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Manapurath R, Chowdhury R, Taneja S, Bhandari N, Strand TA. Epidemiology of overweight in under-five children in India: insights from National Family Health Survey. Br J Nutr 2024:1-9. [PMID: 39295437 DOI: 10.1017/s0007114524001582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Childhood overweight is not only an immediate health concern due to its implications but also significantly increases the risk of persistent obesity and consequently CVD in the future, posing a serious threat to public health. The objective of this study was to examine the trends and associated factors of childhood overweight in India, using nationally representative data from three rounds of the National Family Health Survey (NFHS). For the primary analysis, we used data from 199 375 children aged 0-59 months from fifth round of the NFHS (NFHS-5). Overweight was defined as BMI-for-age Z (BMI Z) score > +2 sd above the WHO growth standards median. We compared the prevalence estimates of childhood overweight with third round of the third round of NFHS and fourth round of the NFHS. Potential risk factors were identified through multiple logistic regression analyses. The prevalence of overweight increased from 1·9 % in third round of NFHS to 4·0 % in NFHS-5, a trend seen across most states and union territories, with the Northeast region showing the highest prevalence. The BMI Z-score distributions from the latest two surveys indicated that the increase in overweight was substantially larger than the decrease in underweight. The consistent upward trend in the prevalence across different demographic groups raises important public health concerns. While undernutrition rates have remained relatively stable, there has been a noticeable rise in the incidence of overweight during the same time frame. The increasing trend of overweight among children in India calls for immediate action.
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Affiliation(s)
- Rukman Manapurath
- Centre for International Health, University of Bergen, Bergen, Norway
- Nutrition, Society for Applied Studies, New Delhi, India
| | | | - Sunita Taneja
- Nutrition, Society for Applied Studies, New Delhi, India
| | - Nita Bhandari
- Nutrition, Society for Applied Studies, New Delhi, India
| | - Tor A Strand
- Centre for International Health, University of Bergen, Bergen, Norway
- Department of Research, Innlandet Hospital Trust, Lillehammer, Norway
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2
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Sheth J, Nair A, Sheth F, Ajagekar M, Dhondekar T, Panigrahi I, Bavdekar A, Nampoothiri S, Datar C, Gandhi A, Muranjan M, Kaur A, Desai M, Mistri M, Patel C, Naik P, Shah M, Godbole K, Kapoor S, Gupta N, Bijarnia-Mahay S, Kadam S, Solanki D, Desai S, Iyer A, Patel K, Patel H, Shah RC, Mehta S, Shah R, Bhavsar R, Shah J, Pandya M, Patel B, Shah S, Shah H, Shah S, Bajaj S, Shah S, Thaker N, Kalane U, Kamate M, Kn VR, Tayade N, Jagadeesan S, Jain D, Chandarana M, Singh J, Mehta S, Suresh B, Sheth H. Burden of rare genetic disorders in India: twenty-two years' experience of a tertiary centre. Orphanet J Rare Dis 2024; 19:295. [PMID: 39138584 PMCID: PMC11323464 DOI: 10.1186/s13023-024-03300-z] [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: 04/18/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Rare disorders comprise of ~ 7500 different conditions affecting multiple systems. Diagnosis of rare diseases is complex due to dearth of specialized medical professionals, testing labs and limited therapeutic options. There is scarcity of data on the prevalence of rare diseases in different populations. India being home to a large population comprising of 4600 population groups, of which several thousand are endogamous, is likely to have a high burden of rare diseases. The present study provides a retrospective overview of a cohort of patients with rare genetic diseases identified at a tertiary genetic test centre in India. RESULTS Overall, 3294 patients with 305 rare diseases were identified in the present study cohort. These were categorized into 14 disease groups based on the major organ/ organ system affected. Highest number of rare diseases (D = 149/305, 48.9%) were identified in the neuromuscular and neurodevelopmental (NMND) group followed by inborn errors of metabolism (IEM) (D = 47/305; 15.4%). Majority patients in the present cohort (N = 1992, 61%) were diagnosed under IEM group, of which Gaucher disease constituted maximum cases (N = 224, 11.2%). Under the NMND group, Duchenne muscular dystrophy (N = 291/885, 32.9%), trinucleotide repeat expansion disorders (N = 242/885; 27.3%) and spinal muscular atrophy (N = 141/885, 15.9%) were the most common. Majority cases of β-thalassemia (N = 120/149, 80.5%) and cystic fibrosis (N = 74/75, 98.7%) under the haematological and pulmonary groups were observed, respectively. Founder variants were identified for Tay-Sachs disease and mucopolysaccharidosis IVA diseases. Recurrent variants for Gaucher disease (GBA:c.1448T > C), β-thalassemia (HBB:c.92.+5G > C), non-syndromic hearing loss (GJB2:c.71G > A), albinism (TYR:c.832 C > T), congenital adrenal hyperplasia (CYP21A2:c.29-13 C > G) and progressive pseudo rheumatoid dysplasia (CCN6:c.298T > A) were observed in the present study. CONCLUSION The present retrospective study of rare disease patients diagnosed at a tertiary genetic test centre provides first insight into the distribution of rare genetic diseases across the country. This information will likely aid in drafting future health policies, including newborn screening programs, development of target specific panel for affordable diagnosis of rare diseases and eventually build a platform for devising novel treatment strategies for rare diseases.
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Affiliation(s)
- Jayesh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India.
| | - Aadhira Nair
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Frenny Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Manali Ajagekar
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | | | - Inusha Panigrahi
- Postgraduate Institute of Medical Education and Research, PGIMER, Chandigarh, India
| | | | | | - Chaitanya Datar
- Bharati Hospital and Research Centre, Dhankawadi, Pune, India
| | | | - Mamta Muranjan
- Department of Pediatrics, KEM Hospital, Parel, Mumbai, India
| | - Anupriya Kaur
- Postgraduate Institute of Medical Education and Research, PGIMER, Chandigarh, India
| | - Manisha Desai
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Mehul Mistri
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Chitra Patel
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Premal Naik
- Rainbow Super speciality Hospital, Ahmedabad, India
| | | | - Koumudi Godbole
- Deenanath Mangeshkar Hospital & Research Centre, Pune, India
| | - Seema Kapoor
- Division of Genetics & Metabolism Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sandeep Kadam
- Department of Pediatrics, K.E.M Hospital, Pune, India
| | | | - Soham Desai
- Shree Krishna Hospital, Karamsad, Anand, India
| | | | - Ketan Patel
- Himalaya Arcade, Homeopathy Clinic, Vastrapur, Ahmedabad, India
| | - Harsh Patel
- Zydus Hospital & Healthcare Research Pvt Ltd, Ahmedabad, India
| | - Raju C Shah
- Ankur Neonatal Hospital, Ashram Road, Ahmedabad, India
| | | | | | - Riddhi Bhavsar
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Jhanvi Shah
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Mili Pandya
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | | | | | - Heli Shah
- Ansa Clinic, S. G. Highway, Ahmedabad, India
| | - Shalin Shah
- Ansa Clinic, S. G. Highway, Ahmedabad, India
| | - Shruti Bajaj
- The Purple Gene Clinic, Simplex Khushaangan, SV Road, Malad West, Mumbai, India
| | | | | | - Umesh Kalane
- Deenanath Mangeshkar Hospital & Research Centre, Pune, India
| | | | - Vykunta Raju Kn
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Naresh Tayade
- Department of Paediatrics, Dr. Panjabrao Deshmukh Memorial Medical College, Amravati, India
| | - Sujatha Jagadeesan
- Department of Clinical Genetics & Genetic Counselling, Mediscan Systems, Chennai, India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Mitesh Chandarana
- Medisquare Superspeciality Hospital and Research Institute, Ahmedabad, India
| | - Jitendra Singh
- Neurology Clinic, Shivranjini Cross Road, Satellite, Ahmedabad, India
| | | | - Beena Suresh
- Department of Clinical Genetics & Genetic Counselling, Mediscan Systems, Chennai, India
| | - Harsh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India.
