Abstract P039: Framework for genomic cancer risk assessment dissemination and implementation in Latin America: The GRACIAS (genetic risk assessment for cancer implementation and sustainment) study

Introduction: Lack of public insurance coverage for genetic testing and a limited trained genomic cancer risk assessment (GCRA) workforce are barriers to cancer screening and prevention and to understanding the genetic epidemiology of cancer in low/middle income countries (LMIC) in Latin America. Methods: We implemented an intervention that included professional education for clinicians in Mexico, Peru and Colombia, support from a community of practice and a federated consortium of collaborators, a versatile research registry with a dual purpose (research and clinical care) centralized relational database and pedigree drawing program (web-accessible), and economical NGS multigene panel tests (MGPT). We report here the outcomes of GCRA for 4181 probands (3170 breast, 301 ovarian, 965 other cancer, and 262 unaffected). Results: With a mean age of 45.2 y.o. (39.9 y.o. at breast cancer dx for carriers), a pathogenic variant (PV) was detected in 605 (14.5%) of 2,710 probands (BRCA testing only for 1387, MGPT for 1323): BRCA1 (n=250); BRCA2 (129); CHEK2 (24); PALB2 (20); ATM (14); TP53 (14); PTEN (6); CDH1 (5); MMR genes (62); RAD51C (6); and BRIP1 (3). We have documented growing reach (proportion of those eligible that access GCRA), increasing cascade testing (family member(s) tested (n=541) for 192/470 [40%] probands with a PV), and with median 2.2 years follow up, 209 risk reduction surgeries were performed. Summary: Remarkably, despite systemic limitations, integration of a skilled multidisciplinary team with access to genetic assays and practice support tools, community, and hospital outreach increased GCRA reach, and the expansion of cascade testing and performance of risk-appropriate surgeries reflect maturing prevention programs. Sustainment of progress requires increased multilevel efforts and establishment of GCRA as a supported standard of care, so the opportunity for prevention is not missed for vulnerable and underserved high-risk patients and families.

Citation Format: Jeffrey N. Weitzel, Julio Abugattas, Cynthia Villarreal-Garza, Adrian Daneri Navarro, Alicia Cock-Rada, Yenni Rodriguez, Pamela Mora-Alferez, Dione Aguilar, Azucena del Toro-Valero, Francisco Gutierrez-Delgado, Ana Ferrigno, Josef Herzog, Danielle Castillo, Gubidxa Gutierrez Seymour, Bita Nehoray, Kathleen R. Blazer, Maria E. Fernandez, Yanin Chavarri Guerra. Framework for genomic cancer risk assessment dissemination and implementation in Latin America: The GRACIAS (genetic risk assessment for cancer implementation and sustainment) study. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P039.

Evaluation of Lynch syndrome risk models in a multicenter diverse population

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Background: Lynch syndrome (LS) is the most common cause of hereditary colorectal cancer (CRC) with an increased CRC lifetime risk of 70-80%. LS affects 1:250 individuals and is caused by pathogenic variants in the mismatch repair (MMR) genes. Statistical prediction models such as MMRpro and PREMM5 are widely used to identify LS carriers. However, these models are trained and validated in mostly white populations, and there remains a gap in understanding their performance in Hispanic populations. The purpose of this study was to evaluate the performance of MMRpro and PREMM5 on a large Hispanic cohort from the Clinical Cancer Genomics Community Research Network (CCGCRN). Methods: We validated MMRpro and PREMM5 on 3,490 CCGCRN families, of which 1,122 are Hispanic and 2,062 Non-Hispanic. The two models were evaluated for discrimination using the C-statistic, calibration using the observed to expected ratio (O/E), and overall performance using the root Brier score and negative and positive predictive value (NPV/PPV) at the 5% carrier probability threshold. Evaluations were stratified by ethnicity, and 95% confidence intervals were obtained via bootstrapping for all measures. Results: The C-statistic is 0.90 for both MMRpro (95% CI: 0.88, 0.92) and PREMM5 (95% CI: 0.87, 0.92). When stratified by ethnicity, the C-statistics are 0.96 (95% CI: 0.94, 0.97) and 0.86 (95% CI: 0.83, 0.89) for Hispanics and Non-Hispanics, respectively, in MMRpro, and 0.96 (95% CI: 0.94, 0.97) and 0.84 (95% CI: 0.79, 0.88) in PREMM5. Both models underpredict mutation probabilities, with O/E ratios ranging from 1.79 to 1.96. At a 5% threshold, variations in PPV between Hispanics and Non-Hispanics are observed in both models: 0.72 (95% CI: 0.63, 0.80) and 0.43 (95% CI: 0.37, 0.50) in Hispanic and Non-Hispanic groups in MMRpro; 0.50 (95% CI: 0.43, 0.57) and 0.25 (95% CI: 0.20, 0.30) in PREMM5. We observe less variation and higher values in NPVs in both models. Conclusions: Overall, MMRpro and PREMM5 perform well in this cohort in predicting the probability of having a pathogenic variant in an MMR gene, with modest underprediction. While these results offer reassurance for the clinical use of MMRpro and PREMM5 in Hispanic populations, further validation studies in underrepresented racial and ethnic populations are crucial.

