ArticleBMC genomics2017
Extremely low-coverage whole genome sequencing in South Asians captures population genomics information.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Human genetic diversity across South Asian populations: A systematic review and meta-analysis.Medicine · 2025Pooled it
- Unified Multi-Caller Ensemble (UME) Generates an Unbiased Maize Haplotype Map for Variable Coverage Whole Genome Data.Molecular ecology resources · 2026Article
- A Multi-Approach for In Silico Detection of Chromosome Inversions in Mosquito Vectors.Microorganisms · 2025Article
- Identifying risk variants for embryo aneuploidy using ultra-low coverage whole-genome sequencing from preimplantation genetic testing.American journal of human genetics · 2023Article
- Reconstruction of the personal information from human genome reads in gut metagenome sequencing data.Nature microbiology · 2023Article
- Nyssorhynchus darlingi genome-wide studies related to microgeographic dispersion and blood-seeking behavior.Parasites & vectors · 2022Article
- A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.Molecular ecology · 2021Article
- CONSULT: accurate contamination removal using locality-sensitive hashing.NAR genomics and bioinformatics · 2021Article
- A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data.BMC bioinformatics · 2021Article
- Whole genome sequencing of elite athletes.Biology of sport · 2020Article
- Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora).Marine biotechnology (New York, N.Y.) · 2019Article
- Genomics of rare genetic diseases-experiences from India.Human genomics · 2019Review
- Systematic evaluation of cancer-specific genetic risk score for 11 types of cancer in The Cancer Genome Atlas and Electronic Medical Records and Genomics cohorts.Cancer medicine · 2019Article
- INDEX-db: The Indian Exome Reference Database (Phase I).Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Scaling read aligners to hundreds of threads on general-purpose processors.Bioinformatics (Oxford, England) · 2019Article
- A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined.
resultsSouth Indian populations are known to have a complex population structure and are an example of a major population group that lacks adequate reference panels. To test the performance of extremely low-coverage WGS (EXL-WGS) in populations with a complex history and to provide a reference resource for South Indian populations, we performed EXL-WGS on 185 South Indian individuals from eight populations to ~1.6x coverage. Using two variant discovery pipelines, SNPTools and GATK, we generated a consensus call set that has ~90% sensitivity for identifying common variants (minor allele frequency ≥ 10%). Imputation further improves the sensitivity of our call set. In addition, we obtained high-coverage for the whole mitochondrial genome to infer the maternal lineage evolutionary history of the Indian samples.
conclusionsOverall, we demonstrate that EXL-WGS with imputation can be a valuable study design for variant discovery with a dramatically lower cost than standard WGS, even in populations with a complex history and without available reference data. In addition, the South Indian EXL-WGS data generated in this study will provide a valuable resource for future Indian genomic studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.