SAGE

SAGE aggregates whole-genome and exome sequencing data from South Asian populations to produce a unified variant compendium for allele-frequency, carrier-rate, and disease-variant analyses, and was developed by the CSIR Institute of Genomics and Integrative Biology.

Key Features:

• Dataset aggregation: Consolidates six distinct whole-genome and exome datasets comprising 1,213 human genomes and exomes from South Asian populations.
• Variant compendium: Produces a comprehensive catalog containing over 154 million genetic variants, including approximately 69 million novel variants.
• Systematic annotation: Performs systematic annotation of variants to support interpretation and downstream analyses.
• Allele-frequency and carrier-rate estimation: Provides allele-frequency and carrier-rate information relevant to rare genetic diseases in South Asian populations.
• Pharmacogenetics and variant prioritization: Enables pharmacogenetic analyses and prioritization/discovery of disease-associated variants.
• Integration into public databases: Integrates annotated variant data into public databases for broader research use.
• Population-specific disease insights: Identifies subsets of variants with high prevalence in population-specific diseases such as retinitis pigmentosa.
• Curated provenance: Curated and assembled by the CSIR Institute of Genomics and Integrative Biology.

Scientific Applications:

• Genetic epidemiology: Estimating allele frequencies and carrier rates to inform population-level disease burden analyses in South Asia.
• Rare disease research: Prioritizing and discovering variants implicated in rare genetic diseases within South Asian cohorts.
• Pharmacogenetics: Assessing variant distributions relevant to drug response and pharmacogenetic marker discovery.
• Population-specific disease studies: Investigating genetic contributors to diseases with regional prevalence, exemplified by analyses of retinitis pigmentosa.
• Precision/personalized medicine: Informing variant interpretation and clinical decision-making tailored to South Asian genetic backgrounds.

Methodology:

Consolidation of six whole-genome and exome datasets (1,213 genomes/exomes), systematic annotation of variants, compilation into a compendium of over 154 million variants including ~69 million novel variants, and integration of annotated variants into public databases.