A Polygenic Risk Score for Breast Cancer in US Latinas and Latin American Women

Background

More than 180 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified; these SNPs can be combined into polygenic risk scores (PRS) to predict breast cancer risk. Because most SNPs were identified in predominantly European populations, little is known about the performance of PRS in non-Europeans. We tested the performance of a 180-SNP PRS in Latinas, a large ethnic group with variable levels of Indigenous American, European, and African ancestry.

Methods

We conducted a pooled case-control analysis of US Latinas and Latin American women (4658 cases and 7622 controls). We constructed a 180-SNP PRS consisting of SNPs associated with breast cancer risk (P < 5 × 10^–8). We evaluated the association between the PRS and breast cancer risk using multivariable logistic regression, and assessed discrimination using an area under the receiver operating characteristic curve. We also assessed PRS performance across quartiles of Indigenous American genetic ancestry. All statistical tests were two-sided.

Results

Of 180 SNPs tested, 142 showed directionally consistent associations compared with European populations, and 39 were nominally statistically significant (P < .05). The PRS was associated with breast cancer risk, with an odds ratio per SD increment of 1.58 (95% confidence interval [CI = 1.52 to 1.64) and an area under the receiver operating characteristic curve of 0.63 (95% CI = 0.62 to 0.64). The discrimination of the PRS was similar between the top and bottom quartiles of Indigenous American ancestry.

Conclusions

The 180-SNP PRS predicts breast cancer risk in Latinas, with similar performance as reported for Europeans. The performance of the PRS did not vary substantially according to Indigenous American ancestry.

Abstract IA13: Advancing gastric cancer precision medicine through minority patient derived modeling

Gastric cancer is a leading cause of cancer mortality in Latinos, who are two times more likely to die of gastric cancer when compared to non-Latino Whites. Gastric cancer outcomes in this minority are poor as most tumors are detected in the metastatic setting, where five-year survival is less than 5%. Despite such a high mortality burden in Latinos and other minority populations, there are only three molecularly-guided therapies approved by the Food and Drug Administration to treat gastric cancer. To advance precision medicine in minority groups, the NCI Center to Reduce Cancer Health Disparities funded our University of California Minority Patient-Derived Xenograft (PDX) Development and Trial Center (UCaMP), which is currently creating and characterizing PDXs and patient-derived organoids from minority patients including those with gastric cancer. In this presentation, we will present an overview of recent advances in gastric cancer precision modeling using patient-derived organoids and xenografts from Latino patients. We will summarize the most promising druggable genes and pathways in gastric tumors and will present initial findings on the development of promising combinations using PIK3CA inhibitors.

Citation Format: Hongyong Zhang, Nicole Coggins, Paul Lott, Ana Estrada, Guadalupe Polanco, Alexa Morales, Sienna Rocha, Amanda Kirane, Shiro Urayama, Javier Torres, Mabel Bohorquez, Magdalena Echeverry, UCaMP Consortium, Luis G. Carvajal-Carmona. Advancing gastric cancer precision medicine through minority patient derived modeling [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr IA13.

Haplotype analysis of the internationally distributed BRCA1 c.3331_3334delCAAG founder mutation reveals a common ancestral origin in Iberia

Background

The BRCA1 c.3331_3334delCAAG founder mutation has been reported in hereditary breast and ovarian cancer families from multiple Hispanic groups. We aimed to evaluate BRCA1 c.3331_3334delCAAG haplotype diversity in cases of European, African, and Latin American ancestry.

Methods

BC mutation carrier cases from Colombia (n = 32), Spain (n = 13), Portugal (n = 2), Chile (n = 10), Africa (n = 1), and Brazil (n = 2) were genotyped with the genome-wide single nucleotide polymorphism (SNP) arrays to evaluate haplotype diversity around BRCA1 c.3331_3334delCAAG. Additional Portuguese (n = 13) and Brazilian (n = 18) BC mutation carriers were genotyped for 15 informative SNPs surrounding BRCA1. Data were phased using SHAPEIT2, and identical by descent regions were determined using BEAGLE and GERMLINE. DMLE+ was used to date the mutation in Colombia and Iberia.

Results

The haplotype reconstruction revealed a shared 264.4-kb region among carriers from all six countries. The estimated mutation age was ~ 100 generations in Iberia and that it was introduced to South America early during the European colonization period.

Conclusions

Our results suggest that this mutation originated in Iberia and later introduced to Colombia and South America at the time of Spanish colonization during the early 1500s. We also found that the Colombian mutation carriers had higher European ancestry, at the BRCA1 gene harboring chromosome 17, than controls, which further supported the European origin of the mutation. Understanding founder mutations in diverse populations has implications in implementing cost-effective, ancestry-informed screening.

