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Racial Disparities in Tumor Profiling Testing Inferred From Continental Genetic Ancestry Determination of 100,000 Cancer Patients

AACR Cancer Health Disparities 2022 PRESENTATION
Authors Francisco M. De La Vega, Yannick Pouliot, Brooke Rhead and Justin Guinney

There are well documented disparities in the incidence of cancer and outcomes of
treatment across patients of different races and ethnicities. This is credited to a variety
of factors which include social, structural, and access to care inequities, as well as
biological differences that may correlate with race/ethnicity. We aimed to measure racial
differences in testing for cancer therapy decision support using real-world data (RWD)
from 100,000 de-identified patients who underwent tumor genomic profiling with the
Tempus xT next-generation sequencing assay (targeting 648 genes). A challenge for
this analysis is that in RWD race/ethnicity is frequently missing from patients’ records.
Instead, we used ancestry-informative markers overlapping assay capture regions to
infer continental ancestry proportions: Africa, Americas, Europe, East Asia, and South
Asia. Our data show that despite a majority of patients being of European descent
(72%), our cohort includes 8 to 12-fold more patients with substantial (>50%)
non-European ancestry when compared to The Cancer Genome Atlas. Recognizing the
complexity of ancestry and race relationships, we imputed several race/ethnicity
categories using ancestry admixture thresholds based on literature and our own
analysis, demonstrating less than 2% error with available race/ethnicity labels. With
imputation, 85% more Black patients were identified within our cohort. Furthermore,
Hispanics/Latinos were substantially overrepresented among those missing ethnicity
metadata; using imputed ethnicity labels increased the numbers of this patient
population by 150%. Patient subpopulation disparities were estimated through
comparison of imputed race/ethnicity distributions with the expected overall cohort-level
distributions. We observed significantly lower than expected percentages of Black
patients with pancreatic (-18%) and urinary tract cancers (-42%), and White patients
with breast (-7%) and colorectal (-5%) cancers, whereas higher than expected numbers
of Hispanic/Latino patients with colorectal (+22%) and thyroid (+48%), and Asian
patients with gallbladder cancer (+32%) were present (p<0.05, chi-squared test). These
disparities are unexpected as compared to the ranking of incidence rates in the SEER
database by race/ethnicity. Our results show that genetic ancestry inference on genomic
data from tumor profiling can partially compensate for the lack of race/ethnicity
information in RWD and allow research on disparities and biological race differences in
cancer etiology and outcomes.