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Sethi S, Mehta P, Andrabi W, Mitra K, Rajender S. SPEM1 Gene Mutation in a Case with Sperm Morphological Defects Leading to Male Infertility. Reprod Sci 2024:10.1007/s43032-024-01612-w. [PMID: 38886283 DOI: 10.1007/s43032-024-01612-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/29/2024] [Indexed: 06/20/2024]
Abstract
The present study aimed at identifying the genetic mutation responsible for teratozoospermic infertility in a case with coiled sperm tails. A 33-year-old infertile male was diagnosed with teratozoospermic infertility, with sperm head in coiled (HIC) tail as the most common deformity. We employed whole exome sequencing to identify the genetic cause in this case. Exome sequencing data was filtered using the following criteria: MAF (< 0.003), ALFA project (< 0.001), 1000 Genomes (< 0.003), Granthem (> 50), Polyphen-2 (> 0.70), SIFT (< 0.03), and PhyloP (> = 0) scores. Shortlisted variants were looked in the in-house 29 exomes data available with us, and the variants that affected conserved amino acid residues or led to insertion/deletion or to protein-truncation with a Combined Annotation Dependent Depletion (CADD) score ≥ 10 were shortlisted. The variants thus populated were prioritized according to their roles in spermiogenesis. The study identified a heterozygous mutation c.826C > T (Arg276Trp) in the SPEM1 gene as a potential pathogenic variant that led to teratozoospermic infertility in the case under investigation. The mutation had a minor allele frequency of 0.00008176 in the gnomAd database and was absent in the Indian Genome Variations database. This is the first human study reporting a mutation in the SPEM1 gene as a cause of coiled sperm tails.
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Affiliation(s)
- Shruti Sethi
- Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Poonam Mehta
- Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - Kalyan Mitra
- Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Singh Rajender
- Central Drug Research Institute, Lucknow, Uttar Pradesh, India.
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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Suroliya V, Uppili B, Kumar M, Jha V, Srivastava AK, Faruq M. Identifying unstable CNG repeat loci in the human genome: a heuristic approach and implications for neurological disorders. Hum Genome Var 2024; 11:25. [PMID: 38871700 DOI: 10.1038/s41439-024-00281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
Tandem nucleotide repeat (TNR) expansions, particularly the CNG nucleotide configuration, are associated with a variety of neurodegenerative disorders. In this study, we aimed to identify novel unstable CNG repeat loci associated with the neurogenetic disorder spinocerebellar ataxia (SCA). Using a computational approach, 15,069 CNG repeat loci in the coding and noncoding regions of the human genome were identified. Based on the feature selection criteria (repeat length >10 and functional location of repeats), we selected 52 repeats for further analysis and evaluated the repeat length variability in 100 control subjects. A subset of 19 CNG loci observed to be highly variable in control subjects was selected for subsequent analysis in 100 individuals with SCA. The genes with these highly variable repeats also exhibited higher gene expression levels in the brain according to the tissue expression dataset (GTEx). No pathogenic expansion events were identified in patient samples, which is a limitation given the size of the patient group examined; however, these loci contain potential risk alleles for expandability. Recent studies have implicated GLS, RAI1, GIPC1, MED15, EP400, MEF2A, and CNKSR2 in neurological diseases, with GLS, GIPC1, MED15, RAI1, and MEF2A sharing the same repeat loci reported in this study. This finding validates the approach of evaluating repeat loci in different populations and their possible implications for human pathologies.
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Affiliation(s)
- Varun Suroliya
- Department of Neurology, All India Institute of Medical Sciences, Ansari Nagar, Delhi, 110020, India
| | - Bharathram Uppili
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy for Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Manish Kumar
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy for Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Vineet Jha
- Persistent LABS, Persistent Systems Ltd., Pune, Maharashtra, India
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, Ansari Nagar, Delhi, 110020, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
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Sadhukhan D, Biswas A, Mishra S, Chatterjee K, Maji D, Mitra P, Mukherjee P, Podder G, Ray BK, Biswas A, Banerjee TK, Hui SP, Deb I. Genetic Variations and Altered Blood mRNA Level of Circadian Genes and BDNF as Risk Factors of Post-Stroke Cognitive Impairment Among Eastern Indians. Neuromolecular Med 2023; 25:586-595. [PMID: 37814155 DOI: 10.1007/s12017-023-08761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
Post-stroke cognitive impairment (PSCI) is a clinical outcome in around 30% of post-stroke survivors. BDNF is a major gene in this regard. It is regulated by circadian rhythm. The circadian genes are correlated with stroke timings at molecular level. However, studies suggesting the role of these on susceptibility to PSCI are limited. We aim here to determine: (a) genetic risk variants in circadian clock genes, BDNF and (b) dysregulation in expression level of CLOCK, BMAL1, and BDNF that may be associated with PSCI. BDNF (rs6265G/A, rs56164415C/T), CLOCK (rs1801260T/C, rs4580704G/C), and CRY2 (rs2292912C/G) genes variants were genotyped among 119 post-stroke survivors and 292 controls from Eastern part of India. In addition, we analyzed their gene expression in Peripheral blood Mononuclear cells (PBMC) from 15 PSCI cases and 12 controls. The mRNA data for BDNF was further validated by its plasma level through ELISA (n = 38). Among the studied variants, only rs4580704/CLOCK showed an overall association with PSCI (P = 0.001) and lower Bengali Mini-Mental State Examination (BMSE) score. Its 'C' allele showed a correlation with attention deficiency. The language and memory impairments showed association with rs6265/BDNF, while the 'CC' genotype of rs2292912/CRY2 negatively influenced language and executive function. A significant decrease in gene expression for CLOCK and BDNF in PBMC (influenced by specific genotypes) of PSCI patients was observed than controls. Unlike Pro-BDNF, plasma-level mBDNF was also lower in them. Our results suggest the genetic variants in CLOCK, CRY2, and BDNF as risk factors for PSCI among eastern Indians. At the same time, a lowering expression of CLOCK and BDNF genes in PSCI patients than controls describes their transcriptional dysregulation as underlying mechanism for post-stroke cognitive decline.
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Affiliation(s)
- Dipanwita Sadhukhan
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India.
| | - Arindam Biswas
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Smriti Mishra
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Koustav Chatterjee
- Department of Neurology, Institute of Neurosciences Kolkata, Kolkata, India
| | - Daytee Maji
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Parama Mitra
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Priyanka Mukherjee
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Gargi Podder
- Institute of Post Graduate of Medical Education & Research and Bangur Institute of Neurosciences, Kolkata, India
| | - Biman Kanti Ray
- Institute of Post Graduate of Medical Education & Research and Bangur Institute of Neurosciences, Kolkata, India
| | - Atanu Biswas
- Institute of Post Graduate of Medical Education & Research and Bangur Institute of Neurosciences, Kolkata, India
| | - Tapas Kumar Banerjee
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Subhra Prakash Hui
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
| | - Ishani Deb
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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Yadav A, Srivastava S, Tyagi S, Krishna N, Katara P. In-silico mining to glean SNPs of pharmaco-clinical importance: an investigation with reference to the Indian populated SNPs. In Silico Pharmacol 2023; 11:17. [PMID: 37484779 PMCID: PMC10356698 DOI: 10.1007/s40203-023-00154-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Drugs pharmacology is defined by pharmacokinetics and pharmacodynamics and both of them are affected by genetic variability. Genetic variability varies from population to population, and sometimes even within the population, it exists. Single nucleotide polymorphisms (SNPs) are one of the major genetic variability factors which are found to be associated with the pharmacokinetics and pharmacodynamics process of a drug and are responsible for variable drug response and clinical phenotypes. Studies of SNPs can help to perform genome-wide association studies for their association with pharmacological and clinical events, at the same time; their information can direct genome-wide association studies for their use as biomarkers. With the aim to mine and characterize Indian populated SNPs of pharmacological and clinical importance. Two hundred six candidate SNPs belonging to 43 genes were retrieved from Indian Genome Variation Database. The distribution pattern of considered SNPs was observed against all five world super-populations (AFR, AMR, EAS, EUR, and SAS). Further, their annotation was done through SNP-nexus by considering Human genome reference builds - hg38, pharmacological and clinical information was supplemented by PharmGKB and ClinVar database. At last, to find out the association between SNPs linkage disequilibrium was observed in terms of r2. Overall, the study reported 53 pharmaco-clinical active SNPs and found 24 SNP-pairs as potential markers, and recommended their clinical and experimental validation. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00154-4.
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Affiliation(s)
- Anamika Yadav
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, 211002 India
| | - Shivani Srivastava
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, 211002 India
- Centre of Biotechnology, University of Allahabad, Prayagraj, 211002 India
| | - Shivani Tyagi
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, 211002 India
| | - Neelam Krishna
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, 211002 India
| | - Pramod Katara
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, 211002 India
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Gupta S, Mathur P, Mishra AK, Medicherla KM, Bandapalli OR, Suravajhala P. Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10050902. [PMID: 37238450 DOI: 10.3390/children10050902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India
| | - Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College and Hospital, JLN Marg, Jaipur 302004, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Department of Bioengineering, Birla Institute of Technology, Mesra, Jaipur Campus, 27-Malaviya Industrial, Area, Jaipur 302017, India
| | | | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita University, Vallikavu, Clappana P.O. Box 690525, Kerala, India
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Vaz M, Warrier P, Wai-Loon Ho C, Bull S. Respecting values and perspectives in biobanking and genetic research governance: Outcomes of a qualitative study in Bengaluru, India. Wellcome Open Res 2023; 7:78. [PMID: 37485294 PMCID: PMC10357076 DOI: 10.12688/wellcomeopenres.17628.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 07/25/2023] Open
Abstract
Background: The promise of biobanking and genetic research (BGR) in the context of translational research towards improving public health and personalised medicine has been recognised in India. Worldwide experience has shown that incorporating stakeholders' expectations and values into the governance of BGR is essential to address ethical aspects of BGR. This paper draws on engagement with various stakeholders in the South Indian city of Bengaluru to understand how incorporating people's values and beliefs can inform policy making decisions and strengthen BGR governance within India. Methods: We adopted a qualitative research approach and conducted six focus group discussions with civil society members and seven in-depth interviews with key informants in BGR, identified through a targeted web search and snowballing methods, until data saturation was reached. Data were thematically analysed to identify emergent patterns. Results: Specific themes relating to the ethics and governance of BGR emerged. Fears and uncertainty about future sample and data use, possibilities of discrimination and exploitation in the use of findings and the lack of comprehensive data protection policies in India along with expectations of enhanced contributor agency, control in future use of samples and data, benefit sharing, enhanced utility of samples, sustained BGR and public good, reflected tensions between different stakeholders' values and beliefs. Fair governance processes through an independent governance committee for biobanks and a system of ongoing engagement with stakeholders emerged as best practice towards building trust and respecting diversity of views and values. Conclusions: Ensuring public trust in BGR requires listening to stakeholders' voices, being open to counter narratives, and a commitment to long term engagement embedded in principles of participatory democracy. This is central to a 'people-centred governance framework' involving a negotiated middle ground and an equilibrium of governance which promotes social justice by being inclusive, transparent, equitable, and trustworthy.
