Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries

Abstract

Reducing disparities is critical to promote equity of access to precision treatments for all patients with cancer. While socioenvironmental factors are a major driver behind such disparities, biological differences also are likely to contribute. The prioritization of cancer drug targets is foundational for drug discovery, yet whether ancestry-related signals in target discovery pipelines exist has not been systematically explored due to the absence of data at the appropriate scale. Here, we analyzed data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models as part of the Cancer Dependency Map to identify ancestry-associated genetic dependencies. Surprisingly, we found that most putative associations between ancestry and dependency arose from artifacts related to germline variants that are present at different frequencies across ancestry groups. In 2-5% of genes profiled in each cellular model, germline variants in sgRNA targeting sequences likely reduced cutting by the CRISPR/Cas9 nuclease. Unfortunately, this bias disproportionately affected cell models derived from individuals of recent African descent because their genomes tended to diverge more from the consensus genome typically used for CRISPR/Cas9 guide design. To help the scientific community begin to resolve this source of bias, we report three complementary methods for ancestry-agnostic CRISPR experiments. This report adds to a growing body of literature describing ways in which ancestry bias impacts cancer research in underappreciated ways.