Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas

Genomics. 2021 May;113(3):1234-1246. doi: 10.1016/j.ygeno.2021.02.020. Epub 2021 Mar 8.


Individuals of African ancestry suffer disproportionally from higher incidence, aggressiveness, and mortality for particular cancers. This disparity likely results from an interplay among differences in multiple determinants of health, including differences in tumor biology. We used The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA aggregate expression datasets and identified differential alternative RNA splicing and transcription events (ARS/T) in cancers between self-identified African American (AA) and White (W) patients. We found that retained intron events were enriched among race-related ARS/T. In addition, on average, 12% of the most highly ranked race-related ARS/T overlapped between any two analyzed cancers. Moreover, the genes undergoing race-related ARS/T functioned in cancer-promoting pathways, and a number of race-related ARS/T were associated with patient survival. We built a web-application, CanSplice, to mine genomic datasets by self-identified race. The race-related targets have the potential to aid in the development of new biomarkers and therapeutics to mitigate cancer disparity.

Keywords: African American; Alternative RNA splicing; Alternative transcription; Breast cancer; Cancer disparity; Prostate cancer; Race; SpliceSeq; Splicing factors; TCGA; White.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alternative Splicing*
  • Black or African American / genetics
  • Gene Expression Regulation, Neoplastic
  • Genomics
  • Humans
  • Neoplasms* / genetics