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Affiliation(s)
- Manjulika Vaz
- Health and Humanities, St John's Research Institute, St John's Medical College, Bangalore, Karnataka, 560 034, India
| | - Prasanna Warrier
- Health and Humanities, St John's Research Institute, St John's Medical College, Bangalore, Karnataka, 560 034, India
| | - Calvin Wai-Loon Ho
- Department of Law and Centre for Medical Ethics and Law, The University of Hong Kong, Hong Kong SAR, China
| | - Susan Bull
- Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, OX3 7LF, UK
- Department of Psychological Medicine, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, 1142, New Zealand
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Chatterjee M, Saha S, Maitra S, Ray A, Sinha S, Mukhopadhyay K. Post-treatment symptomatic improvement of the eastern Indian ADHD probands is influenced by CYP2D6 genetic variations. Drug Metab Pers Ther 2023; 38:45-56. [PMID: 36169235 DOI: 10.1515/dmpt-2022-0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/10/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Symptomatic remediation from attention deficit hyperactivity disorder (ADHD)-associated traits is achieved by treatment with methylphenidate (MPH)/atomoxetine (ATX). We have analyzed the association of functional CYP2D6 variations, rs1065852, rs3892097, rs1135840, and rs1058164, with ADHD in the Indian subjects. METHODS Subjects were recruited following the Diagnostic and Statistical Manual for Mental Disorders. Trait scores were obtained from the Conner's Parents Rating Scale-Revised. After obtaining informed consent, blood was collected for DNA isolation, and genotyping was performed by PCR or TaqMan-based methods. Probands were treated with MPH or ATX based on age, symptoms, and drug availability. Treatment outcome was assessed using a structured questionnaire. Data obtained was analyzed to identify the association of CYP2D6 variations and the SLC6A3 rs28363170 with the treatment outcome. RESULTS The frequency of rs1135840 "G" and rs1065852 "G" was higher in the male ADHD probands. Bias in parental transmission (p=0.007) and association with higher trait scores were observed for rs1065852 "A". Independent influence of rs1065852 on ADHD was also observed. Probands carrying rs1065852 'GG', rs1135840 'CG', and rs28363170 10R exhibited significant symptomatic improvement with MPH, while probands with rs1135840 'CC' and rs28363170 9R showed improvement after ATX treatment. CONCLUSIONS ADHD probands having specific CYP2D6 genetic variations respond differentially to pharmaceutical intervention.
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Affiliation(s)
- Mahasweta Chatterjee
- Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, Kolkata, West Bengal, India
| | - Sharmistha Saha
- Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, Kolkata, West Bengal, India
| | | | - Anirban Ray
- Department of Psychiatry, Institute of Psychiatry, Kolkata, West Bengal, India
| | - Swagata Sinha
- Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, Kolkata, West Bengal, India
| | - Kanchan Mukhopadhyay
- Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, Kolkata, West Bengal, India
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Bose M, Giri A, Varma-Basil M. Comparative Genetic Association Analysis of Human Genetic Susceptibility to Pulmonary and Lymph Node Tuberculosis. Genes (Basel) 2023; 14:genes14010207. [PMID: 36672948 PMCID: PMC9859508 DOI: 10.3390/genes14010207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/08/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) manifests itself primarily in the lungs as pulmonary disease (PTB) and sometimes disseminates to other organs to cause extra-pulmonary TB, such as lymph node TB (LNTB). This study aimed to investigate the role of host genetic polymorphism in immunity related genes to find a genetic basis for such differences. METHODS Sixty-three, Single nucleotide polymorphisms (SNPs) in twenty-three, TB-immunity related genes including eleven innate immunity (SLCA11, VDR, TLR2, TLR4, TLR8, IRGM, P2RX7, LTA4H, SP110, DCSIGN and NOS2A) and twelve cytokine (TNFA, IFNG, IL2, Il12, IL18, IL1B, IL10, IL6, IL4, rs1794068, IL8 and TNFB) genes were investigated to find genetic associations in both PTB and LNTB as compared to healthy community controls. The serum cytokine levels were correlated for association with the genotypes. RESULTS PTB and LNTB showed differential genetic associations. The genetic variants in the cytokine genes (IFNG, IL12, IL4, TNFB and IL1RA and TLR2, 4 associated with PTB susceptibility and cytokine levels but not LNTB (p < 0.05). Similarly, genetic variants in LTA4H, P2RX7, DCSIGN and SP110 showed susceptibility to LNTB and not PTB. Pathway analysis showed abundance of cytokine related variants for PTB and apoptosis related variants for LNTB. CONCLUSIONS PTB and LNTB outcomes of TB infection have a genetic component and should be considered for any future functional studies or studies on susceptibility to pulmonary and extra-pulmonary TB.
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Affiliation(s)
- Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India
- Correspondence: (A.); (M.B.)
| | - Astha Giri
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India
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Aggarwal M, Garg NM, Agrawal A, Sardana V. Lung Function Reference Equations for Indian Ethnic Groups Based on a Handheld Forced Oscillation Device for Age 9-19 Years. Indian J Pediatr 2023; 90:61-68. [PMID: 35713768 DOI: 10.1007/s12098-022-04176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 01/25/2022] [Indexed: 01/10/2023]
Abstract
OBJECTIVE To develop regression equations to predict forced oscillation technique (FOT) parameters in Indian children and adolescents. METHODS Lung function was assessed in a multigeographic cohort of residential school children using a portable FOT-based device (PulmoScan) and spirometry. FOT measurements were performed in 1497 study participants, aged 9-19 y, from 8 Indian districts. Bland-Altman analysis was performed for additional 32 adult subjects to compare the results of PulmoScan to a standard IOS device in an outpatient setting. Reference equations were developed for Rrs and Xrs from the data of healthy subjects with normal spirometry using multivariate regression model for Indo-European, Dravidian, and mixed ethnic groups. RESULTS X5 (bias = 0.02) showed a better agreement than resistance parameters (R5 bias = 0.75, R20 bias = -0.22) in IOS/PulmoScan comparison. Anthropometric variables (age, height, and weight) were positively correlated with reactance (X5) and negatively with resistance parameters (R5, R10, R15, and R20), with most associations being stronger in boys. Final regression model considered ethnicity as a key determinant along with anthropometry. CONCLUSION Multiethnic reference equations were developed for Indian children aged 9-19 y based on a novel handheld FOT device.
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Affiliation(s)
- Mohit Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Neerja Mittal Garg
- CSIR-Central Scientific Instruments Organization, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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OSTA as a screening tool to predict osteoporosis in Indian postmenopausal women - a nationwide study. Arch Osteoporos 2022; 17:121. [PMID: 36087221 DOI: 10.1007/s11657-022-01159-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/22/2022] [Indexed: 02/03/2023]
Abstract
This cross-sectional study done on 5356 postmenopausal women showed that OSTA may be used as a reliable screening tool for osteoporosis across different regions of India, a country known for its ethno-linguistic, cultural, and genetic diversity. BACKGROUND The gold standard for diagnosing osteoporosis is DXA (dual-energy X-ray absorptiometry) scan, and this is not widely available across India. OSTA (Osteoporosis Self-Assessment Tool for Asians) score predicts risk of osteoporosis and can be used as reference tool for DXA. At a cutoff of ≤ + 1, OSTA predicted femoral neck osteoporosis with a sensitivity of 88% in a previous study among south Indian postmenopausal women. This study was done to validate the OSTA score in postmenopausal women across India. METHODOLOGY A cross-sectional study in 5356 postmenopausal women from four regions of India namely south, east, north, and west. Bone mineral density (BMD) and trabecular bone score (TBS) were assessed by DXA. The performance of OSTA in predicting BMD and TBS was assessed using ROC curve. RESULTS The mean (SD) age was 61.6 (7.6) years. The performance of OSTA in predicting osteoporosis was fair (P < 0.001) with an AUC of 0.727 (95% CI 0.705-0.749) in the south, 0.693 (95% CI 0.664-0.723) in east India, 0.730 (95% CI 0.700-0.759) in the north, and 0.703 (95% CI 0.672-0.735) in the western region. At a cut-off below + 1.0, sensitivity was 76-84% and specificity was 45-53% in diagnosing osteoporosis at any site. In predicting degraded microarchitecture, the AUC was 0.500-0.600. CONCLUSION OSTA may be reliably used as a screening tool for women at high risk of osteoporosis across India and may circumvent the limited availability of DXA scanners across the country.
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Abbas T, Chaturvedi G, Prakrithi P, Pathak AK, Kutum R, Dakle P, Narang A, Manchanda V, Patil R, Aggarwal D, Girase B, Srivastava A, Kapoor M, Gupta I, Pandey R, Juvekar S, Dash D, Mukerji M, Prasher B. Whole Exome Sequencing in Healthy Individuals of Extreme Constitution Types Reveals Differential Disease Risk: A Novel Approach towards Predictive Medicine. J Pers Med 2022; 12:jpm12030489. [PMID: 35330488 PMCID: PMC8952204 DOI: 10.3390/jpm12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
Precision medicine aims to move from traditional reactive medicine to a system where risk groups can be identified before the disease occurs. However, phenotypic heterogeneity amongst the diseased and healthy poses a major challenge for identification markers for risk stratification and early actionable interventions. In Ayurveda, individuals are phenotypically stratified into seven constitution types based on multisystem phenotypes termed “Prakriti”. It enables the prediction of health and disease trajectories and the selection of health interventions. We hypothesize that exome sequencing in healthy individuals of phenotypically homogeneous Prakriti types might enable the identification of functional variations associated with the constitution types. Exomes of 144 healthy Prakriti stratified individuals and controls from two genetically homogeneous cohorts (north and western India) revealed differential risk for diseases/traits like metabolic disorders, liver diseases, and body and hematological measurements amongst healthy individuals. These SNPs differ significantly from the Indo-European background control as well. Amongst these we highlight novel SNPs rs304447 (IFIT5) and rs941590 (SERPINA10) that could explain differential trajectories for immune response, bleeding or thrombosis. Our method demonstrates the requirement of a relatively smaller sample size for a well powered study. This study highlights the potential of integrating a unique phenotyping approach for the identification of predictive markers and the at-risk population amongst the healthy.
