Robust Predictor of Breast Cancer Risk

SUMMARY
Approximately 1.5 million women in the United States are at high-risk for developing breast cancer, based on
inheritance of a germline mutation in a gene in the double strand-break (DSB) repair and cyclin-checkpoint
pathways. Many are unaware of their genetic predispositions, because their family history is uninformative or
unknown. Genetic testing is important for identifying mutations in these genes, but in ~80% of cases no
mutation is identified, leading to ambiguous, unsatisfactory results. Identifying women at high risk prior to the
onset of disease is an important challenge for personalized medicine, because disease can be prevented or
treated at the earliest stage when cure is more likely. As more women are seeking genetic testing to identify
their risk of breast cancer, accurate alternatives to sequencing are needed to predict the molecular phenotypic
effects of mutations in genes in breast cancer-predisposing pathways. Risk classification scores based on flow
variant assays (FVAs) are a new technology that can accurately identify women with heterozygous germline
mutations in these pathways. FVAs are rapid, inexpensive and highly reproducible and can be performed on
circulating and cultured human blood cells, thus lending themselves to becoming a Next Generation, non-
sequencing, standalone test. The goal of this STTR project is to develop a simple, rapid and inexpensive
clinical test that will accurately identify those at high risk for breast cancers. Phase I hypothesis: The
standalone FVA test using whole blood samples will identify those at high-risk with 95% accuracy. Specific aim
1. Achieve risk classification score results for 99% of subjects with at least 95% accuracy on 180 subjects from
well-characterized risk groups. Specific aim 2. Achieve risk classification score results for all subjects from Aim
1 with comparable accuracy using an automated analysis protocol and newly created commercial kit. Having
demonstrated the analytical validity in Phase I, MMG will demonstrate clinical utility in Phase II by calculating
and validating 10-year hazard ratios for breast cancer by age decade for 1,800 women followed by up to 20
years by the NCI’s Breast Cancer Family Registry. In addition, MMG will demonstrate the analytical validity of
this test analytical validity and reproducibility of FVA test kits in-house and at collaborating laboratories,
demonstrate the roles of mutations in high and moderate-penetrance DSB repair genes in modifying FVA
traits, and demonstrate the stability of FVA traits over time and whether these are affected by exposure to
chemotherapy. This product will be sold to clinical laboratories in collaboration with a designated good
manufacturing practices facility commercial partner as an FDA approved test. Several factors will drive this
commercialization into the $1B market cancer risk assessment market: 1. low entry and performance costs, 2.
greater accuracy than sequencing, 3. application to understanding risks for ovarian, pancreatic and prostate
cancers, and 4. companion diagnostic for the new class of targeted chemotherapy, called “PARP inhibitors.”
The creation of simplified, commercial FVA kits will be a game changer for assessing cancer risks.PROJECT NARRATIVE
Robust risk probability scores based on FVA analysis to identify those at increased risk for breast cancer will
be a Next Generation high-throughput improvement in sensitivity and specificity, lower cost and shortened time
to reporting over the current standard of cancer gene panel sequencing. Even when a mutation cannot be
found by sequencing, individuals with defects in the DSB repair pathway will be faithfully identified. Direct
testing of the molecular phenotypes associated with genetic defects – initiation of repair of double strand
breaks in response to treatment with radiomimetic agents will circumvent the need to annotate the very
frequent variants of uncertainly significance in the many genes in this pathway. The robust assays and risk
scores are meant to benefit at-risk patients and their health care providers, but these tools will be of
considerable use for preclinical and clinical researchers who may want to investigate the effects of exposures
on increasing the risks for those with DSB repair deficiencies.