Abstract PR15: Intratumoral heterogeneity in Latino gastric adenocarcinomas

The goal of this study was to examine gastric (stomach) cancer mutational intratumoral heterogeneity (ITH) in Latinos using multiregion sequencing (MSEQ). Gastric cancer is the 2nd leading cause of cancer-related death worldwide. It is diagnosed in 25,000 Americans each year, with Latinos twice as likely to succumb as Whites. Treatment is currently limited to a few molecularly guided therapies, but TCGA data show that 70% of GC patients have a mutation in a gene targetable with existing drugs. Significant ITH has been identified in a variety of tumor types to date, although a GC study has yet to be published. ITH is an important consideration for personalized therapy. Driver gene mutations are frequently found to be nonclonal, a crucial factor when assessing effective druggability. In this study, two to five tumor biopsies and adjacent normal tissue were obtained from 33 Latino patients, totaling 120 tumor (T) biopsies and 33 normal (N) samples. DNA was extracted from the tissues and the coding regions of 762 cancer-related genes were sequenced using Agilent target enrichment and Illumina sequencing. For each biopsy, estimates were made of sample purity and ploidy, somatic mutations were called using joint analysis of all T and N sequence data for each patient, cancer cell fraction (CCF) was estimated for each mutation, and copy number variation (CNV) was called across the genome. Somatic mutations and copy number changes were analyzed for clonality in each patient. We found a high degree of heterogeneity, both intratumoral and interpatient, with the fraction of functional somatic mutations that are clonal ranging from 0 to 68%, the fraction private to one biopsy ranging from 32% to 100%, and the fraction shared between multiple but not all biopsies ranging from 0 to 42%. For 10 of the 33 samples there was at least one gene, containing a clonal functional mutation, for which there is an FDA-approved targeted therapy. In summary, our study is the first to assess ITH in GC. Our results are important to understand the genetic diversity and clonal architecture of these tumors and to improve molecular diagnostics.

This abstract is also being presented as Poster D107.

Citation Format: Ted Toal, Guadalupe P. Echeverry, Ruta Sahasrabudhe, Mabel Bohorquez, Javier Torres, Shiro Urayama, Amanda Kirane, Magdalena Echeverry, Luis G. Carvajal Carmona. Intratumoral heterogeneity in Latino gastric adenocarcinomas [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr PR15.

Abstract C030: Gastric tumors from Latino patients show extensive intratumor heterogeneity

Gastric cancer (GC) is the 2nd leading cause of cancer-related death worldwide, with a five-year survival rate lower than 30%. GC is diagnosed in 25,000 Americans each year, with Latinos twice as likely to succumb compared to non-Hispanic whites. Treatment is currently limited to only two molecularly guided therapies. The Cancer Genome Atlas (TCGA) data show that 70% of GC patients have a mutation in a gene targetable with existing drugs. Significant spatial mutational intratumoral heterogeneity (ITH) has been identified in a variety of tumor types to date, although a GC ITH study has yet to be investigated. ITH is an important consideration for personalized therapy. Driver gene mutations are frequently found to be nonclonal, a crucial factor when assessing effective druggability. The goal of the present study was to examine GC ITH in Latino GC patients using targeted multiregional sequencing (MSEQ). Two to five biopsies from different tumor regions and adjacent normal tissue were obtained from 34 GC patients; DNA was extracted from the tumor and the normal tissues and the coding regions of 783 cancer genes were sequenced using Agilent enrichment and Illumina sequencing. Somatic mutations were called in each tumor sample, using joint analysis of all samples for each patient. Tumor cell fractions were estimated for each mutation in each sample, and phylogenetic trees were made for visualize each patient's somatic mutational patterns. We found a high degree of ITH, both intratumoral and interpatient, with the fraction of functional somatic mutations that are clonal ranging from 0 to 52%, the fraction private to one tumor sample ranging from 48% to 94%, and the fraction shared between multiple but not all samples ranging from 0 to 21%. There was at least one known drug interaction with a gene containing a clonal functional mutation for 11 of the 16 samples, and in 6 samples there were two or more known drug interactions. Our study is the first one to assess ITH in GC, and our results are important to understand the clonal architecture of these GCs and to improve molecular diagnostics.

Citation Format: Ted Toal, Guadalupe M. Polanco-Echevery, Ruta Sahasrabudhe, Ana Estrada, Mabel Bohorquez, Magdalena Echeverry, Javier Torres, Luis G. Carvajal-Carmona. Gastric tumors from Latino patients show extensive intratumor heterogeneity [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C030.

Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer Is Associated with Indigenous American Ancestry in Latin American Women

Women of Latin American origin in the United States are more likely to be diagnosed with advanced breast cancer and have a higher risk of mortality than non-Hispanic White women. Studies in U.S. Latinas and Latin American women have reported a high incidence of HER2 positive (+) tumors; however, the factors contributing to this observation are unknown. Genome-wide genotype data for 1,312 patients from the Peruvian Genetics and Genomics of Breast Cancer Study (PEGEN-BC) were used to estimate genetic ancestry. We tested the association between HER2 status and genetic ancestry using logistic and multinomial logistic regression models. Findings were replicated in 616 samples from Mexico and Colombia. Average Indigenous American (IA) ancestry differed by subtype. In multivariate models, the odds of having an HER2+ tumor increased by a factor of 1.20 with every 10% increase in IA ancestry proportion (95% CI, 1.07-1.35; P = 0.001). The association between HER2 status and IA ancestry was independently replicated in samples from Mexico and Colombia. Results suggest that the high prevalence of HER2+ tumors in Latinas could be due in part to the presence of population-specific genetic variant(s) affecting HER2 expression in breast cancer. SIGNIFICANCE: The positive association between Indigenous American genetic ancestry and HER2+ breast cancer suggests that the high incidence of HER2+ subtypes in Latinas might be due to population and subtype-specific genetic risk variants.

