DOI: 10.1158/1538-7755.disp23-c002 ISSN: 1538-7755

Abstract C002: Integrating multiomics data to identify African ancestry-informative markers acting as eQTLs in breast cancer

Samantha Boudeau
  • Oncology
  • Epidemiology


Ancestry-informative markers (AIMs) are SNPs that are found at relatively higher frequencies in a specific population and can be used to estimate genetic ancestry. Genetic ancestry is becoming more commonly used in biomedical research investigating the genetic basis of diseases. For many cancers, the literature suggests that African ancestry is associated with poor response to treatment, poorer prognosis, and poorer survival. More specifically, African American women with breast cancer are more likely to have more aggressive subtypes of the disease and diagnosed with a later stage of the disease at an earlier age compared to their European American counterparts. Some of this disparity remains after accounting for socioeconomic factors, suggesting a genetic basis for the health disparities observed in many cancers.  To evaluate the genetic basis of cancer health disparities in populations of African ancestry, we identified a set of 46,787 African ancestry informative markers (AIMs) using 1000 Genomes Project data from African and European populations. These AIMs were functionally annotated and investigated for potential associations with cancer in the literature, using tools such as VEP, SIFT, and Polyphen. Using multiomics data (RNAseq, genotype, methylation, copy number variation) from The Cancer Genome Atlas and an integrative eQTL modeling approach, we are investigating which of these AIMs act as expression quantitative trait loci in breast cancer. Of the 47K SNPs identified, 0.6% percent was found to be in the coding regions of the genome and AIMS located on chromosomes 8, 10, 11, 15, 18, and 19 were found to be associated with different cancers in the literature including breast and colorectal cancers. Approximately 5K of the AIMs were found in the TCGA breast cancer data and preliminary results identified cis-eqtls in 4 different genes including SERINC2 and ZSCAN23, and trans-eqtls in about 8 genes including CLCN3 and DEDD. These eQTL AIMs are being evaluated for potential association with ancestry-specific differential survival and response to treatment in breast cancer.

Citation Format: Samantha Boudeau. Integrating multiomics data to identify African ancestry-informative markers acting as eQTLs in breast cancer [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C002.

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