Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

BMC Genomics
Navin RustagiJinchuan Xing

Abstract

The 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. South 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 a...Continue Reading

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Jul 19, 2018·Bioinformatics·Ben LangmeadRone Charles
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Methods Mentioned

BETA
genotyping
PCA
exome sequencing
Human Genome Sequencing
PCR

Software Mentioned

Mercury Pipeline
BWA
EIGENSTRAT
STITCH
1000G
EXL
GATK
VariantRecalibrator
PLINK
Genome Analysis Tool Kit ( GATK

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