Melanoma: clinical-pathological and molecular analysis in patients of Ibague city, Colombia

This study aimed to establish the clinicopathological characteristics of patients with melanoma and its association with BRAF gene mutations. The pathology reports and paraffin-embedded tumor samples from 47 women and 30 men with melanoma, with an average age of diagnosis of 60 years, were reviewed at the Hospital Federico Lleras Acosta of Ibague, between 2010 and 2016. The presence of V600E mutation at the exon 15 of BRAF gene, was analyzed in these tumoral samples by Sanger sequencing and visual inspection of the electropherograms. We also studied the clinicopathological variables with X2, t-Student and the Kaplan Meier index. Most of the lesions were located in the lower limbs (46.6%). The most frequent subtype was Acral Lentiginous Melanoma (41.8%). Most lesions were of poor prognosis: Breslow depth greater than 4.1 mm (52.7%), ulceration (61.4%) and medium or high mitotic rate (> 30 %). The V600E mutation was identified in five patients with large, deep and ulcerated tumors, four of them had less than four years of survival. In conclusion, there was a higher frequency of melanoma in women, V600E BRAF mutation was present in patients with advanced disease (high Breslow index) and, the probability of five-year survival was less than 40%.

BRAF and TERT mutations in papillary thyroid cancer patients of Latino ancestry

Papillary thyroid cancer (PTC) is the second most commonly diagnosed malignancy in U.S. Latinas and in Colombian women. Studies in non-Latinos indicate that BRAF and TERT mutations are PTC prognostic markers. This study aimed to determine the prevalence and clinical associations of BRAF and TERT mutations in PTC Latino patients from Colombia. We analyzed mutations of BRAF (V600E) and TERT promoter (C228T, C250T) in tumor DNA from 141 patients (75 with classical variant PTC, CVPTC; 66 with follicular variant PTC, FVPTC) recruited through a multi-center study. Associations between mutations and clinical variables were evaluated with Fisher exact tests. Survival was evaluated with Kaplan-Meier plots. Double-mutant tumors (BRAF+/TERT+, n = 14 patients) were more common in CVPTC (P = 0.02). Relative to patients without mutations (n = 48), double mutations were more common in patients with large tumors (P = 0.03), lymph node metastasis (P = 0.01), extra-thyroid extension (P = 0.03), and advanced stage (P = 6.0 × 10-5). In older patients, TERT mutations were more frequent (mean age 51 years vs 45 years for wild type TERT, P = 0.04) and survival was lower (HR = 1.20; P = 0.017); however, given the small sample size, the decrease in survival was not statically significant between genotypes. Comparisons with published data in US whites revealed that Colombian patients had a higher prevalence of severe pathological features and of double-mutant tumors (10 vs 6%, P = 0.001). Mutations in both oncogenes show prognostic associations in Latinos from Colombia. Our study is important to advance Latino PTC precision medicine and replicates previous prognostic associations between BRAF and TERT in this population.

The Role of Colorectal Cancer Risk Chromosomal Regions in Colombian Admixed Populations

Background: Several colorectal cancer susceptibility disease loci have been discovered through genome-wide association studies. However most of the variants were originally identified in Caucasian populations. Aim: To analyze the role of 20 known risk SNPs for colorectal cancer. Methods: Given that linkage disequilibrium is highly dependent on population demographic history and admixture background, we studied 20 risk SNPs in a pooled sample of 955 cases and 968 controls from admixed populations in Colombia. Results: The replication was reached for 11 out of 20 nominally associated SNPs; with allelic odds ratios (OR) ranging from 1.14 to 1.41, indicating a minimal increase in risk individually, however coinheritance of those SNPs resulted in an overall OR = 5.4 (95% CI: 3.052-9.731, P = 1.16E−08). Most of the variants followed a recessive model consistent with significant homozygous ORs distributed between 1.3 and 1.65. Among the most associated markers we found: rs4939827 (18q21.1, P = 7.35E−6), rs10411210 (19q13.11, P = 0.001), rs10795668 (10p14, P = 0.0024), rs4444235 (14q.2.2, P = 0.005), rs961253 (20p12.3, P = 0.006), rs16892766 (8q23.3, P = 0.011) and rs1050547 (8q24.21, P = 0.017). Conclusion: Our findings in Colombia have addressed the admixture and how this has influenced the risk associated with the known/unknown colorectal cancer regions, providing a comprehensive vision about several CRC-susceptibility SNPs identified in European populations, which also resulted, associated with an increased risk to CRC in the Colombian population, even though frequency and genetic structure differences accounted for those nonreplicated SNPs.

Abstract 5233: Associations between somatic mutations and clinical manifestations in South American Hispanic patients with papillary thyroid cancer