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Affiliation(s)
- Tahseen Abbas
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Gaura Chaturvedi
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - P. Prakrithi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Ankit Kumar Pathak
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Rintu Kutum
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Pushkar Dakle
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Ankita Narang
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
| | - Vijeta Manchanda
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Dhiraj Aggarwal
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Bhushan Girase
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Ankita Srivastava
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA;
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India;
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India;
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Debasis Dash
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Mitali Mukerji
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Jodhpur 342037, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Bhavana Prasher
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Correspondence: (D.D.); (M.M.); (B.P.)
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12
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Vaz M, Warrier P, Wai-Loon Ho C, Bull S. Respecting values and perspectives in biobanking and genetic research governance: Outcomes of a qualitative study in Bengaluru, India. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17628.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The promise of biobanking and genetic research (BGR) in the context of translational research towards improving public health and personalised medicine has been recognised in India. Worldwide experience has shown that incorporating stakeholders’ expectations and values into the governance of BGR is essential to address ethical aspects of BGR. This paper draws on engagement with various stakeholders in the South Indian city of Bengaluru to understand how incorporating people’s values and beliefs can inform policy making decisions and strengthen BGR governance within India. Methods: We adopted a qualitative research approach and conducted six focus group discussions with civil society members and seven in-depth interviews with key informants in BGR, identified through a targeted web search and snowballing methods, until data saturation was reached. Data were thematically analysed to identify emergent patterns. Results: Specific themes relating to the ethics and governance of BGR emerged. Fears and uncertainty about future sample and data use, possibilities of discrimination and exploitation in the use of findings and the lack of comprehensive data protection policies in India along with expectations of enhanced contributor agency, control in future use of samples and data, benefit sharing, enhanced utility of samples, sustained BGR and public good, reflected tensions between different stakeholders’ values and beliefs. Fair governance processes through an independent governance committee for biobanks and a system of ongoing engagement with stakeholders emerged as best practice towards building trust and respecting diversity of views and values. Conclusions: Ensuring public trust in BGR requires listening to stakeholders’ voices, being open to counter narratives, and a commitment to long term engagement embedded in principles of participatory democracy. This is central to a ‘people-centred governance framework’ involving a negotiated middle ground and an equilibrium of governance which promotes social justice by being inclusive, transparent, equitable, and trustworthy.
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13
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Prakrithi P, Lakra P, Sundar D, Kapoor M, Mukerji M, Gupta I, The Indian Genome Variation Consortium. Genetic Risk Prediction of COVID-19 Susceptibility and Severity in the Indian Population. Front Genet 2021; 12:714185. [PMID: 34707636 PMCID: PMC8543005 DOI: 10.3389/fgene.2021.714185] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/08/2021] [Indexed: 01/09/2023] Open
Abstract
Host genetic variants can determine their susceptibility to COVID-19 infection and severity as noted in a recent Genome-wide Association Study (GWAS). Given the prominent genetic differences in Indian sub-populations as well as differential prevalence of COVID-19, here, we compute genetic risk scores in diverse Indian sub-populations that may predict differences in the severity of COVID-19 outcomes. We utilized the top 100 most significantly associated single-nucleotide polymorphisms (SNPs) from a GWAS by Pairo-Castineira et al. determining the genetic susceptibility to severe COVID-19 infection, to compute population-wise polygenic risk scores (PRS) for populations represented in the Indian Genome Variation Consortium (IGVC) database. Using a generalized linear model accounting for confounding variables, we found that median PRS was significantly associated (p < 2 x 10−16) with COVID-19 mortality in each district corresponding to the population studied and had the largest effect on mortality (regression coefficient = 10.25). As a control we repeated our analysis on randomly selected 100 non-associated SNPs several times and did not find significant association. Therefore, we conclude that genetic susceptibility may play a major role in determining the differences in COVID-19 outcomes and mortality across the Indian sub-continent. We suggest that combining PRS with other observed risk-factors in a Bayesian framework may provide a better prediction model for ascertaining high COVID-19 risk groups and to design more effective public health resource allocation and vaccine distribution schemes.
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Affiliation(s)
- P Prakrithi
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Priya Lakra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, United States
| | - Mitali Mukerji
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - The Indian Genome Variation Consortium
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.,Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, United States
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14
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Padh H. Sequencing and comparative genome analysis of three Indians. Mamm Genome 2021; 32:401-412. [PMID: 34086082 DOI: 10.1007/s00335-021-09882-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/26/2021] [Indexed: 11/27/2022]
Abstract
Remarkable advancement in DNA sequencing (NGS) technology has made personal genome analysis feasible and affordable. Here we present the whole genome sequencing and analysis of three individuals, two males and one female, from different parts of India. Comparison with the Reference Human Genome and the variant database showed a total of 4.0-4.85 million variants, primarily single nucleotide variants (SNVs), 350-600 K small insertions and deletions (INDELs), and previously unreported novel variants. The analysis of Y-chromosome and mitochondrial haplogroups revealed that the ancestors of the individual arrived on the subcontinent at very different times using distinctly different migration routes. Approximately, 500,000 novel SNPs and about 89,000 novel INDELs have been submitted to the NCBI as novel variants. PCA and Admix analysis revealed that the IHGP03, a Mizoram male from the Northeast region, is strikingly different from the other two Indian genomes. Collectively, the data suggest the complexity of the Indian population admix developed from several distinct waves of human migration over tens of thousands of years.
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Affiliation(s)
- Harish Padh
- Former Vice-Chancellor, Sardar Patel University, Vallabh Vidyanagar, Gujarat, 388120, India.
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15
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Kumar A, Chauhan G, Sharma S, Dabla S, Sylaja PN, Chaudhary N, Gupta S, Agrawal CS, Anand KS, Srivastava AK, Vibha D, Sagar R, Raj R, Maheshwari A, Vivekanandhan S, Kaul B, Raghavan S, Gorthi SP, Mohania D, Kaushik S, Yadav RK, Hazarika A, Sharma P, Prasad K. Association of SUMOylation Pathway Genes With Stroke in a Genome-Wide Association Study in India. Neurology 2021; 97:e345-e356. [PMID: 34031191 DOI: 10.1212/wnl.0000000000012258] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/21/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To undertake a genome-wide association study (GWAS) to identify genetic variants for stroke in an Indian population. METHODS In a hospital-based case-control study, 8 teaching hospitals in India recruited 4,088 participants, including 1,609 stroke cases. Imputed genetic variants were tested for association with stroke subtypes using both single-marker and gene-based tests. Association with vascular risk factors was performed with logistic regression. Various databases were searched for replication, functional annotation, and association with related traits. Status of candidate genes previously reported in the Indian population was also checked. RESULTS Associations of vascular risk factors with stroke were similar to previous reports and show modifiable risk factors such as hypertension, smoking, and alcohol consumption as having the highest effect. Single-marker-based association revealed 2 loci for cardioembolic stroke (1p21 and 16q24), 2 for small vessel disease stroke (3p26 and 16p13), and 4 for hemorrhagic stroke (3q24, 5q33, 6q13, and 19q13) at p < 5 × 10-8. The index single nucleotide polymorphism of 1p21 is an expression quantitative trait locus (p lowest = 1.74 × 10-58) for RWDD3 involved in SUMOylation and is associated with platelet distribution width (1.15 × 10-9) and 18-carbon fatty acid metabolism (p = 7.36 × 10-12). In gene-based analysis, we identified 3 genes (SLC17A2, FAM73A, and OR52L1) at p < 2.7 × 10-6. Eleven of 32 candidate gene loci studied in an Indian population replicated (p < 0.05), and 21 of 32 loci identified through previous GWAS replicated according to directionality of effect. CONCLUSIONS This GWAS of stroke in an Indian population identified novel loci and replicated previously known loci. Genetic variants in the SUMOylation pathway, which has been implicated in brain ischemia, were identified for association with stroke.
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Affiliation(s)
- Amit Kumar
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Ganesh Chauhan
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Shriram Sharma
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Surekha Dabla
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - P N Sylaja
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Neera Chaudhary
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Salil Gupta
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Chandra Sekhar Agrawal
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Kuljeet Singh Anand
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Achal Kumar Srivastava
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Deepti Vibha
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Ram Sagar
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Ritesh Raj
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Ankita Maheshwari
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Subbiah Vivekanandhan
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Bhavna Kaul
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Samudrala Raghavan
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Sankar Prasad Gorthi
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Dheeraj Mohania
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Samander Kaushik
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Rohtas Kanwar Yadav
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Anjali Hazarika
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Pankaj Sharma
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India
| | - Kameshwar Prasad
- From the Department of Neurology (A.K., A.K.S., D.V., R.S., R.R., A.M., K.P.), Department of Neurobiochemisty (S.V.), Dr. R. P. Centre for Ophthalmic Sciences (D.M.), and Cardio-Neuro Centre (A.H.), All India Institute of Medical Sciences, New Delhi; Centre for Brain Research (G.C.), Indian Institute of Science, Bangalore; Department of Neurology (S.S.), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya; Department of Neurology (S.D.), Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana; Department of Neurology (P.N.S.), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kerala; Department of Neurology (N.C., B.K., S.R.), Vardhman Mahavir Medical College and Safdarjung Hospital; Department of Neurology (S.G., S.P.G.), Army Research and Referral Hospital; Department of Neurology (C.S.A.), Sir Ganga Ram Hospital; Ram Manohar Lohia Hospital (K.S.A.); Department of Biotechnology (S.K.), Maharshi Dayanand University, Government of India, New Delhi; Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences (R.K.Y.), Rohtak, Haryana, India; and Institute of Cardiovascular Research Royal Holloway (P.S.), University of London, Imperial College London, UK. Amit Kumar, Kameshwar Prasad, and Ganesh Chauhan are currently at Rajendra Institute of Medical Sciences, Ranchi, India.
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Bose A, Platt DE, Parida L, Drineas P, Paschou P. Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India. Mol Biol Evol 2021; 38:1809-1819. [PMID: 33481022 PMCID: PMC8097304 DOI: 10.1093/molbev/msaa321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.
