuals with Fanconi anemia have an extremely high incidence of cancer. The mutations identified in BRIP1 in this study among the Icelandic population are frame-shift mutations that result in a truncated form of the protein.

Like the BRCA1, BRCA2 and MMR genes, the current study found that the BRIP1 mutations are also associated with a higher risk of other cancer types. The National Icelandic Cancer Registry and genotype information from individuals with cancer (excluding those with ovarian cancer) was analyzed to find that BRIP1 mutations are also associated with pancreatic and rectal cancers. Specifically, the Icelandic frame-shift mutations in BRIP1 increase the risk of developing a cancer, excluding ovarian cancer, by 36%.

Further sequencing and analysis of 144 ovarian cancer and 896 control individuals from Spain revealed that the frame-shift mutations are very rare but are associated with a “greatly increased risk” of ovarian cancer and a “significant risk” of breast cancer.

Based on this published work, it appears that BRIP1 behaves like a classic tumor suppressor gene whereby loss of the wild-type allele is seen in ovarian tumors of heterozygous carriers. The authors suggest that ovarian tumors that have lost both alleles of BRIP1 may be good targets for therapeutic agents (such as PARP inhibitors) that affect the DNA repair pathway.

The Uniqueness of the Icelandic Population for Population Genetic Studies

The authors propose that while mutations in BRIP1 have a low penetrance, they may cause sporadic ovarian cancer cases. The ability to detect these rare mutations is attributed to using the Icelandic population, a founder population where the mutation may reach a frequency that allows its detection, in contrast to more outbred populations. Support for this, as cited by the researchers, is the crucial role that Icelandic populations had in the discovery of the BRCA2 gene.

“This study underscores the important contribution that the Icelandic population can make to the discovery of low frequency sequence variants with large effect.  The potential to do this has been clear since the critical role played by Iceland in the discovery of the BRCA2 gene.  Until now, however, the combination of sequencing technology and analytical techniques were insufficient to unleash the flood of discoveries that we and our collaborators are now making,” said Stefnsson.

CancerNetwork spoke with Stefnsson about the new findings and the utility of using the Icelandic database created by deCODE. “I think the only historical example of something like this is the BRCA2 gene, that was discovered by two groups almost simultaneously: Mark Skolnick’s group in Utah, who subsequently founded Myriad Genetics and Michael Stratton who is now the Head of the Sanger Institute.  Both of these groups were using Icelandic materials and were able to find the gene because in Iceland there is only one mutation in BRCA2 and it is a five base-pair deletion. This five-base deletion has an allelic frequency of 0.4% which means that 0.8% of people in Iceland carry it. In the U.S., Myriad has found 6,500 mutations in the BRCA2 gene, and the combined allelic frequency of these 6,500 mutations is about 0.1%.  You can just imagine how impossible a task it would be to try to show that each one of these 6,500 mutations associate with breast cancer.  So they've called mutations that interfere with the formation of the BRCA2 protein “positive.”  What it basically shows is that the mutations that lead to a truncated protein lead to higher risk for breast cancer. We have shown this unequivocal association of a truncating mutation in BRIP1 with ovarian cancer and we'll most likely describe other truncating mutations in BRIP1 as "positive," so I think that's probably the way that the story will evolve.  Right now we're mapping out these mutations in BRIP1 in other populations; we have samples from America and samples from several European populations,” said Stefnsson.

Broadly, Stefnsson and his team aim to turn their population-based findings into novel tests that will provide better early-detection and treatments for patients. “Our objective is to translate our discoveries rapidly into benefit for patients.  We are committed to working with our collaborators, as we did in this case, to identify the spectrum of mutations occurring in other populations.  This allows us to use the Icelandic resource as a unique discovery cohort, and quickly elucidate the broader utility,”  Stefansson added, saying that there is potential for a BRIP1 diagnostic test to be developed over the next two years.

Stefnsson believes that genetic testing will become as common as an annual PAP smear or PSA test.  “We are encouraging women to have breast exams hoping that we could pick up early cancer, we are encouraging women to have mammography, we are encouraging both men and women to have colonoscopies every five to ten years after age 50, we are encouraging men to have PSA and digital exam of prostate once they become 50 so, as a society, we are leaning on people to pay attention to preventative medicine. The best way to systematically do preventative medicine is to tally people's risk of various diseases.  Who are you when it comes to risk of disease?  Are you a person with higher risk of colon cancer, are you a person with high risk of ovarian cancer? and then use the annual manual medical check up to focus on the regions where people are vulnerable."