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Abu-Amara H, Zhao W, Li Z, Leung YY, Schellenberg GD, Wang LS, Moorjani P, Dey AB, Dey S, Zhou X, Gross AL, Lee J, Kardia SLR, Smith JA. Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India. RESEARCH SQUARE 2024:rs.3.rs-4712660. [PMID: 39149469 PMCID: PMC11326367 DOI: 10.21203/rs.3.rs-4712660/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The prevalence of dementia among South Asians across India is approximately 7.4% in those 60 years and older, yet little is known about genetic risk factors for dementia in this population. Most known risk loci for Alzheimer's disease (AD) have been identified from studies conducted in European Ancestry (EA) but are unknown in South Asians. Using whole-genome sequence data from 2680 participants from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study of India (LASI-DAD), we performed a gene-based analysis of 84 genes previously associated with AD in EA. We investigated associations with the Hindi Mental State Examination (HMSE) score and factor scores for general cognitive function and five cognitive domains. For each gene, we examined missense/loss-of-function (LoF) variants and brain-specific promoter/enhancer variants, separately, both with and without incorporating additional annotation weights (e.g., deleteriousness, conservation scores) using the variant-Set Test for Association using Annotation infoRmation (STAAR). In the missense/LoF analysis without annotation weights and controlling for age, sex, state/territory, and genetic ancestry, three genes had an association with at least one measure of cognitive function (FDR q<0.1). APOE was associated with four measures of cognitive function, PICALM was associated with HMSE score, and TSPOAP1 was associated with executive function. The most strongly associated variants in each gene were rs429358 (APOE ε4), rs779406084 (PICALM), and rs9913145 (TSPOAP1). rs779406084 is a rare missense mutation that is more prevalent in LASI-DAD than in EA (minor allele frequency=0.075% vs. 0.0015%); the other two are common variants. No genes in the brain-specific promoter/enhancer analysis met criteria for significance. Results with and without annotation weights were similar. Missense/LoF variants in some genes previously associated with AD in EA are associated with measures of cognitive function in South Asians from India. Analyzing genome sequence data allows identification of potential novel causal variants enriched in South Asians.
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Affiliation(s)
| | | | | | | | | | | | | | - A B Dey
- All India Institute of Medical Sciences
| | | | | | - Alden L Gross
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University
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4
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Subramanian K, Chopra M, Kahali B. Landscape of genomic structural variations in Indian population-based cohorts: Deeper insights into their prevalence and clinical relevance. HGG ADVANCES 2024; 5:100285. [PMID: 38521976 PMCID: PMC11007539 DOI: 10.1016/j.xhgg.2024.100285] [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: 09/14/2023] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
Structural variations (SV) are large (>50 base pairs) genomic rearrangements comprising deletions, duplications, insertions, inversions, and translocations. Studying SVs is important because they play active and critical roles in regulating gene expression, determining disease predispositions, and identifying population-specific differences among individuals of diverse ancestries. However, SV discoveries in the Indian population using whole-genome sequencing (WGS) have been limited. In this study, using short-read WGS having an average 42X depth of coverage, we identify and characterize 36,210 SVs from 529 individuals enrolled in population-based cohorts in India. These SVs include 24,574 deletions, 2,913 duplications, 8,710 insertions, and 13 inversions; 1.26% (456 out of 36,210) of the identified SVs can potentially impact the coding regions of genes. Furthermore, 56 of these SVs are highly intolerant to loss-of-function changes to the mapped genes, and five SVs impacting ADAMTS17, CCDC40, and RHCE are common in our study individuals. Seven rare SVs significantly impact dosage sensitivity of genes known to be associated with various clinical phenotypes. Most of the SVs in our study are rare and heterozygous. This fine-scale SV discovery in the underrepresented Indian population provides valuable insights that extend beyond Eurocentric human genetic studies.