Papillary thyroid cancer (PTC) is the second most commonly diagnosed tumor in U.S. Hispanic women, representing ~9% of all incident female cancer cases in this minority. In Colombia, a country with a predominantly Hispanic population, PTC is the fifth most commonly diagnosed cancer in women. Several studies, predominantly in non-Hispanic whites (NHW), have associated the RAS-RAF gene and TERT promoter mutations with severe PTC clinical manifestations. We investigated associations between mutations in these genes and clinicopathologic data (age, gender, histologic type, tumor features and AJCC stage) in 143 Colombian cases (76 with classical variant PTC, CVPTC and 65 with follicular variant PTC, FVPTC). DNA from archival samples was isolated using standard methods and mutation status at hotspots in BRAF (V600E), NRAS (Q61R, Q61K), HRAS (Q61R, Q61K), and TERT (C228T, C250T) were assessed using Sanger sequencing. Clinicopathologic data between mutation carriers and noncarriers and with data from NHWs in the TCGA were carried out with t-tests and odds ratios (OR). BRAF V600E was detected in 59% of all cases, a rate that is similar to NHW (64%; P=0.29). When we stratified the data by subtype, we found a similar V600E frequency in CVPTC in Colombian cases than in NHWs (67% vs 68%; P=0.87) but a borderline significantly higher frequency of the mutation in FVPTC (49% vs 29%; P=0.06). TERT promoter mutations were found in 17% of all cases, a rate that is significantly higher than in NHW (10%, p= 0.03). 5% of cases had mutations in HRAS/NRAS, which is lower than in NHW (11%; P=0.04). Given the low RAS gene mutation frequency, comparisons with clinical data were carried out only with BRAF and TERT data. BRAF/TERT mutation-positive samples (BRAF+/TERT+, n=18) were compared to mutation-negative cases for either or both genes (n=123). BRAF+/TERT+ tumors were more common in CVPTC than in FVPTC (17% vs. 7%; OR=4.1; P=0.02), and in cases with tumors &gt;2cm (20% vs. 6%; OR=4.0; P=0.03), with capsular invasion (18% vs. 5%; OR=5.6; P=0.02), with lymph node metastasis (19% vs. 6%; OR=7.1; P=0.006), with extrathyroidal extension (23% vs. 6%; OR=4.8; P=0.03), and advanced AJCC stage (29% vs. 4%; OR= 8.7; P=5.00 x 10-4). PTC is considered a relatively benign malignancy with good prognosis and survival in the U.S., but we found a high fraction of Colombian cases in advanced AJCC stage (32%) and with distant metastasis (6%), suggesting that most cases were not the result of incidental findings, a common phenomenon in developed countries where most PTCs are likely the result of overdiagnosis. In summary, we present the first report of BRAF/RAS/TERT mutations in Hispanics with PTC from Latin America, demonstrate the utility of these mutations to identify cases with severe disease, and generate a body of data that will be important for the establishment of PTC precision medicine in the region.

Citation Format: Ana P. Estrada-Florez, Mabel E. Bohorquez, Carlos S. Duque, Jorge Donado, Gilbert Mateus, Fernando Bolaños, Alejandro Velez, Erika Estrada, Guadalupe Polanco-Echeverry, Ruta Sahasrabudhe, Elisha Garcia, Magdalena Echeverry, Luis G. Carvajal-Carmona. Associations between somatic mutations and clinical manifestations in South American Hispanic patients with papillary thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5233.

Abstract LB-158: Germline mutations in PALB2, BRCA1 and RAD51C observed in gastric cancer cases

Gastric cancer (GC) is the third common cause of cancer related deaths worldwide and its risk is partially mediated by inherited factors. However, the majority of GC heritability remains to be discovered. The goal of this study was to identify novel GC genes. To identify novel GC genes, we undertook a multi-staged approach of whole exome sequencing (WES), followed by targeted sequencing and genotyping in germline DNA samples from hereditary diffuse GC (HDGC) and isolated GC cases recruited in Europe and Latin America. We also performed WES in 4 available tumor samples to analyze loss of heterozygosity and somatic mutation signature. Our study identified eleven cases with mutations in homologous recombination repair (HR) genes, including seven with PALB2 mutations, three with BRCA1 mutations and one with a RAD51C mutation. Out of 361 total unrelated GC cases analyzed, 6.45% of the HDGC cases (2 out of 31) and 2.7% (9 out of 330) of isolated/non-HDGC cases had mutations in PALB2, BRCA1 or RAD51C. Most of these mutations are known as pathogenic in other cancer types and three were shared by multiple Hispanic and European cases. None of these mutations were present in 1,170 population-matched controls (P=5.75x10-7). Tumor samples from four mutation carriers exhibited mutational signature indicative of defects in HR pathway. Our results suggest that mutations in HR genes are likely involved in GC susceptibility. Our findings have potential clinical implications as these cases and their families could benefit from risk reducing surveillance and possibly benefit from platinum or PARP inhibitor based therapies.

Citation Format: Ruta Sahasrabudhe, Paul Lott, Mabel Bohorquez, Ted Toal, Ana Estrada, John Suarez, Alejandro Brea-Fernández, Jose Cameselle-Teijeiro, Carla Pinto, Irma Ramos, Alejandra Mantilla, Rodrigo Prieto, Alejandro Corvalan, Enrique Norero, Carolina Alvarez, Teresa Tapia, Pilar Carvallo, Luz Gonzalez, Alicia Cock-Rada, Angela Solano, Florencia Neffa, Adriana Della Valle, Chris Yau, Gabriela Soares, Alexander Borowsky, Xiao-You Han, Li-JI He, Phillip Taylor, Alisa Goldstein, Nan Hu, Javier Torres, Magdalena Echeverry, Clara Ruiz-Ponte, Manuel Teixeira, Luis G. Carvajal-Carmona. Germline mutations in PALB2, BRCA1 and RAD51C observed in gastric cancer cases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-158. doi:10.1158/1538-7445.AM2017-LB-158

Germline Mutations in PALB2, BRCA1, and RAD51C, Which Regulate DNA Recombination Repair, in Patients With Gastric Cancer

Up to 10% of cases of gastric cancer are familial, but so far, only mutations in CDH1 have been associated with gastric cancer risk. To identify genetic variants that affect risk for gastric cancer, we collected blood samples from 28 patients with hereditary diffuse gastric cancer (HDGC) not associated with mutations in CDH1 and performed whole-exome sequence analysis. We then analyzed sequences of candidate genes in 333 independent HDGC and non-HDGC cases. We identified 11 cases with mutations in PALB2, BRCA1, or RAD51C genes, which regulate homologous DNA recombination. We found these mutations in 2 of 31 patients with HDGC (6.5%) and 9 of 331 patients with sporadic gastric cancer (2.8%). Most of these mutations had been previously associated with other types of tumors and partially co-segregated with gastric cancer in our study. Tumors that developed in patients with these mutations had a mutation signature associated with somatic homologous recombination deficiency. Our findings indicate that defects in homologous recombination increase risk for gastric cancer.