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Affiliation(s)
- Aritra Bose
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Daniel E Platt
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Laxmi Parida
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Petros Drineas
- Computer Science Department, Purdue University, West Lafayette, IN, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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Kausthubham N, Shukla A, Gupta N, Bhavani GS, Kulshrestha S, Das Bhowmik A, Moirangthem A, Bijarnia-Mahay S, Kabra M, Puri RD, Mandal K, Verma IC, Bielas SL, Phadke SR, Dalal A, Girisha KM. A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians. Hum Mutat 2021; 42:e15-e61. [PMID: 33502066 PMCID: PMC10052794 DOI: 10.1002/humu.24172] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 12/16/2022]
Abstract
Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.
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Affiliation(s)
- Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gandham S Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Aneek Das Bhowmik
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,ASPIRE (Diagnostics Facility), CSIR-Centre for Cellular & Molecular Biology, CCMB Annexe II, Hyderabad, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna D Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin Dalal
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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18
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Pant AB. The Implementation of the Three Rs in Regulatory Toxicity and Biosafety Assessment: The Indian Perspective. Altern Lab Anim 2021; 48:234-251. [PMID: 33523713 DOI: 10.1177/0261192920986811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Animal models have long served as a basis for scientific experimentation, biomedical research, drug development and testing, disease modelling and toxicity studies, as they are widely thought to provide meaningful, human-relevant predictions. However, many of these systems are resource intensive and time-consuming, have low predictive value and are associated with great social and ethical dilemmas. Often drugs appear to be effective and safe in these classical animal models, but later prove to be ineffective and/or unsafe in clinical trials. These issues have paved the way for a paradigm shift from the use of in vivo approaches, toward the 'science of alternatives'. This has fuelled several research and regulatory initiatives, including the ban on the testing of cosmetics on animals. The new paradigm has been shifted toward increasing the relevance of the models for human predictivity and translational efficacy, and this has resulted in the recent development of many new methodologies, from 3-D bio-organoids to bioengineered 'human-on-a-chip' models. These improvements have the potential to significantly advance medical research globally. This paper offers a stance on the existing strategies and practices that utilise alternatives to animals, and outlines progress on the incorporation of these models into basic and applied research and education, specifically in India. It also seeks to provide a strategic roadmap to streamline the future directions for the country's policy changes and investments. This strategic roadmap could be a useful resource to guide research institutions, industries, regulatory agencies, contract research organisations and other stakeholders in transitioning toward modern approaches to safety and risk assessment that could replace or reduce the use of animals without compromising the safety of humans or the environment.
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Affiliation(s)
- Aditya B Pant
- System Toxicology and Health Risk Assessment Group, 538266Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, India
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19
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Kanakan A, Mishra N, Srinivasa Vasudevan J, Sahni S, Khan A, Sharma S, Pandey R. Threading the Pieces Together: Integrative Perspective on SARS-CoV-2. Pathogens 2020; 9:E912. [PMID: 33158051 PMCID: PMC7694192 DOI: 10.3390/pathogens9110912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has challenged the research community globally to innovate, interact, and integrate findings across hierarchies. Research on SARS-CoV-2 has produced an abundance of data spanning multiple parallels, including clinical data, SARS-CoV-2 genome architecture, host response captured through transcriptome and genetic variants, microbial co-infections (metagenome), and comorbidities. Disease phenotypes in the case of COVID-19 present an intriguing complexity that includes a broad range of symptomatic to asymptomatic individuals, further compounded by a vast heterogeneity within the spectrum of clinical symptoms displayed by the symptomatic individuals. The clinical outcome is further modulated by the presence of comorbid conditions at the point of infection. The COVID-19 pandemic has produced an expansive wealth of literature touching many aspects of SARS-CoV-2 ranging from causal to outcome, predisposition to protective (possible), co-infection to comorbidity, and differential mortality globally. As challenges provide opportunities, the current pandemic's challenge has underscored the need and opportunity to work for an integrative approach that may be able to thread together the multiple variables. Through this review, we have made an effort towards bringing together information spanning across different domains to facilitate researchers globally in pursuit of their response to SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | | | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India; (A.K.); (N.M.); (J.S.V.); (S.S.); (A.K.); (S.S.)
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20
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Pemmasani SK, Raman R, Mohapatra R, Vidyasagar M, Acharya A. A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation. Front Genet 2020; 11:753. [PMID: 32793285 PMCID: PMC7387655 DOI: 10.3389/fgene.2020.00753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/24/2020] [Indexed: 11/13/2022] Open
Abstract
Today, genomic data holds great potential to improve healthcare strategies across various dimensions – be it disease prevention, enhanced diagnosis, or optimized treatment. The biggest hurdle faced by the medical and research community in India is the lack of genotype-phenotype correlations for Indians at a population-wide and an individual level. This leads to inefficient translation of genomic information during clinical decision making. Population-wide sequencing projects for Indian genomes help overcome hurdles and enable us to unearth and validate the genetic markers for different health conditions. Machine learning algorithms are essential to analyze huge amounts of genotype data in synergy with gene expression, demographic, clinical, and pathological data. Predictive models developed through these algorithms help in classifying the individuals into different risk groups, so that preventive measures and personalized therapies can be designed. They also help in identifying the impact of each genetic marker with the associated condition, from a clinical perspective. In India, genome sequencing technologies have now become more accessible to the general population. However, information on variants associated with several major diseases is not available in publicly-accessible databases. Creating a centralized database of variants facilitates early detection and mitigation of health risks in individuals. In this article, we discuss the challenges faced by genetic researchers and genomic testing facilities in India, in terms of dearth of public databases, people with knowledge on machine learning algorithms, computational resources and awareness in the medical community in interpreting genetic variants. Potential solutions to enhance genomic research in India, are also discussed.
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Affiliation(s)
| | - Rasika Raman
- Research and Development Division, Mapmygenome India Limited, Hyderabad, India
| | | | | | - Anuradha Acharya
- Research and Development Division, Mapmygenome India Limited, Hyderabad, India
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21
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Angural A, Spolia A, Mahajan A, Verma V, Sharma A, Kumar P, Dhar MK, Pandita KK, Rai E, Sharma S. Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India. Front Genet 2020; 11:415. [PMID: 32425985 PMCID: PMC7203485 DOI: 10.3389/fgene.2020.00415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the "Pandora's Box of genetic disorders." Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) - India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region's typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K - India.
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Affiliation(s)
- Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankit Mahajan
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Vijeshwar Verma
- Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankush Sharma
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu, India
| | | | - Kamal Kishore Pandita
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
- Independent Researcher, Health Clinic, Jammu, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
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22
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Sivasubbu S, Scaria V. Genomics of rare genetic diseases-experiences from India. Hum Genomics 2019; 14:52. [PMID: 31554517 PMCID: PMC6760067 DOI: 10.1186/s40246-019-0215-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Home to a culturally heterogeneous population, India is also a melting pot of genetic diversity. The population architecture characterized by multiple endogamous groups with specific marriage patterns, including the widely prevalent practice of consanguinity, not only makes the Indian population distinct from rest of the world but also provides a unique advantage and niche to understand genetic diseases. Centuries of genetic isolation of population groups have amplified the founder effects, contributing to high prevalence of recessive alleles, which translates into genetic diseases, including rare genetic diseases in India.Rare genetic diseases are becoming a public health concern in India because a large population size of close to a billion people would essentially translate to a huge disease burden for even the rarest of the rare diseases. Genomics-based approaches have been demonstrated to accelerate the diagnosis of rare genetic diseases and reduce the socio-economic burden. The Genomics for Understanding Rare Diseases: India Alliance Network (GUaRDIAN) stands for providing genomic solutions for rare diseases in India. The consortium aims to establish a unique collaborative framework in health care planning, implementation, and delivery in the specific area of rare genetic diseases. It is a nation-wide collaborative research initiative catering to rare diseases across multiple cohorts, with over 240 clinician/scientist collaborators across 70 major medical/research centers. Within the GUaRDIAN framework, clinicians refer rare disease patients, generate whole genome or exome datasets followed by computational analysis of the data for identifying the causal pathogenic variations. The outcomes of GUaRDIAN are being translated as community services through a suitable platform providing low-cost diagnostic assays in India. In addition to GUaRDIAN, several genomic investigations for diseased and healthy population are being undertaken in the country to solve the rare disease dilemma.In summary, rare diseases contribute to a significant disease burden in India. Genomics-based solutions can enable accelerated diagnosis and management of rare diseases. We discuss how a collaborative research initiative such as GUaRDIAN can provide a nation-wide framework to cater to the rare disease community of India.
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Affiliation(s)
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
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23
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Prasad G, Bandesh K, Giri AK, Kauser Y, Chanda P, Parekatt V, Mathur S, Madhu SV, Venkatesh P, Bhansali A, Marwaha RK, Basu A, Tandon N, Bharadwaj D. Genome-Wide Association Study of Metabolic Syndrome Reveals Primary Genetic Variants at CETP Locus in Indians. Biomolecules 2019; 9:E321. [PMID: 31366177 PMCID: PMC6723498 DOI: 10.3390/biom9080321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
Indians, a rapidly growing population, constitute vast genetic heterogeneity to that of Western population; however they have become a sedentary population in past decades due to rapid urbanization ensuing in the amplified prevalence of metabolic syndrome (MetS). We performed a genome-wide association study (GWAS) of MetS in 10,093 Indian individuals (6,617 MetS and 3,476 controls) of Indo-European origin, that belong to our previous biorepository of The Indian Diabetes Consortium (INDICO). The study was conducted in two stages-discovery phase (N = 2,158) and replication phase (N = 7,935). We discovered two variants within/near the CETP gene-rs1800775 and rs3816117-associated with MetS at genome-wide significance level during replication phase in Indians. Additional CETP loci rs7205804, rs1532624, rs3764261, rs247617, and rs173539 also cropped up as modest signals in Indians. Haplotype association analysis revealed GCCCAGC as the strongest haplotype within the CETP locus constituting all seven CETP signals. In combined analysis, we perceived a novel and functionally relevant sub-GWAS significant locus-rs16890462 in the vicinity of SFRP1 gene. Overlaying gene regulatory data from ENCODE database revealed that single nucleotide polymorphism (SNP) rs16890462 resides in repressive chromatin in human subcutaneous adipose tissue as characterized by the enrichment of H3K27me3 and CTCF marks (repressive gene marks) and diminished H3K36me3 marks (activation gene marks). The variant displayed active DNA methylation marks in adipose tissue, suggesting its likely regulatory activity. Further, the variant also disrupts a potential binding site of a key transcription factor, NRF2, which is known for involvement in obesity and metabolic syndrome.
