Sandra Perdomo

Identification of Circulating Tumor DNA for the Early Detection of Small-cell Lung Cancer

Circulating tumor DNA (ctDNA) is emerging as a key potential biomarker for post-diagnosis surveillance but it may also play a crucial role in the detection of pre-clinical cancer. Small-cell lung cancer (SCLC) is an excellent candidate for early detection given there are no successful therapeutic options for late-stage disease, and it displays almost universal inactivation of TP53. We assessed the presence of TP53 mutations in the cell-free DNA (cfDNA) extracted from the plasma of 51 SCLC cases and 123 non-cancer controls. We identified mutations using a pipeline specifically designed to accurately detect variants at very low fractions. We detected TP53 mutations in the cfDNA of 49% SCLC patients and 11.4% of non-cancer controls. When stratifying the 51 initial SCLC cases by stage, TP53 mutations were detected in the cfDNA of 35.7% early-stage and 54.1% late-stage SCLC patients. The results in the controls were further replicated in 10.8% of an independent series of 102 non-cancer controls. The detection of TP53 mutations in 11% of the 225 non-cancer controls suggests that somatic mutations in cfDNA among individuals without any cancer diagnosis is a common occurrence, and poses serious challenges for the development of ctDNA screening tests.

Analysis of DNA repair gene polymorphisms in glioblastoma

BACKGROUND Glioblastoma is the most common and aggressive primary brain tumor in adults. Despite several factors such as ionizing radiation exposure or rare genetic syndromes have been associated with the development of glioblastoma, no underlying cause has been identified for the majority of cases. We thus aimed to investigate the role of DNA repair polymorphisms in modulating glioblastoma risk. METHODS Genotypic and allelic frequencies of seven common polymorphisms in DNA repair genes involved in nucleotide excision repair (ERCC1 rs11615, ERCC2 rs13181, ERCC6 rs4253079), base excision repair (APEX1 rs1130409, XRCC1 rs25487), double-strand break repair (XRCC3 rs861539) and mismatch repair (MLH1 rs1800734) pathways were analyzed in 115 glioblastoma patients and 200 healthy controls. Haplotype analysis was also performed for ERCC1 rs11615 and ERCC2 rs13181 polymorphisms, located on the same chromosomal region (19q13.32). RESULTS Our results indicated that carriers of the ERCC2 Gln/Gln genotype were associated with a lower glioblastoma risk (OR=0.32, 95% CI 0.12-0.89; P=0.028), whereas carriers of the MLH1 AA genotype were associated with an increased risk of glioblastoma (OR=3.14, 95% CI 1.09-9.06; P=0.034). Furthermore, the haplotype containing the C allele of ERCC2 rs13181 polymorphism and the T allele of ERCC1 rs11615 polymorphism was significantly associated with a protective effect of developing glioblastoma (OR=0.34, 95% CI 0.16-0.71; P=0.004). CONCLUSIONS These results pointed out that MLH1 rs1800734 and ERCC2 rs13181 polymorphisms might constitute glioblastoma susceptibility factors, and also suggested that the chromosomal region 19q could be important in glioblastoma pathogenesis.

Head and neck cancer burden and preventive measures in Central and South America

RATIONALE AND OBJECTIVE Central and South America comprise one of the areas characterized by high incidence rates for head and neck cancer. We describe the geographical and temporal trends in incidence and mortality of head and neck cancers in the Central and South American region in order to identify opportunities for intervention on the major identified risk factors: tobacco control, alcohol use and viral infections. METHODS We obtained regional- and national-level incidence data from 48 population-based cancer registries in 13 countries and cancer deaths from the WHO mortality database for 18 countries. Age-standardized incidence (ASR) and mortality (ASMR) rates per 100,000 person-years were estimated. RESULTS Brazil had the highest incidence rates for oral and pharyngeal cancer in the region for both sexes, followed by Cuba, Uruguay and Argentina. Cuba had the highest incidence and mortality rates of laryngeal cancer in the region for males and females. Overall, males had rates about four times higher than those in females. Most countries in the region have implemented WHO recommendations for both tobacco and alcohol public policy control. CONCLUSION Head and neck squamous-cell cancer (HNSCC) incidence and mortality rates in the Central and South America region vary considerably across countries, with Brazil, Cuba, French Guyana, Uruguay and Argentina experiencing the highest rates in the region. Males carry most of the HNSCC burden. Improvement and implementation of comprehensive tobacco and alcohol control policies as well as the monitoring of these factors are fundamental to prevention of head and neck cancers in the region.

