Association of Somatic Variants with Ethnicity in Patients with Colon Cancer
Open AccessAbstractAssociation of Somatic Variants with Ethnicity in Patients with Colon CancerThe occurrence and outcome of colon cancer vary considerably between racial and ethnic groups, with the highest incidence occurring in African American. These disparities were primarily explained by socioeconomic factors and lower healthcare services utilization. Few studies indicated genetic determinants for specific cancer types have also significant contributions to disparities, however, disparities remain significant. Hence, studying the genetic alterations that may have implications for colon cancer disparities is important in the effort to eliminate disparities. In this project, we studied the association of somatic mutation with ethnicity computationally inferred from the patient’s genome. The data set of our study consists of exome sequencing NGS data of 37 colon cancer patients. Germline and somatic variant calling were performed using the Genome Analysis Tool Kit (GATK) and matched normal samples were used as a reference genome. Ethnicity annotation was performed using an R package EthSEQ. Statistical analysis was performed using R software, and P values <0.05 were considered statistically significant. The EthSEQ ethnicity annotation classified our study subjects into nine African (AFR), twenty Caucasian (EUR), and eight admixed American (AMR). For mixed ethnicity, the percent contribution of each ethnic group was used to compute associations with gene mutations. We found a statistically significant difference in the number and frequency of genes mutated in AFR and EUR colon cancers in our data set, with the mutation frequency in the AFR group lower than in EUR. This result is not consistent with other previous studies, probably due to the sample size and gene set differences between the two groups and a high proportion of mixed genetic ethnicity in our study subjects. Tumor mutation burden didn’t show a significant difference between the AFR and other ethnic groups. Logistic regression models indicated that alterations in DNAH5, MUC12, MUC16, RYR3, HMCN1, AHNAK2, DNAH14, TMEM132C, TCF7L2, UBE20, DCHS1 and SMAD45 were associated with the AFR ethnicity. Further studies of these associations in larger samples are warranted to investigate their impact on the disparities of colon cancer in different ethnic groups.
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Demessie_gwu_0075M_16436.pdf | 2023-11-14 | Open Access |
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