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Affiliation(s)
- Gauri Prasad
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi 110020, India
| | - Khushdeep Bandesh
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi 110020, India
| | - Anil K Giri
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi 110020, India
| | - Yasmeen Kauser
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi 110020, India
| | - Prakriti Chanda
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vaisak Parekatt
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sandeep Mathur
- Department of Endocrinology, S.M.S. Medical College, Jaipur, Rajasthan 302004, India
| | - Sri Venkata Madhu
- Division of Endocrinology, University College of Medical Sciences, New Delhi 110095, India
| | - Pradeep Venkatesh
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Anil Bhansali
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh 160012, India
| | - Raman K Marwaha
- Department of Endocrinology, International Life Sciences Institute, New Delhi 110024, India
| | - Analabha Basu
- National Institute of Bio Medical Genomics, Netaji Subhas Sanatorium (Tuberculosis Hospital), Kalyani 741251, West Bengal, India
| | - Nikhil Tandon
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi 110020, India.
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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24
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Ahmed P H, V V, More RP, Viswanath B, Jain S, Rao MS, Mukherjee O. INDEX-db: The Indian Exome Reference Database (Phase I). J Comput Biol 2019; 26:225-234. [PMID: 30615482 PMCID: PMC6441288 DOI: 10.1089/cmb.2018.0199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.
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Affiliation(s)
- Husayn Ahmed P
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
| | - Vidhya V
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Ravi Prabhakar More
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Mahendra S. Rao
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Odity Mukherjee
- Address correspondence to: Dr. Odity Mukherjee, Investigator & Chief Technologist, Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bellary Road, Bengaluru–560065, Karnataka, India
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25
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Hetu M, Koutouki K, Joly Y. Genomics for All: International Open Science Genomics Projects and Capacity Building in the Developing World. Front Genet 2019; 10:95. [PMID: 30828348 PMCID: PMC6384230 DOI: 10.3389/fgene.2019.00095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
Genomic medicine applications have the potential to considerably improve health care in developing countries in the coming years. However, if developing countries do not improve their capacity for research and development (R&D) in the field, they might be left out of the genomics revolution. Large-scale and widely accessible databases for storing and analyzing genomic data are crucial tools for the advancement of genomic medicine. Building developing countries' capacity in genomics is accordingly closely linked to their involvement in international human genomics research initiatives. The purpose of this paper is to conduct a pilot study on the impact of international open science genomics projects on capacity building in R&D in developing countries. Using indicators we developed in previous work to measure the performance of international open science genomics projects, we analyse the policies and practices of four key projects in the field: the International HapMap Project, the Human Heredity and Health in Africa Initiative, the Malaria Genomic Epidemiology Network and the Structural Genomics Consortium. The results show that these projects play an important role in genomics capacity building in developing countries, but play a more limited role with regard to the potential redistribution of the benefits of research to the populations of these countries. We further suggest concrete initiatives that could facilitate the involvement of researchers from developing countries in the international genomics research community and accelerate capacity building in the developing world.
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Affiliation(s)
- Martin Hetu
- Department of Human Genetics, Faculty of Medicine, Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | | | - Yann Joly
- Department of Human Genetics, Faculty of Medicine, Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
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26
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Natarajan S, Chowdappa S, Yellapurkar S, Boaz K, Pai M, Sriranjani DS, Nayak V. Permanent tooth emergence patterns in Dakshina Kannada region, India: an analysis of polymorphisms. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Sivadas A, Scaria V. Population-scale genomics-Enabling precision public health. ADVANCES IN GENETICS 2018; 103:119-161. [PMID: 30904093 DOI: 10.1016/bs.adgen.2018.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The current excitement for affordable genomics technologies and national precision medicine initiatives marks a turning point in worldwide healthcare practices. The last decade of global population sequencing efforts has defined the enormous extent of genetic variation in the human population resulting in insights into differential disease burden and response to therapy within and between populations. Population-scale pharmacogenomics helps to provide insights into the choice of optimal therapies and an opportunity to estimate, predict and minimize adverse events. Such an approach can potentially empower countries to formulate national selection and dosing policies for therapeutic agents thereby promoting public health with precision. We review the breadth and depth of worldwide population-scale sequencing efforts and its implications for the implementation of clinical pharmacogenetics toward making precision medicine a reality.
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Affiliation(s)
- Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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28
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Evaluation of FGF 20 variants for susceptibility to Parkinson’s disease in Eastern Indians. Neurosci Lett 2018; 675:68-73. [DOI: 10.1016/j.neulet.2018.03.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 11/18/2022]
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29
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Recapitulation of Ayurveda constitution types by machine learning of phenotypic traits. PLoS One 2017; 12:e0185380. [PMID: 28981546 PMCID: PMC5628820 DOI: 10.1371/journal.pone.0185380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/10/2017] [Indexed: 01/19/2023] Open
Abstract
In Ayurveda system of medicine individuals are classified into seven constitution types, “Prakriti”, for assessing disease susceptibility and drug responsiveness. Prakriti evaluation involves clinical examination including questions about physiological and behavioural traits. A need was felt to develop models for accurately predicting Prakriti classes that have been shown to exhibit molecular differences. The present study was carried out on data of phenotypic attributes in 147 healthy individuals of three extreme Prakriti types, from a genetically homogeneous population of Western India. Unsupervised and supervised machine learning approaches were used to infer inherent structure of the data, and for feature selection and building classification models for Prakriti respectively. These models were validated in a North Indian population. Unsupervised clustering led to emergence of three natural clusters corresponding to three extreme Prakriti classes. The supervised modelling approaches could classify individuals, with distinct Prakriti types, in the training and validation sets. This study is the first to demonstrate that Prakriti types are distinct verifiable clusters within a multidimensional space of multiple interrelated phenotypic traits. It also provides a computational framework for predicting Prakriti classes from phenotypic attributes. This approach may be useful in precision medicine for stratification of endophenotypes in healthy and diseased populations.
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30
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Saw WY, Tantoso E, Begum H, Zhou L, Zou R, He C, Chan SL, Tan LWL, Wong LP, Xu W, Moong DKN, Lim Y, Li B, Pillai NE, Peterson TA, Bielawny T, Meikle PJ, Mundra PA, Lim WY, Luo M, Chia KS, Ong RTH, Brunham LR, Khor CC, Too HP, Soong R, Wenk MR, Little P, Teo YY. Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study. Nat Commun 2017; 8:653. [PMID: 28935855 PMCID: PMC5608948 DOI: 10.1038/s41467-017-00413-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/28/2017] [Indexed: 11/09/2022] Open
Abstract
The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups. Consistent patterns of correlations between lipid species also suggest the possibility of lipid tagging to simplify future lipidomics assays. The Singapore Integrative Omics Study is expected to allow the characterization of intra-omic and inter-omic correlations within and across all three ethnic groups through a systems biology approach.The Singapore Genome Variation projects characterized the genetics of Singapore's Chinese, Malay, and Indian populations. The Singapore Integrative Omics Study introduced here goes further in providing multi-omic measurements in individuals from these populations, including genetic, transcriptome, lipidome, and lifestyle data, and will facilitate the study of common diseases in Asian communities.
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Affiliation(s)
- Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore.,Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Erwin Tantoso
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Husna Begum
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Lihan Zhou
- MiRXES, Agency for Science, Technology and Research Singapore, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Ruiyang Zou
- MiRXES, Agency for Science, Technology and Research Singapore, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Cheng He
- MiRXES, Agency for Science, Technology and Research Singapore, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Sze Ling Chan
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research Singapore, 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Linda Wei-Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Lai-Ping Wong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Wenting Xu
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Yenly Lim
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Bowen Li
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Nisha Esakimuthu Pillai
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Trevor A Peterson
- Department of Medical Microbiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, Canada, R3E 0Z2.,National Microbiology Laboratory, 1015 Arlington St, Winnipeg, MB, Canada, R3E
| | - Tomasz Bielawny
- Department of Medical Microbiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, Canada, R3E 0Z2.,National Microbiology Laboratory, 1015 Arlington St, Winnipeg, MB, Canada, R3E
| | - Peter J Meikle
- Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21, 30 Flemington Road, Melbourne, VIC, 3010, Australia
| | - Piyushkumar A Mundra
- Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, Canada, R3E 0Z2.,National Microbiology Laboratory, 1015 Arlington St, Winnipeg, MB, Canada, R3E
| | - Kee-Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Liam R Brunham
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research Singapore, 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research Singapore, 60 Biopolis St, Singapore, 138672, Singapore.,Singapore Eye Research Institute, 20 College Road, Singapore, 169856, Singapore
| | - Heng Phon Too
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,Molecular Engineering of Biological and Chemical System/Chemical Pharmaceutical Engineering, Singapore-Massachusetts Institute of Technology Alliance, 4 Engineering Drive 3, Singapore, 117576, Singapore.,Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research, Singapore), 20 Biopolis Way, Singapore, 138668, Singapore
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Markus R Wenk
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543, Singapore
| | - Peter Little
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore. .,Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Genome Institute of Singapore, Agency for Science, Technology and Research Singapore, 60 Biopolis St, Singapore, 138672, Singapore. .,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Department of Statistics and Applied Probability, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore.
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Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy. Sci Rep 2017; 7:6733. [PMID: 28751670 PMCID: PMC5532257 DOI: 10.1038/s41598-017-06905-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/20/2017] [Indexed: 12/23/2022] Open
Abstract
Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.
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Sengupta D, Choudhury A, Basu A, Ramsay M. Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset. Genome Biol Evol 2016; 8:3460-3470. [PMID: 27797945 PMCID: PMC5203783 DOI: 10.1093/gbe/evw244] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India.
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Affiliation(s)
- Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, India
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa .,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Arvind P, Jayashree S, Jambunathan S, Nair J, Kakkar VV. Understanding gene expression in coronary artery disease through global profiling, network analysis and independent validation of key candidate genes. J Genet 2016; 94:601-10. [PMID: 26690514 DOI: 10.1007/s12041-015-0548-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molecular mechanism underlying the patho-physiology of coronary artery disease (CAD) is complex. We used global expression profiling combined with analysis of biological network to dissect out potential genes and pathways associated with CAD in a representative case-control Asian Indian cohort. We initially performed blood transcriptomics profiling in 20 subjects, including 10 CAD patients and 10 healthy controls on the Agilent microarray platform. Data was analysed with Gene Spring Gx12.5, followed by network analysis using David v 6.7 and Reactome databases. The most significant differentially expressed genes from microarray were independently validated by real time PCR in 97 cases and 97 controls. A total of 190 gene transcripts showed significant differential expression (fold change>2,P<0.05) between the cases and the controls of which 142 genes were upregulated and 48 genes were downregulated. Genes associated with inflammation, immune response, cell regulation, proliferation and apoptotic pathways were enriched, while inflammatory and immune response genes were displayed as hubs in the network, having greater number of interactions with the neighbouring genes. Expression of EGR1/2/3, IL8, CXCL1, PTGS2, CD69, IFNG, FASLG, CCL4, CDC42, DDX58, NFKBID and NR4A2 genes were independently validated; EGR1/2/3 and IL8 showed >8-fold higher expression in cases relative to the controls implying their important role in CAD. In conclusion, global gene expression profiling combined with network analysis can help in identifying key genes and pathways for CAD.
