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Whole genome variant analysis in three ethnically diverse Indians
Seema Malhotra1, Sayar Singh1, Soma Sarkar2
1Defence Institute of Physiology and Allied Sciences (DIPAS), Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India.
Genes & Genomics
|June 13, 2018
Summary
This study analyzes genomic variations in three diverse Indian populations, revealing significant genetic diversity and novel variations. The findings establish a baseline for understanding human genomic variation across India and Asia.
Area of Science:
- Genomics
- Population Genetics
- Human Genetic Variation
Background:
- India harbors a vast array of geographically, linguistically, and socially diverse ethnic populations.
- Understanding the genetic diversity within the Indian population is complex and challenging.
Purpose of the Study:
- To analyze genomic variations in three healthy Indian males from distinct geographical and linguistic regions.
- To investigate the extent of genetic diversity across different Indian populations.
- To create a baseline and comprehensive catalog of human genomic variation in India and Asia.
Main Methods:
- High-depth (approx. 30x) whole-genome sequencing using the Illumina Hiseq 2000 platform.
- Analysis of genomic data from individuals representing high-altitude (Ladakh), sub-mountainous (Kumaun), and sea-level (Telangana) regions.
- Comparison with the human reference genome to identify single nucleotide variations (SNVs).
Main Results:
- High-quality sequencing data with over 95% read alignment to the human reference genome.
- Identification of millions of single nucleotide variations (SNVs) across the three genomes (4.3M, 3.7M, 4.3M).
- A significant percentage of variants (17.3-18.2%) were unique to each genome, with numerous novel variations identified per individual.
Conclusions:
- The study highlights substantial genetic diversity within the Indian population.
- Identified novel variations contribute to a growing understanding of human genomic variation.
- The comprehensive catalog serves as a crucial resource for future genomic studies in India and Asia.
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