Circulating tumor DNA detection in head and neck cancer: evaluation of two different detection approaches

The use of non-invasive biomarkers such as circulating tumor DNA (ctDNA) in head and neck tumors may be of relevance in early diagnosis and eventually improved outcome. We evaluated two different approaches from two case series in Europe and South America including (i) targeted screening of ctDNA mutations, and (ii) detection of TP53 mutations in plasma and oral rinses without previous knowledge of mutational status in tumor samples. Targeted sequencing in 5 genes identified ctDNA mutations in plasma among 42% of HNSCC cases, 67% of who were early stage cases. No association was found between ctDNA mutation detection and overall survival. Sequencing of the entire coding region of the TP53 gene resulted in identification of TP53 mutations in 76% of tumor cases. However, concordance of mutation detection was low between tumor, oral rinses (11%) and plasma (2,7%) samples. Identification of 5 pathogenic TP53 mutations in oral rinses from 3 non-cancer controls gives additional evidence of mutation occurrence in individuals without a diagnosed cancer and presents an additional challenge for the development of ctDNA diagnostic assays.

Genomic analysis of head and neck cancer cases from two high incidence regions

We investigated how somatic changes in HNSCC interact with environmental and host risk factors and whether they influence the risk of HNSCC occurrence and outcome. 180-paired samples diagnosed as HNSCC in two high incidence regions of Europe and South America underwent targeted sequencing (14 genes) and evaluation of copy number alterations (SCNAs). TP53, PIK3CA, NOTCH1, TP63 and CDKN2A were the most frequently mutated genes. Cases were characterized by a low copy number burden with recurrent focal amplification in 11q13.3 and deletion in 15q22. Cases with low SCNAs showed an improved overall survival. We found significant correlations with decreased overall survival between focal amplified regions 4p16, 10q22 and 22q11, and losses in 12p12, 15q14 and 15q22. The mutational landscape in our cases showed an association to both environmental exposures and clinical characteristics. We confirmed that somatic copy number alterations are an important predictor of HNSCC overall survival.

Human papilloma virus: An etiological and prognostic factor for oral cancer?

The increasing prevalence of human papilloma virus (HPV)-positive oral tumors can be considered an epidemic. Although the incidence of HPV cervical cancer is decreasing, the incidence of oral cavity and oropharyngeal cancers associated with HPV is increasing. The presence of certain HPV genotypes could be a predictor of future oral cancer lesions, although lesions associated with HPV could be less aggressive and exhibit a higher survival rate. In the present study, we review the most important biologic, clinic, epidemiologic, and prognostic factors associated with HPV infection and oral cancer.

Predictors of Survival After Head and Neck Cancer in South America: Preliminary Results of the InterCHANGE Study

Abstract 65PurposeIncidence of head and neck cancer (HNC) is high in South America, and survival data are scarce in this region. The InterCHANGE study was established by clinical groups from across South America and the International Agency for Research on Cancer, with the primary aim to study the impact of human papillomavirus (HPV) infection and sociodemographic, clinic, and lifestyle factors on survival after this malignancy. The current study examined the main predictors of survival after HNC in South America and estimated overall and conditional survival probabilities.MethodsPatients were recruited during 2010 to 2016 from seven centers in Argentina, Brazil, Colombia, and Uruguay. A questionnaire obtained information on age, stage, and body mass index at diagnosis; sex; education; race; and comprehensive smoking and alcohol history. Blood samples were collected for HPV16 E6 testing—a surrogate marker for HPV16 infection. The Kaplan-Meier method and Cox proportional hazards regression were used for st...