Clinical manifestations of colorectal cancer patients from a large multicenter study in Colombia

Colorectal cancer (CRC) is a major public health problem, and its incidence is rising in developing countries. However, studies characterizing CRC clinicopathological features in cases from developing countries are still lacking. The goal of this study was to evaluate clinicopathological and demographic features in one of the largest CRC studies in Latin America.The study involved over 1525 CRC cases recruited in a multicenter study in Colombia between 2005 and 2014 as part of ongoing genetic and epidemiological studies. We gathered clinicopathological data such as age at diagnosis, sex, body mass index, tobacco and alcohol consumption, family history of cancer, and tumor features including location, histological type, and stage. Statistical analyses were performed to test the association between age of onset, sex, and clinical manifestations.The average age at CRC diagnosis was 57.4 years, with 26.5% of cases having early-onset CRC (diagnosed by age 50 years). Most cases were women (53.2%; P = 0.009), 49.2% were overweight or obese, 49.1% were regular alcohol drinkers, 52% were smokers/former smokers, and 12.2% reported relatives with cancer. Most tumors in the study were located in the rectum (42.7%), were adenocarcinomas (91.5%), and had advanced stage (T3-T4, 79.8%). Comparisons by sex found that male cases were more likely to be obese (36.5% vs 31.1%; P = 0.001), less likely to have a family history of cancer (9.7% vs 15.3%; P = 0.016), and more likely to have advanced-stage tumors (83.9% vs 76.1%; P = 0.036). Comparisons by age of onset found that early-onset cases were more likely to be women (59.3% vs 51.0%; P = 0.005) and report a family history of cancer (17.4% vs 10.2%; P = 0.001).To our knowledge, our study is the largest report of clinicopathological characterization of Hispanic CRC cases, and we suggest that further studies are needed to understand CRC etiology in diverse Hispanic populations.

Clinical features of Hispanic thyroid cancer cases and the role of known genetic variants on disease risk

Thyroid cancer (TC) is the second most common cancer among Hispanic women. Recent genome-wide association (GWA) and candidate studies identified 6 single nucleotide polymorphisms (SNPs; rs966423, rs2439302, rs965513, rs6983267, rs944289, and rs116909374), associated with increased TC risk in Europeans but their effects on disease risk have not been comprehensively tested in Hispanics. In this study, we aimed to describe the main clinicopathological manifestations and to evaluate the effects of known SNPs on TC risk and on clinicopathological manifestations in a Hispanic population.We analyzed 281 nonmedullary TC cases and 1146 cancer-free controls recruited in a multicenter population-based study in Colombia. SNPs were genotyped by Kompetitive allele specific polymerase chain reaction (KASP) technique. Association between genetic variants and TC risk was assessed by computing odds ratios (OR) and confidence intervals (CIs).Consistent with published data in U.S. Hispanics, our cases had a high prevalence of large tumors (>2 cm, 43%) and a high female/male ratio (5:1). We detected significant associations between TC risk and rs965513A (OR = 1.41), rs944289T (OR = 1.26), rs116909374A (OR = 1.96), rs2439302G (OR = 1.19), and rs6983267G (OR = 1.18). Cases carried more risk alleles than controls (5.16 vs. 4.78, P = 4.8 × 10). Individuals with ≥6 risk alleles had >6-fold increased TC risk (OR = 6.33, P = 4.0 × 10) compared to individuals with ≤2 risk alleles. rs944289T and rs116909374A were strongly associated with follicular histology (ORs = 1.61 and 3.33, respectively); rs2439302G with large tumors (OR = 1.50); and rs965513A with regional disease (OR = 1.92).To our knowledge, this is the first study of known TC risk variants in South American Hispanics and suggests that they increase TC susceptibility in this population and can identify patients at higher risk of severe disease.

The HABP2 G534E polymorphism does not increase nonmedullary thyroid cancer risk in Hispanics

Familial nonmedullary thyroid cancer (NMTC) has not been clearly linked to causal germline variants, despite the large role that genetic factors play in risk. Recently, HABP2 G534E (rs7080536A) has been implicated as a causal variant in NMTC. We have previously shown that the HABP2 G534E variant is not associated with TC risk in patients from the British Isles. Hispanics are the largest and the youngest minority in the United States and NMTC is now the second most common malignancy in women from this population. In order to determine if the HABP2 G534E variant played a role in NMTC risk among Hispanic populations, we analyzed 281 cases and 1105 population-matched controls from a multicenter study in Colombia, evaluating the association through logistic regression. We found that the HABP2 G534E variant was not significantly associated with NMTC risk (P=0.843) in this Hispanic group. We also stratified available clinical data by multiple available clinicopathological variables and further analyzed the effect of HABP2 on NMTC presentation. However, we failed to detect associations between HABP2 G534E and NMTC risk, regardless of disease presentation (P≥0.273 for all cases). Therefore, without any significant associations between the HABP2 G534E variant and NMTC risk, we conclude that the variant is not causal of NMTC in this Hispanic population.

