Researchers investigate genomic data discrepancies among racial groups

The Cancer Genome Atlas, one of the biggest and most commonly used cancer research databases, was used by Mayo Clinic researchers to investigate disparities in genomic data quality among racial groups.

Image Credit: Mayo Clinic

We found lower quality genomic sequencing data in self-reported Black patients and patients of African ancestry. This finding serves as a reminder that when designing, conducting and interpreting cancer genomic studies, the underlying data quality differences between patients need to be carefully examined.”

Yan Asmann., PhD, Study Senior Author and Bioinformatician, Mayo Clinic

The study, which was published in the Journal of the National Cancer Institute, is the first to show racial inequalities in data quality. It is indeed significant since ethnic minorities in the United States frequently endure cancer disparities, with Blacks and African Americans having higher death rates and shorter survival rates for many forms of cancer.

These differences are the result of a complex interaction between nonbiological (socioeconomic, environmental, and behavioral) and biological (genetic and genomic) variables. Dr Asmann emphasizes that data that is equitable in quantity and quality among racial groups is essential to find genetic factors behind cancer discrepancies.

Researchers examined the characteristics of germline and tumor exomes in ancestrally African and European patients using The Cancer Genome Atlas.

The study included 7 types of cancer:

1. Breast
2. Colon
3. Prostate
4. Kidney renal clear cell carcinomas
5. Kidney renal papillary cell
6. Uterine corpus endometrial
7. Lung adenocarcinomas

More than 50 patients with African ancestry were added in these tumor groups.

The researchers looked at the depth of sequencing, tumor purity, and the characteristics of germline and somatic mutations.

We found germline and tumor exomes from Black patients were sequenced at a significantly lower depth in six out of the seven cancers we studied. Lower sequencing depths of tumor and germline exomes likely resulted in less-complete data, underdetection of germline variants and somatic mutations, and inferior variant quality among patients with African ancestry.”

Yan Asmann., PhD, Study Senior Author and Bioinformatician, Mayo Clinic

Future considerations

It is abundantly obvious that minority groups have historically been outnumbered in DNA databases when compared to those of European heritage. As a result, a database of genetic variants has been created that is unlikely to reflect the complete range of human genetic variability.

Patients’ genomics data are often used in clinical decision-making, including patient selection for personalized therapies, and prediction of therapy responses and clinical outcomes. We plan to study the impact of this finding on patient care.”

Aaron Mansfield, M.D. Study Co-Corresponding Author, Mayo Clinic

The results serve as a reminder to researchers using The Cancer Genome Atlas datasets about the possible underdetection of germline variations and somatic mutations among ancestrally African people, according to Dr Asmann.

“These data highlight the need to consider epidemiological factors when designing and conducting future genomic and genetic studies,” concludes Dr Asmann.

“The scientific community and The Cancer Genome Atlas may consider resequencing residual DNA, if still available, from these Black patients with cancer with confirmed African ancestry, or additional ancestrally African patients could be sequenced at high coverage to compensate for the current disparity,” Dr Asmann adds.