India’s Genetic Map

Context: India’s Genetic Mapping Study Uncovers Deep Ancestry and Hidden Disease Risks

A groundbreaking study published in Cell has provided the most comprehensive genomic map of India to date. Researchers sequenced the genomes of 2,762 individuals from 23 States and Union Territories, representing a wide range of caste, tribal, linguistic, and geographic diversity.

Key Findings:

1. Ancestral Origins

• Single out-of-Africa migration (~50,000 years ago) forms the major ancestry of present-day Indians.

• Earlier archaeological evidence of humans in India suggests that those populations left no genetic trace.

• Indian ancestry is modeled as a blend of:

  • Ancient Ancestral South Indians (AASI) – indigenous hunter-gatherers.

  • Iranian-related Neolithic farmers – linked to Sarazm (modern-day Tajikistan).

  • Eurasian Steppe pastoralists – arrived ~2000 BCE, associated with Indo-European languages.

2. East and Northeast Indian Ancestry

• These regions, and parts of Central India, show East Asian-related ancestry (up to 5% in Bengal), likely arriving after 520 CE or earlier through rice farming.

3. Population Structure and Genetic Isolation

• India’s endogamous marriage practices (within-caste/community) led to strong founder effects.

• South Indians show 2–9 times more homozygosity than Europeans/East Asians—raising the risk of recessive genetic diseases.

• Every individual had at least one genetic relative in the study—indicating tight genetic clustering.

4. Disease Risks and Undocumented Variants

• Over 2.6 crore previously undocumented genetic variants were discovered.

  • 1.6 lakh are protein-altering and absent in global databases.

  • 7% are linked to conditions like:

    • Thalassemia

    • Congenital deafness

    • Cystic fibrosis

    • Metabolic disorders

• A pathogenic BCHE variant (causing severe anesthetic reactions) was found enriched in Telangana.

5. Interbreeding with Archaic Humans

• Indians carry up to 1.5% Neanderthal and Denisovan DNA, including the widest range of Neanderthal sequences globally.

• This diversity may be due to multiple migrations + caste-based endogamy, fixing certain archaic sequences within communities.

• Neanderthal DNA is enriched in immune genes, including a segment on chromosome 3 associated with severe COVID-19—especially common in East and Northeast India.

• Denisovan variants appear in:

  • MHC region (key to infection response)

  • TRIM and BTNL2 genes, involved in antiviral immunity.

6. Neglect of Indian Populations in Genomic Research

• The study emphasizes how global genetic databases underrepresent Indian variation, weakening:

  • Scientific discovery

  • Risk prediction accuracy

  • Precision medicine

To make medicine inclusive and effective, India’s genetic diversity must be prioritized in both global research and localised healthcare strategies. The study reveals not only India’s rich genetic ancestry but also urgent public health implications of underrepresentation in genomic science.