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Affiliation(s)
- Prathima Arvind
- Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bengaluru 560 099, India.
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Mookherjee S, Banerjee D, Chakraborty S, Mukhopadhyay I, Sen A, Ray K. Evaluation of the IL1 Gene Cluster Single Nucleotide Polymorphisms in Primary Open-Angle Glaucoma Pathogenesis. Genet Test Mol Biomarkers 2016; 20:633-636. [PMID: 27533638 DOI: 10.1089/gtmb.2015.0344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
AIMS Dysregulation of the immune system has previously been implicated in glaucoma pathogenesis. In this study, we investigated the potential association of SNPs in the IL1 gene cluster, consisting of nine genes, with primary open-angle glaucoma (POAG) cases. These cases presented with low to normal intraocular pressures (<20 mmHg), and are referred to as non-high tension glaucoma (non-HTG) cases. MATERIALS AND METHODS In this biphasic study, the discovery phase was conducted with 198 non-HTG cases and 112 controls from eastern India. A total of 68 single nucleotide polymorphisms (SNPs) spanning the IL1 nine-gene cluster region were genotyped using the MALDI-TOF based Sequenom platform. SNPs, which were found to be significantly associated with non-HTG cases in the first phase of the study, were further genotyped by Sanger sequencing in a replication cohort consisting of 194 non-HTG cases and 242 controls. RESULTS In the discovery phase, two nonsynonymous SNPs (rs3811046 and rs3811047), located in the IL1F7 gene and in an intergenic region, respectively were found to be weakly associated with non-HTG cases. However, the association was not sustained in the replication cohort. CONCLUSION Our study did not reveal any reproducible association of SNPs in the IL1 gene cluster with POAG.
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Affiliation(s)
- Suddhasil Mookherjee
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
| | - Deblina Banerjee
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
| | - Subhadip Chakraborty
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
| | | | | | - Kunal Ray
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
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Abstract
Coronary artery disease (CAD) has emerged as a major cause of morbidity and mortality worldwide. Recent findings on the role of genetic factors in the aetiopathology of CAD have implicated novel genes and variants in addition to those involved in lipid and lipoprotein metabolism. However, our present knowledge is limited due to lack of clarity on their exact identity and the quantum of impact on disease susceptibility, and incident risk. It is a matter of great interest to understand the role of genetic factors in ethnic populations that have a strong underlying predisposition to CAD such as the South Asian populations, particularly among Asian Indians living in India and abroad. Although, a number of isolated studies do implicate certain gene polymorphisms towards enhanced disease susceptibility, the available data remains scanty and inconclusive as they have not been validated in large, prospective cohorts. The present review aims to consolidate the available literature on the genetics of CAD in Asian Indians and seeks to provide insights on the concerns that need to be addressed in future studies to generate information having clinical value.
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Upadhyay P, Gardi N, Desai S, Sahoo B, Singh A, Togar T, Iyer P, Prasad R, Chandrani P, Gupta S, Dutt A. TMC-SNPdb: an Indian germline variant database derived from whole exome sequences. Database (Oxford) 2016; 2016:baw104. [PMID: 27402678 PMCID: PMC4940432 DOI: 10.1093/database/baw104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/08/2016] [Indexed: 02/05/2023]
Abstract
Cancer is predominantly a somatic disease. A mutant allele present in a cancer cell genome is considered somatic when it's absent in the paired normal genome along with public SNP databases. The current build of dbSNP, the most comprehensive public SNP database, however inadequately represents several non-European Caucasian populations, posing a limitation in cancer genomic analyses of data from these populations. We present the T: ata M: emorial C: entre-SNP D: ata B: ase (TMC-SNPdb), as the first open source, flexible, upgradable, and freely available SNP database (accessible through dbSNP build 149 and ANNOVAR)-representing 114 309 unique germline variants-generated from whole exome data of 62 normal samples derived from cancer patients of Indian origin. The TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface with the ability to deplete additional Indian population specific SNPs over and above dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb could deplete 42, 33 and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. In addition to dbSNP build 149 and ANNOVAR, the TMC-SNPdb along with the subtraction tool is available for download in the public domain at the following:Database URL: http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html.
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Affiliation(s)
- Pawan Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Nilesh Gardi
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Sanket Desai
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Bikram Sahoo
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Ankita Singh
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Trupti Togar
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Prajish Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Ratnam Prasad
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Pratik Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, Maharashtra 410012, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
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Abstract
CONTEXT India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses. OBJECTIVE AND METHODS Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications. RESULTS The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country. CONCLUSION This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations.
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Affiliation(s)
- Sarabjit S Mastana
- Human Genomics Lab, Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
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Aggarwal S, Gheware A, Agrawal A, Ghosh S, Prasher B, Mukerji M. Combined genetic effects of EGLN1 and VWF modulate thrombotic outcome in hypoxia revealed by Ayurgenomics approach. J Transl Med 2015; 13:184. [PMID: 26047609 PMCID: PMC4457985 DOI: 10.1186/s12967-015-0542-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Extreme constitution "Prakriti" types of Ayurveda exhibit systemic physiological attributes. Our earlier genetic study has revealed differences in EGLN1, key modulator of hypoxia axis between Prakriti types. This was associated with differences in high altitude adaptation and susceptibility to high altitude pulmonary edema (HAPE). In this study we investigate other molecular differences that contribute to systemic attributes of Prakriti that would be relevant in predictive marker discovery. METHODS Genotyping of 96 individuals of the earlier cohort was carried out in a panel of 2,800 common genic SNPs represented in Indian Genomic Variation Consortium (IGVC) panel from 24 diverse populations. Frequency distribution patterns of Prakriti differentiating variations (FDR correction P < 0.05) was studied in IGVC and 55 global populations (HGDP-CEPH) panels. Genotypic interactions between VWF, identified from the present analysis, and EGLN1 was analyzed using multinomial logistic regression in Prakriti and Indian populations from contrasting altitudes. Spearman's Rank correlation was used to study this genotypic interaction with respect to altitude in HGDP-CEPH panel. Validation of functional link between EGLN1 and VWF was carried out in a mouse model using chemical inhibition and siRNA studies. RESULT Significant differences in allele frequencies were observed in seven genes (SPTA1, VWF, OLR1, UCP2, OR6K3, LEPR, and OR10Z1) after FDR correction (P < 0.05). A non synonymous variation (C/T, rs1063856) associated with thrombosis/bleeding susceptibility respectively, differed significantly between Kapha (C-allele) and Pitta (T-allele) constitution types. A combination of derived EGLN1 allele (HAPE associated) and ancestral VWF allele (thrombosis associated) was significantly high in Kapha group compared to Pitta (p < 10(-5)). The combination of risk-associated Kapha alleles was nearly absent in natives of high altitude. Inhibition of EGLN1 using (DHB) and an EGLN1 specific siRNA in a mouse model lead to a marked increase in vWF levels as well as pro-thrombotic phenotype viz. reduced bleeding time and enhanced platelet count and activation. CONCLUSION We demonstrate for the first time a genetic link between EGLN1 and VWF in a constitution specific manner which could modulate thrombosis/bleeding susceptibility and outcomes of hypoxia. Integration of Prakriti in population stratification may help assemble common variations in key physiological axes that confers differences in disease occurrence and patho-phenotypic outcomes.
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Affiliation(s)
- Shilpi Aggarwal
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, India.
| | - Atish Gheware
- CSIR's Ayurgenomics Unit-TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110 020, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
| | - Anurag Agrawal
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
| | | | - Bhavana Prasher
- CSIR's Ayurgenomics Unit-TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110 020, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
| | - Mitali Mukerji
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, India. .,CSIR's Ayurgenomics Unit-TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110 020, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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Datta De D, Roychoudhury S. To be or not to be: The host genetic factor and beyond in Helicobacter pylori mediated gastro-duodenal diseases. World J Gastroenterol 2015; 21:2883-2895. [PMID: 25780285 PMCID: PMC4356907 DOI: 10.3748/wjg.v21.i10.2883] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/28/2014] [Accepted: 01/08/2015] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) have long been associated with a spectrum of disease outcomes in the gastro-duodenal system. Heterogeneity in bacterial virulence factors or strains is not enough to explain the divergent disease phenotypes manifested by the infection. This review focuses on host genetic factors that are involved during infection and eventually are thought to influence the disease phenotype. We have summarized the different host genes that have been investigated for association studies in H. pylori mediated duodenal ulcer or gastric cancer. We discuss that as the bacteria co-evolved with the host; these host gene also show much variation across different ethnic population. We illustrate the allelic distribution of interleukin-1B, across different population which is one of the most popular candidate gene studied with respect to H. pylori infections. Further, we highlight that several polymorphisms in the pathway gene can by itself or collectively affect the acid secretion pathway axis (gastrin: somatostatin) thereby resulting in a spectrum of disease phenotype
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Jajodia A, Kaur H, Kumari K, Gupta M, Baghel R, Srivastava A, Sood M, Chadda RK, Jain S, Kukreti R. Evidence for schizophrenia susceptibility alleles in the Indian population: An association of neurodevelopmental genes in case-control and familial samples. Schizophr Res 2015; 162:112-7. [PMID: 25579050 DOI: 10.1016/j.schres.2014.12.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/26/2014] [Accepted: 12/21/2014] [Indexed: 02/05/2023]
Abstract
Schizophrenia is a severe psychiatric disorder with lifetime prevalence of ~1% worldwide. A genotyping study was conducted using a custom panel of Illumina 1536 SNPs in 840 schizophrenia cases and 876 controls (351 patients and 385 controls from North India; and 436 patients, 401 controls and 143 familial samples with 53 probands containing 37 complete and 16 incomplete trios from South India). Meta-analysis of this population of Indo-European and Dravidian ancestry identified three strongly associated variants with schizophrenia: STT3A (rs548181, p=1.47×10(-5)), NRG1 (rs17603876, p=8.66×10(-5)) and GRM7 (rs3864075, p=4.06×10(-3)). Finally, a meta-analysis was conducted comparing our data with data from the Schizophrenia Psychiatric Genome-Wide Association Study Consortium (PGC-SCZ) that supported rs548181 (p=1.39×10(-7)). In addition, combined analysis of sporadic case-control association and a transmission disequilibrium test in familial samples from South Indian population identified three associations: rs1062613 (p=3.12×10(-3)), a functional promoter variant of HTR3A; rs6710782 (p=3.50×10(-3)), an intronic variant of ERBB4; and rs891903 (p=1.05×10(-2)), an intronic variant of EBF1. The results support the risk variants observed in the earlier published work and suggest a potential role of neurodevelopmental genes in the schizophrenia pathogenesis.