The 8q24 rs6983267G variant is associated with increased thyroid cancer risk

The G allele of the rs6983267 single-nucleotide polymorphism, located on chromosome 8q24, has been associated with increased risk of several cancer types. The association between rs6983267G and thyroid cancer (TC) has been tested in different populations, mostly of European ancestry, and has led to inconclusive results. While significant associations have been reported in the British and Polish populations, no association has been detected in populations from Spain, Italy and the USA. To further investigate the role of rs6983267G in TC susceptibility, we evaluated rs6983267 genotypes in three populations of different continental ancestry (British Isles, Colombia and Japan), providing a total of 3067 cases and 8575 controls. We detected significant associations between rs6983267G and TC in the British Isles (odds ratio (OR)=1.19, 95% CI: 1.11-1.27, P=4.03×10(-7)), Japan (OR=1.20, 95% CI: 1.03-1.41, P=0.022) and a borderline significant association of similar effect direction and size in Colombia (OR=1.19, 95% CI: 0.99-1.44, P=0.069). A meta-analysis of our multi-ethnic study and previously published non-overlapping datasets, which included a total of 5484 cases and 12 594 controls, confirmed the association between rs6983267G and TC (P=1.23×10(-7), OR=1.13, 95% CI: 1.08-1.18). Our results therefore support the notion that rs6983267G is a bona fide TC risk variant that increases the risk of disease by ∼13%.

Abstract 2759: Possible later age of breast cancer onset for Hispanic BRCA1 carriers with the protective rs140068132-G allele

Hispanic women in the U.S. have lower incidence of breast cancer compared to Non-Hispanic Whites (NHW). A genome-wide association study (GWAS) of breast cancer in Hispanics reported a relatively strong protective variant near the ESR1 gene, only observed among women with Indigenous American ancestry (rs140068132-A/G). The study also reported lower mammographic density among women who were homozygous for the Indigenous American variant (G) and a stronger protective effect for estrogen receptor negative (ER-) breast cancer. In the present study, we assessed if this variant had an effect on age at breast cancer diagnosis among Hispanic BRCA1 carriers, who commonly present with ER- disease. We combined data from four studies of Hispanic BRCA1 mutation carriers with breast cancer: the Clinical Cancer Genetics Community Research Network (CCGCRN; N = 152), Northern California Breast Cancer Family Registry (NC-BCFR, N = 27), and two studies in Latin America, one from Colombia (N = 33) and one from Chile (N = 27). We genotyped the rs140068132 variant using a Taqman assay following the recommended protocol. We used a non-parametric Kruskal-Wallis equality-of-populations rank test to evaluate if the age of breast cancer diagnosis was associated with the rs140068132 polymorphism among BRCA1 carriers. We conducted separate analyses of Hispanic women from California and women from Colombia and Chile. For the California studies, we also had information on ovarian cancer status and were able to conduct stratified analyses. Among 239 BRCA1 carriers, we observed 201 homozygous AA, 36 heterozygous AG, and 2 missing genotypes, with an overall allele frequency of the G allele of 7.6%. We did not find a statistically significant effect of rs140068132 on age at diagnosis among Hispanic BRCA1 carriers overall. However, we found a suggestion of later age at diagnosis, with median age at diagnosis of 39.8 years (33-46 years) in AA homozygous compared to 44 years (34-50 years) in heterozygous (p value = 0.1) women from California. Among women without ovarian cancer either before or after the breast cancer diagnosis, the difference in age at breast cancer diagnosis by genotype was slightly stronger (p value 0.06). We did not observe an association among the patients from Colombia and Chile. Studies of BRCA mutation carriers are often limited by selection for breast cancer cases, thus there may be a bias against enrollment of BRCA carriers with the protective allele in the present analysis. The observed suggestion of a difference in age at diagnosis in the samples from California, similar to genome-wide identified variants that have been shown to have an effect among BRCA1 and BRCA2 carriers, warrants further investigation.

Citation Format: Laura Fejerman, Jeffrey N. Weitzel, Esther M. John, Cynthia Villarreal, Gary Unzeitig, Darling Horcasitas, Charite Ricker, Adrian Daneri, Kayla Castaneda, Alexander Miron, Ana Marie Tuazon, Magdalena Echeverry, Pilar Carvallo, Carolina Alvarez, Teresa Tapia, Columbus Consortium, Luis Carvajal-Carmona, Susan Neuhausen, Elad Ziv. Possible later age of breast cancer onset for Hispanic BRCA1 carriers with the protective rs140068132-G allele. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2759. doi:10.1158/1538-7445.AM2015-2759

Abstract 4620: Somatic mutation profile of gastric cancer cases from the Hispanic population

Gastric cancer contributes to a significant health care burden, being the third most common cause of cancer related deaths worldwide. In the US, gastric cancer incidence and mortality in the Hispanic population is more than double compared to Non-Hispanic whites (NHW). However, a majority of the large-scale gastric cancer genome characterization studies that have been carried so far have been largely limited to non-Hispanic (NH) populations, predominantly Non-Hispanic Whites (NHW). This “mono-ethnic” approach is likely to miss driver mutations that are unique or common in Hispanics but rare in NHWs and can lead to future genomic-driven cancer health disparities. Identification of driver mutations is important to understand the molecular basis of tumorigenesis and to develop better preventive and therapeutic strategies in minority groups like Hispanics. Therefore, the purpose of this study was to characterize gastric cancer somatic changes in the understudied Hispanic population. Somatic mutations were identified using whole exome sequencing (WES) of 36 tumor-normal pairs from Hispanic gastric cancer patients. Microsatellite stability tasting was also performed on all the samples and samples were divided into 27 microsatellite stable (MSS) and 9 microsatellite instable (MSI) cases. Interestingly, preliminary analysis of exome sequencing data delineates differences in mutational profile in our study population compared to publish studies in NH. For example, we found that the frequency of TP53, the most commonly mutated gastric cancer driver in NHs, had a significantly lower frequency in our Hispanic sample (33% in MSS tumors and 11% in MSI tumors compared to 50% in MSS and 35% in MSI tumors reported in TCGA dataset). Similar differences were also found in other frequently mutated gastric cancer genes, which suggest that the genetic pathways leading to gastric cancer in Hispanics are likely to be different to the ones involved in NHW tumors. In summary, our sequencing study of Hispanic gastric cancer cases have identified important differences with other populations, are likely to identify novel cancer drivers in this tumor type and would help bridge the gap in heath care disparities