Abstract PS8-15: The spectrum of germline susceptibility gene variants in Mexican patients with breast cancer (BC): A Prospective Multicenter study

Background: BRCA mutations are responsible for a significant proportion of hereditary breast and ovarian cancers. However, other cancer susceptibility genes are also associated with an increased risk of developing breast cancer (BC). In Mexico, approximately 15% of patients with BC have been identified with BRCA mutations. Despite our growing understanding of BRCA mutations, the contribution and characterization of non-BRCA mutations in Mexican patients with a BC diagnosis remains unknown. We aimed to investigate the spectrum of BC-associated mutations among Mexican patients with BC referred for genetic cancer risk assessment (GCRA) in the multinational Clinical Cancer Genomics Community Research Network (CCGCRN). Methods: Mexican patients with a primary BC who were enrolled in the IRB-approved CCGCRN registry protocol and underwent genetic counseling and multigene panel testing (MGPT) were included. Pathogenic and likely pathogenic variants (PV) in genes associated with increased BC risk were used for analyses. Clinical and demographic characteristics of BRCA and non-BRCA carriers were compared. Results: From December 2012 to February 2020, 725 Mexican patients with BC who had MGPT results with a median age (years) of 41 (range 25-76) were included. 142 (19.6%) patients carried a BC-associated PV. Of these, 98 (69.0%) carried BRCA PVs: 58 in BRCA1 (41.5%) and 40 in BRCA2 (26.7%). PVs in other BC-associated genes (n = 42) accounted for 29.5% of all observed PVs and were distributed as follows: PALB2 (n = 13), CHEK2 (n = 11), RAD51C (n = 6), ATM (n = 3), PTEN (n = 3), TP53 (n = 3), BRIP1 (n = 2), and CDH1(n = 1). Other actionable genes represented 3.5% of all PVs (PMS2 [n = 3]; MSH6 [n = 1]; MSH2 [n = 1]). Suspected founder mutations in Latinas, PALB2 c.2167_2168delAT (n = 5) and CHEK2 c.707T>C (n = 9), represented 33.3% (n = 14/42) of the detected non-BRCA PVs. Mean age at first cancer diagnosis (years) for BRCA and non-BRCA carriers was: 37 (range 26-58) and 42 (range 25-76) (p<0.05), respectively. Among carriers, those with BRCA PVs had a significantly greater proportion of triple-negative (TN) tumors compared to non-BRCA PVs (45.2% vs 9.5%; p<0.05). Conclusion: A significant proportion of Mexican women carried a BC-associated mutation and a third were non-BRCA PVs. Among non-BRCA PVs, recurrent PALB2 and CHEK2, which had previously been characterized in BRCA-negative US Latinas with BC, were the most common and confirms their presence and clinical impact in Mexico. BRCA carriers were younger and more commonly had the TN molecular subtype.

Citation Format: Yanin Chavarri-Guerra, Cynthia Villarreal-Garza, Gubidxa Gutierrez Seymour, Dione Aguilar y Mendez, Jazmin Arteaga-Vazquez, Servando Cardona-Huerta, Adrian Daneri-Navarro, Azucena del Toro Valero, Alejandro Mohar-Betancourt, Andrés Rodríguez-Faure, Jose Luis Rodriguez-Olivares, Gregorio Quintero Beulo, Danielle Castillo, Kai Yang, Joseph Herzog, Rosa Mejia, Sharon Sand, Jeffrey N Weitzel. The spectrum of germline susceptibility gene variants in Mexican patients with breast cancer (BC): A Prospective Multicenter study [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-15.