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Frequency spectrum of rare and clinically relevant markers in multi-ethnic Indian populations (ClinIndb): A resource for genomic medicine in India
  • +19
  • Ankita Narang,
  • Bharathram Uppilli,
  • Vivek Anand,
  • Salwa Naushin,
  • Arti Yadav,
  • Khushboo Singhal,
  • Uzma Shamim,
  • Pooja Sharma,
  • Sana Zahra,
  • Aradhana Mathur,
  • Malika Seth,
  • Shaista Parveen,
  • Archana Vats,
  • Sara Hillman,
  • Padma Dolma,
  • Binuja Varma,
  • Vandana Jain,
  • Trisutra Consortium,
  • Bhavana Parasher,
  • Shantanu Sengupta,
  • Mitali Mukerji,
  • Mohammed Faruq
Ankita Narang
CSIR Institute of Genomics & Integrative Biology
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Bharathram Uppilli
CSIR Institute of Genomics & Integrative Biology
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Vivek Anand
CSIR Institute of Genomics & Integrative Biology
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Salwa Naushin
CSIR Institute of Genomics & Integrative Biology
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Arti Yadav
CSIR Institute of Genomics & Integrative Biology
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Khushboo Singhal
CSIR Institute of Genomics & Integrative Biology
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Uzma Shamim
Institute of Genomics & Integrative Biology (IGIB)
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Pooja Sharma
CSIR Institute of Genomics & Integrative Biology
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Sana Zahra
CSIR Institute of Genomics & Integrative Biology
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Aradhana Mathur
CSIR Institute of Genomics & Integrative Biology
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Malika Seth
CSIR Institute of Genomics & Integrative Biology
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Shaista Parveen
CSIR Institute of Genomics & Integrative Biology
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Archana Vats
CSIR Institute of Genomics & Integrative Biology
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Sara Hillman
UCL Institute for Women’s Health 25 Grafton Way, London UK
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Padma Dolma
Sonam Norboo Memorial Hospital, Leh Ladakh
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Binuja Varma
CSIR Institute of Genomics & Integrative Biology
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Vandana Jain
All India Institute of Medical Sciences, New Delhi
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Trisutra Consortium
CSIR Institute of Genomics & Integrative Biology
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Bhavana Parasher
CSIR Institute of Genomics & Integrative Biology
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Shantanu Sengupta
CSIR Institute of Genomics & Integrative Biology
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Mitali Mukerji
Institute of genomics and integrative biology
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Mohammed Faruq
Institute of Genomics and Integrative Biology
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Abstract

Purpose:There have been concerted efforts towards cataloging rare and deleterious variants in different world population using high throughput genotyping and sequencing based methods. The Indian populations are underrepresented or its information w.r.t. clinically relevant variants are sparse in public datasets. The aim of this study was to estimate the burden of monogenic disease causing variants in Indian populations. Towards this, we have assessed the frequency profile of monogenic phenotype associated ClinVar variants. Methods: The study utilized genotype dataset (global-screening-array, Illumina) from 2795 individuals (multiple in-house genomics cohorts) representing diverse ethnic and geographically distinct Indian populations. Results: Of the analyzed variants from GSA, ~12% were found to be informative and were either not known earlier or underrepresented in public databases in terms of their frequencies. These variants were linked to disorders, viz. Inborn-errors of Metabolism, Monogenic-diabetes, hereditary cancers and various other hereditary conditions. We have also shown that our study cohort is genetically better representatives of Indian populations than its representation in1000 genome project (South-Asians). Conclusion: We have created a database, ClinIndb [(http://clinindb.igib.res.in) and (https://databases.lovd.nl/shared/variants?search_owned_by_=%3D%22Mohamed%20Faruq%22)], to help clinicians and researchers in diagnosis, counseling and development of appropriate genetic screening tools relevant to the Indian populations and Indians living abroad.

Peer review status:ACCEPTED

03 Apr 2020Submitted to Human Mutation
04 Apr 2020Submission Checks Completed
04 Apr 2020Assigned to Editor
16 Apr 2020Reviewer(s) Assigned
24 May 2020Review(s) Completed, Editorial Evaluation Pending
07 Jun 2020Editorial Decision: Revise Major
10 Jul 20201st Revision Received
11 Jul 2020Assigned to Editor
11 Jul 2020Submission Checks Completed
13 Jul 2020Reviewer(s) Assigned
21 Jul 2020Review(s) Completed, Editorial Evaluation Pending
04 Aug 2020Editorial Decision: Revise Minor
17 Aug 20202nd Revision Received
18 Aug 2020Assigned to Editor
18 Aug 2020Submission Checks Completed
18 Aug 2020Review(s) Completed, Editorial Evaluation Pending
28 Aug 2020Editorial Decision: Accept