Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations

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Abstract

Background: Historically, geneticists have relied on genotyping arrays and imputation to study human genetic variation. However, an underrepresentation of diverse populations has resulted in arrays that poorly capture global genetic variation, and a lack of reference panels. This has contributed to deepening global health disparities. Whole genome sequencing (WGS) better captures genetic variation but remains prohibitively expensive. Thus, we explored WGS at “mid-pass” 1-7x coverage. Results: Here, we developed and benchmarked methods for mid-pass sequencing. When applied to a population without an existing genomic reference panel, 4x mid-pass performed consistently well across ethnicities, with high recall (98%) and precision (97.5%). Conclusion: Compared to array data imputed into 1000 Genomes, mid-pass performed better across all metrics and identified novel population-specific variants with potential disease relevance. We hope our work will reduce financial barriers for geneticists from underrepresented populations to characterize their genomes prior to biomedical genetic applications.

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APA

Emde, A. K., Phipps-Green, A., Cadzow, M., Gallagher, C. S., Major, T. J., Merriman, M. E., … Castel, S. E. (2021). Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations. BMC Genomics, 22(1). https://doi.org/10.1186/s12864-021-07949-9

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