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Affiliation(s)
- Ajay Jajodia
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Harpreet Kaur
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Kalpana Kumari
- Department of Psychiatry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Meenal Gupta
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Ruchi Baghel
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Ankit Srivastava
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Mamta Sood
- Department of Psychiatry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rakesh Kumar Chadda
- Department of Psychiatry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sanjeev Jain
- Molecular Genetic Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Hosur Road, Bengaluru 560029, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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Goel A, Patnaik V, Puri N. Lip morphometry in 600 North Indian adults: a data base study for sexual dimorphism. MEDICINE, SCIENCE, AND THE LAW 2015; 55:16-21. [PMID: 24644225 DOI: 10.1177/0025802414524382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The study comprised lip morphometry of 600 North Indian adults (300 males and 300 females). The aim of the study was to create base data of various linear and vertical measurements of the upper and lower lips and width of the mouth. This standard may serve as a guideline for sexual dimorphism as well as for restoration or enhancement of esthetic and plastic surgery for the lips in the north Indian population, which will enable the surgeon to offer a better cosmetic result. Prior informed written consent from all the subjects was obtained. The exclusion and inclusion criteria for the subjects were predefined. The analysis shows the sexual dimorphism in most parameters of lips being greater in males. The results were compared with the available data for north white Americans, Malays, Malaysian Indians, Italians, western Indians and Caucasians. In the population under study, the measurements differ in all dimensions with Malays, Italians and Caucasians and show resemblance to the Malaysian Indians. Knowledge of the proportion between the upper and lower lips helps in surgical correction of the region. This study highlights the applied significance of observations of the present study to forensic, namely racial and sex dimorphic, criteria of identification.
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Affiliation(s)
- Archana Goel
- Department of Anatomy, MMMCH Kumarhati Solan, India
| | - Vvg Patnaik
- Department of Anatomy, MMIMSR Mullana (Ambala), India
| | - Nidhi Puri
- Department of Anatomy, MMIMSR Mullana (Ambala), India
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LIG1 polymorphisms: the Indian scenario. J Genet 2014; 93:459-69. [PMID: 25189241 DOI: 10.1007/s12041-014-0415-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Elucidation of the genetic diversity and relatedness of the subpopulations of India may provide a unique resource for future analysis of genetic association of several critical community-specific complex diseases.We performed a comprehensive exploration of single nucleotide polymorphisms (SNPs) within the gene DNA ligase 1 (LIG1) among a multiethnic panel of Indian subpopulations representative of the ethnic, linguistic and geographical diversity of India using a two-stage design involving DNA resequencing-based SNP discovery followed by SNP validation using sequenom-based genotyping. Thirty SNPs were identified in LIG1 gene using DNA resequencing including three promoter SNPs and one coding SNP. Following SNP validation, the SNPs rs20580/C19008A and rs3730862/C8804T were found to have the most widespread prevalence with noticeable variations in minor allele frequencies both between the Indian subpopulation groups and also from those reported on other major world populations. Subsequently, SNPs found in Indian subpopulations were analysed using bioinformatics-based approaches and compared with SNP data available on major world populations. Further, we also performed genotype-phenotype association analysis of LIG1 SNPs with publicly available data on LIG1 mRNA expression in HapMap samples. Results showed polymorphisms in LIG1 affect its expression and may therefore change its function. Our results stress upon the uniqueness of the Indian population with respect to the worldwide scenario and suggest that any epidemiological study undertaken on the global population should take this distinctiveness in consideration and avoid making generalized conclusions.
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Giri AK, Khan NM, Grover S, Kaur I, Basu A, Tandon N, Scaria V, Consortium IGV, Kukreti R, Brahmachari SK, Bharadwaj D. Genetic epidemiology of pharmacogenetic variations in CYP2C9, CYP4F2 and VKORC1 genes associated with warfarin dosage in the Indian population. Pharmacogenomics 2014; 15:1337-54. [DOI: 10.2217/pgs.14.88] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Warfarin, a widely used anticoagulant, exhibits large interindividual variability in dose requirements. CYP2C9 and VKORC1 polymorphisms in various ethnic groups have been extensively studied as genetic markers associated with variable drug response. However, allele frequencies of these variants have not been assessed in major ethnic groups in the Indian population. Materials & methods: To study the functional variants known to affect warfarin dosing, we reanalyzed genotype microarray datasets generated as a part of genome-wide association studies as well as data from the Indian Genome Variation database. We examined data from 2680 individuals across 24 ethnically diverse Indian subpopulations. Results: Allelic distribution of VKORC1 (-1639G>A) showed a greater degree of variation across Indian subpopulations, with frequencies as low as 6.5% in an out-group subpopulation to >70% in Tibeto–Burmans. Risk allele frequency of CYP4F2*3 (V433M) was higher in north Indians (0.30–0.44), as compared with other world populations, such as African–American (0.12), Caucasian (0.34) and Hispanic (0.23). TheVKORC1 variant (-1639A) was shown to be prevalent amongst Tibeto–Burmans, whereas CYP2C9 (R144C, I359L) and CYP4F2 (V433M) variants were observed in considerable variability amongst Indo–Europeans. The frequency of CYP2C9*3 (I359L) in north Indians was found to be higher than in most Asian populations. Furthermore, geographical distribution patterns of these variants in north India showed an increased trend of warfarin extensive metabolizers from the Himalayan to Gangetic region. Combined allele frequency (CYP2C9*3 and CYP4F2*3) data suggest that poor metabolizers varied in the range of 0.38–1.85% in Indo–Europeans. Conclusion: Based on genotypic distribution, the majority of the Indian subpopulation might require higher doses for stable anticoagulation, whereas careful assessment is required for Tibeto–Burmans who are expected to have intermediate dose requirement. This is the largest global genetic epidemiological study examining variants associated with warfarin that could potentially be valuable to clinicians in optimizing dosage strategies. Original submitted 4 April 2014; Revision submitted 23 May 2014
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Affiliation(s)
- Anil K Giri
- CSIR-Institute of Genomics & Integrative Biology, Delhi, 110 020, India
- Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhavan, 2 Rafi Marg Delhi, 110 001, India
| | - Nazir M Khan
- CSIR-Institute of Genomics & Integrative Biology, Delhi, 110 020, India
| | - Sandeep Grover
- CSIR-Institute of Genomics & Integrative Biology, Delhi, 110 020, India
| | - Ismeet Kaur
- CSIR-Institute of Genomics & Integrative Biology, Delhi, 110 020, India
| | - Analabha Basu
- National Institute of BioMedical Genomics, Kalyani, 741 251, India
| | - Nikhil Tandon
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Vinod Scaria
- Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhavan, 2 Rafi Marg Delhi, 110 001, India
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi, 110 020, India
| | | | - Ritushree Kukreti
- CSIR-Institute of Genomics & Integrative Biology, Delhi, 110 020, India
| | | | - Dwaipayan Bharadwaj
- CSIR-Institute of Genomics & Integrative Biology, Delhi, 110 020, India
- Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhavan, 2 Rafi Marg Delhi, 110 001, India
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Juyal G, Mondal M, Luisi P, Laayouni H, Sood A, Midha V, Heutink P, Bertranpetit J, Thelma BK, Casals F. Population and genomic lessons from genetic analysis of two Indian populations. Hum Genet 2014; 133:1273-87. [PMID: 24980708 DOI: 10.1007/s00439-014-1462-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/05/2014] [Indexed: 12/25/2022]
Abstract
Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.
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Affiliation(s)
- Garima Juyal
- Department of Genetics, University of Delhi South Campus, New Delhi, 110 021, India
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Dey A, Bhowmik K, Chatterjee A, Chakrabarty PB, Sinha S, Mukhopadhyay K. Down Syndrome Related Muscle Hypotonia: Association with COL6A3 Functional SNP rs2270669. Front Genet 2013; 4:57. [PMID: 23626599 PMCID: PMC3631610 DOI: 10.3389/fgene.2013.00057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/02/2013] [Indexed: 12/03/2022] Open
Abstract
Down syndrome (DS), the principal cause for intellectual disability, is also associated with hormonal, immunological, and gastrointestinal abnormalities. Muscle hypotonia (MH) and congenital heart diseases (CHD) are also frequently observed. Collagen molecules are essential components for maintaining muscle integrity and are formed by the assembly of three chains, alpha 1–3. The type VI collagen is crucial for cardiac as well as skeletal muscles. The COL α1 (VI) and α2 (VI) chains are encoded by genes located at the 21st chromosome and are expected to have higher dosage in individuals with DS. The α 3 (VI) chain is encoded by the COL6A3 located at the chromosome 2. We hypothesized that apart from COL6A1 and COL6A2, COL6A3 may also have some role in the MH of subjects with DS. To find out the relevance of COL6A3 in DS associated MH and CHD, we genotyped two SNPs in COL6A3, rs2270669 and rs2270668, in individuals with DS. Subjects with DS were recruited based on the Diagnostic and Statistical Manual for Mental Disorders-IV and having trisomy of the 21st chromosome. Parents of individuals with DS and ethnically matched controls were enrolled for comparison. Informed written consent was obtained for participation. Peripheral blood was used for isolation of genomic DNA. Target genetic loci were studied by DNA sequence analysis. Data obtained was subjected to population – as well as family-based statistical analysis. rs2270668 was found to be non-polymorphic in the studied population. rs2270669 showed significant association of the “C” allele and “CC” genotype with DS probands having MH (P = 0.02). Computational analysis showed that rs2270669 may induce structural and functional alterations in the COL α3 (VI). Interaction of COLα3 (VI) with different proteins, crucial for muscle integrity, was also noticed by computational methods. This pioneering study on COL6A3 with DS related MH thus indicates that rs2270669 “C” could be considered as a risk factor for DS related MH.