Citation Format: Rodrigo Prieto-Sanchez, Ruta Madhusudan Sahasrabudhe, Paul Lott, Mabel Bohorquez, Jhon Jairo Suarez, Gilbert Mateus, Javier Torres, Magdalena Echeverry, Luis Carvajal-Carmona. Somatic mutation profile of gastric cancer cases from the Hispanic population. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4620. doi:10.1158/1538-7445.AM2015-4620

Abstract 2739: Transcontinental characterization of the Hispanic BRCA1 3450del4 breast cancer founder mutation

Breast cancer (BC) is the most commonly diagnosed cancer among women, with 1 in every 7 women in the U.S. developing BC in their lifetime. While BC may not be the leading cause of cancer incidence in many minority populations, such as Hispanics, it is the leading cause of cancer death, highlighting a cancer disparity. Moreover, the contribution of mutations in BC susceptibility genes remains poorly investigated in Hispanic populations. To begin to address these voids, we screened Colombian BC patients for common BRCA1 and BRCA2 mutations using the KASP genotyping system. Strikingly, 27 of 722 unselected cases (4%) harbored the same BRCA1 3450del4 mutation. Clinical data and family history indicate that these individuals originate from a distinct geographic region in Colombia, Neiva. Significantly, 10% of the unselected BC cases in Neiva and the surrounding region harbor the 3450del4 mutation, potentially representing one of the most profound founder effects reported in human populations. Interesting, this BRCA1 mutation has also been reported in other countries, including Portugal, Spain, and Chile. To determine whether this mutation stems from a single origin, mutation carriers from each of these countries (n = 26), along with mutation carriers from Colombia (n = 27), were subjected to the Affymetrix Axiom Human UK Biobank Array (&gt;800 thousand markers). Haplotypes in which the BRCA1 mutation resides were estimated by SHAPEIT, and pairwise segmental sharing was determined using GERMLINE. Our data suggest that the mutation carriers, although from different countries and continents, share a core haplotype, likely to have originated from Spain. Additionally, the mutation seems to be fairly new to Colombia, with individuals sharing up to a 40Mb haplotype comprising the mutation. We are currently estimating the age of the mutation using the bioinformatic software DMLE+, which exploits the rate of linkage disequilibrium decay due to recombination. By understanding the prevalence of mutations in known breast cancer risk genes in minority populations, cancer disparities can be better addressed and breast cancer screening can be improved. Furthermore, these findings have direct implications in robust and cost-effective targeted screening in regions where there is a high prevalence of the BRCA1 3450del4 mutation.

Citation Format: Anna Marie De Asis Tuazon, Carolina Ramirez, Mabel Bohorquez, Rodrigo Prieto, Paul Lott, Angel Criollo, Ana Estrada, Gillbert Mateus, Alejandro Velez, Justo Ramirez, COLUMBUS Consortium, Manuel Teixeira, Ana Vega, Conxi Lazaro, Eva Tornero, Cristina Martinez, Mar Infante, Miguel De La Hoya, Orland Diez, Pilar Carvallo, Magdalena Echeverry, Luis Carvajal-Carmona. Transcontinental characterization of the Hispanic BRCA1 3450del4 breast cancer founder mutation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2739. doi:10.1158/1538-7445.AM2015-2739

Abstract B10: Development of high-throughput screening methods for detecting germline cancer causing mutations in the Hispanic population

Colorectal and breast cancers are leading causes of cancer morbidity and mortality in Hispanics. Most of the genes predisposing to these common malignancies are yet to be identified. Moreover, the prevalence of mutations in known cancer genes in Hispanic populations remains largely undetermined. Our present study aims to establish the prevalence of mutations that predispose to cancer susceptibility syndromes in Hispanics using a high throughput next-generation sequencing approach. We have developed an amplicon sequencing method that uses microfluidics PCR to simultaneously identify mutations in up to 480 amplicons. This amount of sequence data is enough to cover, at a high depth, the coding sequence of ∼20 different genes in a single reaction. To do so, the samples are barcoded individually using indexing adapters that allows pooling of multiple amplicon libraries for up to 384 samples in a single MiSeq run. The sequence data is analyzed with a locally developed bioinformatics pipeline that uses BWA, VarScan V2.0 and custom shell and Perl scripts. Our preliminary data, in several hundred familial and early-onset colon and breast cancer patients from South America, have identified many individuals with mutations in known cancer genes, such as APC, MSH2, MLH1, BRCA1 and BRCA2, and that have been previously reported in Southern European populations. We have also identified several mutations that have not been reported previously and that appear to have an Amerindian origin. Interestingly, a large fraction of these mutations are shared by multiple patients and suggest that founder effects are common in some of these populations. We have also found that more than over 50% of the patients screened so far are mutation negative. We plan to use this latter set of samples for novel gene discovery by whole exome or genome sequencing in the next phase of our study. In conclusion, we have developed a rapid, cost effective, and efficient method for screening mutations in known cancer genes in the Hispanic population. Hispanics are the youngest, largest and the fastest growing US minority and the largest population group living in the Americas. However, to a large extent, this population remains under-studied and under-screened, contributing to health care disparities. Prevalence of mutations in known cancer genes as well as novel mutations identified in our study can be used during initial steps of genetic testing programs that can improve the detection of early cancers among Hispanic communities.