Comprehensive Analysis of Germline Variants in Mexican Patients with Hereditary Breast and Ovarian Cancer Susceptibility

Hereditary breast and ovarian cancer syndrome (HBOC) represents 5–10% of all patients with breast cancer and is associated with high-risk pathogenic alleles in BRCA1/2 genes, but only for 25% of cases. We aimed to find new pathogenic alleles in a panel of 143 cancer-predisposing genes in 300 Mexican cancer patients with suspicion of HBOC and 27 high-risk patients with a severe family history of cancer, using massive parallel sequencing. We found pathogenic variants in 23 genes, including BRCA1/2. In the group of cancer patients 15% (46/300) had a pathogenic variant; 11% (33/300) harbored variants with unknown clinical significance (VUS) and 74% (221/300) were negative. The high-risk group had 22% (6/27) of patients with pathogenic variants, 4% (1/27) had VUS and 74% (20/27) were negative. The most recurrent mutations were the Mexican founder deletion of exons 9-12 and the variant p.G228fs in BRCA1, each found in 5 of 17 patients with alterations in this gene. Rare VUS with potential impact at the protein level were found in 21 genes. Our results show for the first time in the Mexican population a higher contribution of pathogenic alleles in other susceptibility cancer genes (54%) than in BRCA1/2 (46%), highlighting the high locus heterogeneity of HBOC and the necessity of expanding genetic tests for this disease to include broader gene panels.

Cancer Genomic Resources and Present Needs in the Latin American Region

In Latin America (LA), cancer is the second leading cause of death, and little is known about the capacities and needs for the development of research in the field of cancer genomics. In order to evaluate the current capacity for and development of cancer genomics in LA, we collected the available information on genomics, including the number of next-generation sequencing (NGS) platforms, the number of cancer research institutions and research groups, publications in the last 10 years, educational programs, and related national cancer control policies. Currently, there are 221 NGS platforms and 118 research groups in LA developing cancer genomics projects. A total of 272 articles in the field of cancer genetics/genomics were published by authors affiliated to Latin American institutions. Educational programs in genomics are scarce, almost exclusive of graduate programs, and only few are concerning cancer. Only 14 countries have national cancer control plans, but all of them consider secondary prevention strategies for early diagnosis, opportune treatment, and decreasing mortality, where genomic analyses could be implemented. Despite recent advances in introducing knowledge about cancer genomics and its application to LA, the region lacks development of integrated genomic research projects, improved use of NGS platforms, implementation of associated educational programs, and health policies that could have an impact on cancer care.

Abstract 3263: Is Latin America ready for the use of genomics in cancer care and control

In Latin American (LA) countries cancer is the second most frequent cause of death after cardiovascular disease. Disease patterns have changed from infectious to chronic, the population is increasing and becoming elderly, and countries lack planning to respond adequately to this epidemiological and socio-demographic transition. By 2025 and increment of nearly 30% of new cases and 35% of deaths from cancer are predicted. Genomic studies have profoundly changed cancer management from improved cancer diagnosis to reformulating cancer prognosis and treatment. However, all these key advances have been mainly concentrated in highly developed nations and little is known about the capacities and needs of cancer genomics in the LA context. In order to evaluate the capacity and development of cancer genomics in LA, we collected available information for all countries in Central, South America and Cuba. Data reviewed included: number of NGS platforms, number of cancer research institutions, research groups working in cancer genetics, publications on cancer genetics and genomics in the last 10 years, educational programs on genomics and related national cancer control policies. Currently, there are a total of 212 NGS platforms in LA. Mexico and Brazil are the countries with more users, and Peru and Ecuador have the fewest. 118 research groups in South America have been working in cancer genetics and started developing cancer genomics related projects. No data on research groups was available for countries in Central America. In the last 10 years, 231 articles in cancer genetic/genomic related topics were published by authors affiliated to LA institutions. Educational programs in genomics are scarce, almost exclusive of graduate programs and few applied to cancer. Twelve countries in LA have national cancer control plans (NCCP). All NCCPs reviewed consider secondary prevention strategies for early diagnosis, opportune treatment and decrease of mortality, areas where genomic analysis could be implemented. Only 5 NCCPs include cancer research as an action plan to increase cancer prevention strategies and reduce both incidence and mortality. Despite the recent advances in introducing cancer genomics knowledge and application in LA, the region lacks development of integrated genomic research projects, improved use of platforms, associated educational programs and health policies that might focus on the most frequent cancers and could impact cancer care. Citation Format: Sandra Perdomo, Angela Torres, Javier Olivier, Cecilia Frecha, Rosalia Quezada-Urban, Clara Estela Diaz-Velasquez, Felipe Vaca. Is Latin America ready for the use of genomics in cancer care and control [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 3263. doi:10.1158/1538-7445.AM2017-3263