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Peer-reviewedCC BY 4.0NPJ Parkinson's Disease

Whole-genome sequencing of 197 cases with Parkinson’s disease reveals novel pathogenic variants in the Indian population

  • Hiba Ali1
  • Banashree Mondal1
  • Andie Pinto1
  • Camellia Sarkar1
  • Bikram Kumar Panda2
  • Khader Valli Rupanagudi1
  • Vikram V. Holla3
  • Tarunya Nagaraj3
  • Shubha GS Bhat3
  • Shweta Prasad3
  • Mahima Bhardwaj3
  • Pooja Mailankody3
7 more authors
  • Rohan R. Mahale3
  • Nitish Kamble3
  • Ravi Yadav3
  • Pramod Kumar Pal3
  • Albert Stezin1
  • Latha Diwakar1
  • Shweta Ramdas1
  1. 1Centre for Brain Research (CBR), Indian Institute of Science, Bengaluru, India
  2. 2Computational and Data Science Department (CDS), Indian Institute of Science, Bengaluru, India
  3. 3National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
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Abstract

Most insights into the genetics of Parkinson’s disease (PD) arise from European cohorts, leaving the genomic diversity of India underexplored. To address this gap, we performed whole-genome sequencing of 197 Indian PD cases (106 with early-onset PD (EOPD) and 91 with late-onset PD (LOPD)), capturing SNVs, indels, splice, and structural variants. We identified pathogenic variants in 31 cases across seven PD-associated genes (GBA1, PRKN, PINK1, DJ1, SYNJ1, SNCA, and PLA2G6), giving a diagnostic rate of 27.6% in EOPD and 2.2% in LOPD. Seven of these variants were novel to Indian populations. GBA1 and PRKN were the most frequently mutated genes. Candidate genes with pathogenic variants were enriched in lysosomal pathways. Cases had significantly higher polygenic risk scores, supporting a polygenic contribution to PD risk. Our study establishes one of the first comprehensive sequencing-based resources for PD genetics in India, and underscores the need for large-scale genomic studies across diverse populations.

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Cite

BibTeXRIS
BibTeX
@article{ali2026wholegenome,
  title = {{Whole-genome sequencing of 197 cases with Parkinson’s disease reveals novel pathogenic variants in the Indian population}},
  author = {Hiba Ali and Banashree Mondal and Andie Pinto and Camellia Sarkar and Bikram Kumar Panda and Khader Valli Rupanagudi and Vikram V. Holla and Tarunya Nagaraj and Shubha GS Bhat and Shweta Prasad and Mahima Bhardwaj and Pooja Mailankody and Rohan R. Mahale and Nitish Kamble and Ravi Yadav and Pramod Kumar Pal and Albert Stezin and Latha Diwakar and Shweta Ramdas},
  journal = {NPJ Parkinson's Disease},
  year = {2026},
  month = jul,
  doi = {10.1038/s41531-026-01462-0},
  url = {https://doi.org/10.1038/s41531-026-01462-0},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Whole-genome sequencing of 197 cases with Parkinson’s disease reveals novel pathogenic variants in the Indian population
AU  - Hiba Ali
AU  - Banashree Mondal
AU  - Andie Pinto
AU  - Camellia Sarkar
AU  - Bikram Kumar Panda
AU  - Khader Valli Rupanagudi
AU  - Vikram V. Holla
AU  - Tarunya Nagaraj
AU  - Shubha GS Bhat
AU  - Shweta Prasad
AU  - Mahima Bhardwaj
AU  - Pooja Mailankody
AU  - Rohan R. Mahale
AU  - Nitish Kamble
AU  - Ravi Yadav
AU  - Pramod Kumar Pal
AU  - Albert Stezin
AU  - Latha Diwakar
AU  - Shweta Ramdas
PY  - 2026
DA  - 2026/07/06
JO  - NPJ Parkinson's Disease
DO  - 10.1038/s41531-026-01462-0
UR  - https://doi.org/10.1038/s41531-026-01462-0
AB  - Most insights into the genetics of Parkinson’s disease (PD) arise from European cohorts, leaving the genomic diversity of India underexplored. To address this gap, we performed whole-genome sequencing of 197 Indian PD cases (106 with early-onset PD (EOPD) and 91 with late-onset PD (LOPD)), capturing SNVs, indels, splice, and structural variants. We identified pathogenic variants in 31 cases across seven PD-associated genes (GBA1, PRKN, PINK1, DJ1, SYNJ1, SNCA, and PLA2G6), giving a diagnostic rate of 27.6% in EOPD and 2.2% in LOPD. Seven of these variants were novel to Indian populations. GBA1 and PRKN were the most frequently mutated genes. Candidate genes with pathogenic variants were enriched in lysosomal pathways. Cases had significantly higher polygenic risk scores, supporting a polygenic contribution to PD risk. Our study establishes one of the first comprehensive sequencing-based resources for PD genetics in India, and underscores the need for large-scale genomic studies across diverse populations.
SN  - 2373-8057
ER  -