Citation Format: Ruta Sahasrabudhe, Anna-Marie Tuazon, Paul Lott, Ana Estrada, Mabel Bohorquez, Rodrigo Prieto, Angel Criollo, Carolina Ramirez, Magdalena Echeverry, Luis G. Carvajal-Carmona. Development of high-throughput screening methods for detecting germline cancer causing mutations in the Hispanic population. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr B10. doi:10.1158/1538-7755.DISP13-B10

Abstract LB-299: Genome wide association study of breast cancer in Latinas identifies protective variants of Indigenous American origin on 6q25

Background: Multiple breast cancer genome-wide association studies (GWAS) have been conducted, with most samples analyzed being of European or Asian origin. No GWAS has been published to date on US Latinas or Latin American women. Previous studies have demonstrated that among Latina women, those with the highest Indigenous American ancestry are protected from breast cancer. We performed the first genome-wide association study of breast cancer in Latinas in a total of 1523 cases and 3221 controls and validated the strongest associations in an additional 977 Latina cases and 1158 controls.

Methods: For the discovery phase, samples were genotyped with either the 6.0 Affymetrix array or Illumina Infinitum 660W/Omni 2.5 arrays. Additional genotypes were imputed from 1000 genomes and the final analysis included ∼7 million SNPs. SNPs for replication were genotyped using Sequenom. Logistic regression analyses included the first 10 principal components as covariates.

Results: We identified two new variants, located 5’ of the ESR1 gene (6q25 region), which are strongly associated with breast cancer in this population. The minor allele for these variants is strongly protective (rs140068132: OR 0.61, 95%CI 0.48-0.75, p=3x10-13 & rs147157845: OR 0.63 95% CI 0.49-0.76; p =2x10-12). These alleles are present only in Latinos, correlate with Indigenous American ancestry, and are uncorrelated with previously reported risk variants in the ESR1 region. We found a strong association for both ER-positive and ER-negative breast cancer, but significantly more protection for ER-negative disease (p=0.014). The rs140068132 variant is also associated with breast density. The average breast density among women who are homozygous for the protective allele is approximately half of that of women homozygous for the common allele [Mean (sd) density for Homozygous GG = 9 (8); Homozygous AA = 17 (14), p 0.0009]. rs140068132, is located within a putative binding region for multiple transcription factors. MAPPER predicts disruption of putative transcription factor binding sites for the rare allele at rs140068132 but not rs147157845. Electromotility shift assays showed differential binding of the two alleles at the rs140068132 locus, with the protective allele (G) showing substantially reduced binding affinity compared to the common A allele.

Conclusions: The variants at this locus represent, to our knowledge, the strongest genome wide effect size on breast cancer for a common variant (frequency &gt;0.05 in any major population). These results may help in understanding the previous observations of lower breast cancer risk among Latina women with more Indigenous American ancestry and highlight the importance of conducting GWAS in diverse populations.

Citation Format: Laura Fejerman, Nasim Ahmadiyeh, Donglei Hu, Scott Huntsman, Kenneth Beckman, Jennifer Caswell, Esther M. John, Gabriela Torres-Mejia, Luis Carvajal-Carmona, Magdalena Echeverry, Anna Marie Tuazon, Carolina Ramirez, COLUMBUS Consortium, Christopher Gignoux, Celeste Eng, Esteban Gonzalez-Burchard, Brian Henderson, Loic Le Marchand, Eliseo J. Perez-Stable, Christopher A. Haiman, Elad Ziv. Genome wide association study of breast cancer in Latinas identifies protective variants of Indigenous American origin on 6q25. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-299. doi:10.1158/1538-7445.AM2014-LB-299

Abstract 5166: Characterization of somatic mutation spectrum in gastric cancer cases from Hispanic populations

Gastric cancer is the second leading cause of cancer related deaths worldwide. Identification of gastric cancer drivers and somatic changes are essential to understand the molecular basis of tumorigenesis and to develop better preventive and therapeutic strategies. Till date, the large-scale initiatives to characterize somatic changes have been largely limited to Caucasian and Asian populations. This approach is likely to miss potential driver mutations that can be unique to other populations. Therefore, identification of somatic changes in cancers from multi-ethnic populations is essential to advance our understanding of tumor biology as well to bridge the gap in heath-care disparities. Hispanics are the largest and fastest growing minority in the USA and gastric cancer is a significant health care concern in this population. To understand molecular signatures of somatic alterations in gastric cancer in Hispanic population, we performed exome sequencing of 36 tumor samples and matched normal mucosa from gastric cancer patients from Colombia. In addition, we also performed microsatellite instability (MSI) testing and determined Epstein Barr virus and Helicobacter Pylori infection status for these samples. Our preliminary analysis of exome sequencing data by a locally developed pipeline indicates that the frequency of known cancer drivers in our study population in different than that has been reported previously and a subset of these cancers are following unique genetic pathways. In summary, our sequencing efforts in gastric cancer cases from Hispanic population are likely to identify novel cancer drivers and can help to further our understanding of molecular basis of this tumor type.

Citation Format: Rodrigo Prieto, Paul Lott, Ruta Sahasrabudhe, Mabel Bohorquez, Jorge Castro, Gilbert Mateus, Magdalena Echeverry, Luis G. Carvajal Carmona. Characterization of somatic mutation spectrum in gastric cancer cases from Hispanic populations. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5166. doi:10.1158/1538-7445.AM2014-5166