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- Title
Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations.
- Authors
Emde, Anne-Katrin; Phipps-Green, Amanda; Cadzow, Murray; Gallagher, C. Scott; Major, Tanya J.; Merriman, Marilyn E.; Topless, Ruth K.; Takei, Riku; Dalbeth, Nicola; Murphy, Rinki; Stamp, Lisa K.; de Zoysa, Janak; Wilcox, Philip L.; Fox, Keolu; Wasik, Kaja A.; Merriman, Tony R.; Castel, Stephane E.
- 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.
- Subjects
WHOLE genome sequencing; HUMAN genetic variation; GENETIC variation; HEALTH equity; GENETICISTS
- Publication
BMC Genomics, 2021, Vol 22, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-021-07949-9