]. The IndiGenomes dataset serves as one of the starting points for deriving Indian population-specific genotypic prevalence estimates in context of various rare genetic disease conditions.
In this study, we utilised the IndiGenomes dataset to discover the genetic spectrum underlying cardiac channelopathies in self-declared healthy Indian individuals. Analysis of 1029 personal genomes revealed 440 nonsynonymous and 30 high confidence pLoF variants. Although copy number variations and other structural genomic variants can also be important genetic players for cardiac channelopathies, we limited our analysis to nonsynonymous variants and loss of function variants.
Patient cohort WES: Whole-exome sequencing libraries were prepared from the fragmented DNA samples using Illumina TruSeq DNA or Nextera exome kit as instructed by the manufacturer . The pooled libraries were sequenced on the Illumina sequencing platform generating paired-end reads. The IndiGenomes dataset was generated exclusively on Novaseq6000 platform in 6 months whereas the exome sequencing dataset from the patient cohort was generated over a time period of 5 years using both HiSeq2500 and NovaSeq6000 platforms.IndiGen WGS: Alignment, post-processing and default quality filtered variant calling was performed on the Illumina DRAGEN v3.4 Bio-IT platform using GRCh38 as a human reference genome. The joint variant calling was performed using Sentieon.
Patient cohort WES: Alignment, post-processing and default quality filtered variant calling was performed on the Illumina DRAGEN v3.4 Bio-IT platform using GRCh38 as a human reference genome. The variants were systematically annotated using ANNOVAR.The variant positions were based on the build GRCh38/hg38 of human genome assembly and were annotated using ANNOVAR [
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