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Affiliation(s)
- Arpita Dey
- Manovikas Biomedical Research and Diagnostic Centre Kolkata, West Bengal, India
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Tabassum R, Chauhan G, Dwivedi OP, Mahajan A, Jaiswal A, Kaur I, Bandesh K, Singh T, Mathai BJ, Pandey Y, Chidambaram M, Sharma A, Chavali S, Sengupta S, Ramakrishnan L, Venkatesh P, Aggarwal SK, Ghosh S, Prabhakaran D, Srinath RK, Saxena M, Banerjee M, Mathur S, Bhansali A, Shah VN, Madhu SV, Marwaha RK, Basu A, Scaria V, McCarthy MI, Venkatesan R, Mohan V, Tandon N, Bharadwaj D. Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21. Diabetes 2013; 62:977-86. [PMID: 23209189 PMCID: PMC3581193 DOI: 10.2337/db12-0406] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Indians undergoing socioeconomic and lifestyle transitions will be maximally affected by epidemic of type 2 diabetes (T2D). We conducted a two-stage genome-wide association study of T2D in 12,535 Indians, a less explored but high-risk group. We identified a new type 2 diabetes-associated locus at 2q21, with the lead signal being rs6723108 (odds ratio 1.31; P = 3.32 × 10⁻⁹). Imputation analysis refined the signal to rs998451 (odds ratio 1.56; P = 6.3 × 10⁻¹²) within TMEM163 that encodes a probable vesicular transporter in nerve terminals. TMEM163 variants also showed association with decreased fasting plasma insulin and homeostatic model assessment of insulin resistance, indicating a plausible effect through impaired insulin secretion. The 2q21 region also harbors RAB3GAP1 and ACMSD; those are involved in neurologic disorders. Forty-nine of 56 previously reported signals showed consistency in direction with similar effect sizes in Indians and previous studies, and 25 of them were also associated (P < 0.05). Known loci and the newly identified 2q21 locus altogether explained 7.65% variance in the risk of T2D in Indians. Our study suggests that common susceptibility variants for T2D are largely the same across populations, but also reveals a population-specific locus and provides further insights into genetic architecture and etiology of T2D.
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Affiliation(s)
- Rubina Tabassum
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Ganesh Chauhan
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Om Prakash Dwivedi
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anubha Mahajan
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Alok Jaiswal
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Ismeet Kaur
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Khushdeep Bandesh
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Tejbir Singh
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Benan John Mathai
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Yogesh Pandey
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Manickam Chidambaram
- Department of Molecular Genetics, Madras Diabetes Research Foundation-Indian Council of Medical Research Advanced Centre for Genomics of Diabetes, Chennai, India
| | - Amitabh Sharma
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Sreenivas Chavali
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Lakshmi Ramakrishnan
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Pradeep Venkatesh
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay K. Aggarwal
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Ghosh
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | | | - Madhukar Saxena
- Department of Zoology, University of Lucknow, Lucknow, India
| | | | - Sandeep Mathur
- Department of Endocrinology, SMS Medical College and Hospital, Jaipur, India
| | - Anil Bhansali
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, India
| | - Viral N. Shah
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, India
| | - Sri Venkata Madhu
- Division of Endocrinology, University College of Medical Sciences, Delhi, India
| | - Raman K. Marwaha
- Department of Endocrinology and Thyroid Research, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
| | - Analabha Basu
- National Institute of BioMedical Genomics, Kalyani, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | | | | | - Radha Venkatesan
- Department of Molecular Genetics, Madras Diabetes Research Foundation-Indian Council of Medical Research Advanced Centre for Genomics of Diabetes, Chennai, India
| | - Viswanathan Mohan
- Department of Molecular Genetics, Madras Diabetes Research Foundation-Indian Council of Medical Research Advanced Centre for Genomics of Diabetes, Chennai, India
| | - Nikhil Tandon
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
- Corresponding authors: Dwaipayan Bharadwaj, , and Nikhil Tandon,
| | - Dwaipayan Bharadwaj
- Genomics and Molecular Medicine Unit, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
- Corresponding authors: Dwaipayan Bharadwaj, , and Nikhil Tandon,
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Zaumsegel D, Rothschild MA, Schneider PM. A 21 marker insertion deletion polymorphism panel to study biogeographic ancestry. Forensic Sci Int Genet 2013; 7:305-12. [PMID: 23352554 DOI: 10.1016/j.fsigen.2012.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/21/2012] [Accepted: 12/26/2012] [Indexed: 11/19/2022]
Abstract
Insertion/deletion polymorphisms have recently received increased interest in the forensic genetics community. This class of markers combines the advantageous genetic properties of single nucleotide polymorphisms (i.e., low mutation rate, genetic stability, and short amplicon size) with the technical advantage of short tandem repeat markers (simple detection by fluorescence-labelled PCR and capillary electrophoresis). For a large number of indel markers significant differences in allele frequencies between the major populations have been reported, making this class of markers suitable for the analysis of biogeographic ancestry. We have developed a multiplex PCR assay designed to establish the biogeographic ancestry of forensic DNA samples based on insertion/deletion polymorphisms. A panel of 21 short indels with allele frequency differences between three major population groups (European, African and Asian) was selected to be incorporated into a single-tube multiplex PCR assay. The assay is highly sensitive, requiring less than 0.5 ng of genomic DNA for successful typing. Due to the short fragment lengths below 200 bp, the assay is ideally suited for the typing of challenging forensic genetic case work samples. A population genetic study has been performed proving the performance of the assay in inferring the ancestral population of individuals. The chosen 21 markers are sufficient to distinguish between three major global population groups. Furthermore, the assay design leaves room for an extension in order to cover additional population groups.
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Affiliation(s)
- Daniel Zaumsegel
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Köln, Germany.
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Reddy DS. Citizens in the commons: blood and genetics in the making of the civic. CONTEMPORARY SOUTH ASIA 2013; 21:275-290. [PMID: 24478538 PMCID: PMC3902168 DOI: 10.1080/09584935.2013.826626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This essay is based on ethnographic fieldwork conducted with the Indian community in Houston, as part of a NIH/NHGRI-sponsored ethics study and sample collection initiative entitled 'Indian and Hindu Perspectives on Genetic Variation Research.' Taking a cue from my Indian interlocutors who largely support and readily respond to such initiatives on the grounds that they will undoubtedly serve 'humanity' and the common good, I explore notions of the commons that are created in the process of soliciting blood for genetic research. How does blood become the stuff of which a civic discourse is made? How do idealistic individual appeals to donate blood, ethics research protocols, open-source databases, debates on approaches to genetic research, patents and Intellectual Property regulations, markets and the nation-state itself variously engage, limit or further ideas of the common good? Moving much as my interlocutors do, between India and the United States, I explore the nature of the commons that is both imagined and pragmatically reckoned in both local and global diasporic contexts.
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Goswami R, Singh A, Gupta N, Rani R. Presence of strong association of the major histocompatibility complex (MHC) class I allele HLA-A*26:01 with idiopathic hypoparathyroidism. J Clin Endocrinol Metab 2012; 97:E1820-4. [PMID: 22723329 DOI: 10.1210/jc.2012-1328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT The pathogenesis of isolated hypoparathyroidism, also referred to as idiopathic hypoparathyroidism (IH), is not clear. There is a paucity of information related to the immunogenetic basis of the disease due to its rarity. A recurrent theme of several autoimmune disorders is aberrant antigen presentation. OBJECTIVE We investigated for the association of alleles of the human leukocyte antigen (HLA) class I and II loci with IH. PATIENTS AND CONTROLS A total of 134 patients with IH and 902 healthy controls from the same ethnic background participated in the study. RESULTS There was a significant increase of HLA class I alleles HLA-A*26:01 [P < 1.71 × 10(-34); odds ratio (OR) = 9.29; 95% confidence interval (CI) = 6.08-14.16] and HLA-B*08:01 (P < 8.19 × 10(-6); OR = 2.59; 95% CI = 1.63-4.04) in patients with IH compared to healthy controls. However, the association of A*26:01 was primary because B*08:01 was in linkage disequilibrium with A*26:01. Although the major histocompatibility complex (MHC) is very polymorphic, several alleles of HLA loci share key residues at anchor positions in the peptide binding pockets such that similar peptides may be presented by different MHC molecules encoded by the same locus. These allelic forms with similar anchoring amino acids have been clustered in supertypes. An analysis of HLA-A locus supertypes A01, A02, A03, and A04 revealed that supertype A01 was significantly increased (P < 9.18 × 10(-9); OR = 2.95) in IH compared to controls. However, this increase in the supertype A01 was contributed by A*26:01 because 68.7% of the A01 samples had A*26:01. Other alleles of the supertype did not show any significant differences. CONCLUSION The strong association of HLA-A*26:01 suggests an important role of MHC class I-mediated presentation of autoantigenic peptides to CD8(+) cytotoxic T cells in the pathogenesis of IH. These data provide evidence for the autoimmune etiology of IH akin to other autoimmune disorders like type 1 diabetes and rheumatoid arthritis.
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Affiliation(s)
- Ravinder Goswami
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi 110029, India
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Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S, Scaria V. Systematic analysis and functional annotation of variations in the genome of an Indian individual. Hum Mutat 2012; 33:1133-40. [PMID: 22461382 DOI: 10.1002/humu.22091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/05/2012] [Indexed: 01/02/2023]
Abstract
Whole genome sequencing of personal genomes has revealed a large repertoire of genomic variations and has provided a rich template for identification of common and rare variants in genomes in addition to understanding the genetic basis of diseases. The widespread application of personal genome sequencing in clinical settings for predictive and preventive medicine has been limited due to the lack of comprehensive computational analysis pipelines. We have used next-generation sequencing technology to sequence the whole genome of a self-declared healthy male of Indian origin. We have generated around 28X of the reference human genome with over 99% coverage. Analysis revealed over 3 million single nucleotide variations and about 490,000 small insertion-deletion events including several novel variants. Using this dataset as a template, we designed a comprehensive computational analysis pipeline for the systematic analysis and annotation of functionally relevant variants in the genome. This study follows a systematic and intuitive data analysis workflow to annotate genome variations and its potential functional effects. Moreover, we integrate predictive analysis of pharmacogenomic traits with emphasis on drugs for which pharmacogenomic testing has been recommended. This study thus provides the template for genome-scale analysis of personal genomes for personalized medicine.
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Affiliation(s)
- Ashok Patowary
- Genomics and Molecular Medicine, CSIR Institute of Genomics and IntegrativeBiology, Council of Scientific and Industrial Research, Delhi, India
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