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Affiliation(s)
- Krithika Subramanian
- Centre for Brain Research, Indian Institute of Science, Bangalore 560012, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mehak Chopra
- Centre for Brain Research, Indian Institute of Science, Bangalore 560012, India
| | - Bratati Kahali
- Centre for Brain Research, Indian Institute of Science, Bangalore 560012, India.
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5
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Biddanda A, Bandyopadhyay E, de la Fuente Castro C, Witonsky D, Urban Aragon JA, Pasupuleti N, Moots HM, Fonseca R, Freilich S, Stanisavic J, Willis T, Menon A, Mustak MS, Kodira CD, Naren AP, Sikdar M, Rai N, Raghavan M. Distinct positions of genetic and oral histories: Perspectives from India. HGG ADVANCES 2024; 5:100305. [PMID: 38720459 PMCID: PMC11153255 DOI: 10.1016/j.xhgg.2024.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024] Open
Abstract
Over the past decade, genomic data have contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great's army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.
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Affiliation(s)
- Arjun Biddanda
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Esha Bandyopadhyay
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Constanza de la Fuente Castro
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | | | - Nagarjuna Pasupuleti
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Karnataka 574199, India
| | - Hannah M Moots
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Institute for the Study of Ancient Cultures Museum, University of Chicago, Chicago, IL, USA
| | - Renée Fonseca
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Suzanne Freilich
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
| | - Jovan Stanisavic
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tabitha Willis
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Anoushka Menon
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Karnataka 574199, India
| | | | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Cystic Fibrosis Research Center, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mithun Sikdar
- Anthropological Survey of India, Mysore, Karnataka 570026, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Uttar Pradesh, Lucknow, Uttar Pradesh 226007, India.
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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6
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Kumar S, Singh PP, Pasupuleti N, Tripathy VM, Chauley MK, Chaubey G, Rai N. The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India. Hum Mol Genet 2024; 33:1015-1019. [PMID: 38538568 DOI: 10.1093/hmg/ddae054] [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: 11/14/2023] [Revised: 03/02/2024] [Accepted: 03/14/2024] [Indexed: 04/23/2024] Open
Abstract
The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations.
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Affiliation(s)
- Sachin Kumar
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226607, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | | | - Veena Mushrif Tripathy
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra 411006, India
| | - Milan Kumar Chauley
- Archaeological Survey of India, Nagpur Circle, Seminary Hills, Nagpur, Maharashtra 440001, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226607, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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7
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Varghese JS, Ghosh A, Stein AD, Narayan KMV, Patel SA. The association of hypertension among married Indian couples: a nationally representative cross-sectional study. Sci Rep 2024; 14:10411. [PMID: 38710852 PMCID: PMC11074266 DOI: 10.1038/s41598-024-61169-1] [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: 01/15/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024] Open
Abstract
Mounting evidence demonstrates that intimate partners sharing risk factors have similar propensities for chronic conditions such as hypertension. The objective was to study whether spousal hypertension was associated with one's own hypertension status independent of known risk factors, and stratified by socio-demographic subgroups (age, sex, wealth quintile, caste endogamy). Data were from heterosexual married couples (n = 50,023, women: 18-49 years, men: 21-54 years) who participated in the National Family Health Survey-V (2019-2021). Hypertension was defined as self-reported diagnosis of hypertension or average of three blood pressure measurements ≥ 140 systolic or 90 mmHg diastolic BP. Among married adults, the prevalence of hypertension among men (38.8 years [SD 8.3]) and women (33.9 years [SD 7.9]) were 29.1% [95% CI 28.5-29.8] and 20.6% [95% CI 20.0-21.1] respectively. The prevalence of hypertension among both partners was 8.4% [95% CI 8.0-8.8]. Women and men were more likely to have hypertension if their spouses had the condition (husband with hypertension: PR 1.37 [95% CI 1.30-1.44]; wife with hypertension: PR 1.32 [95% CI 1.26-1.38]), after adjusting for known risk factors. Spouse's hypertension status was consistently associated with own status across all socio-demographic subgroups examined. These findings present opportunities to consider married couples as a unit in efforts to diagnose and treat hypertension.
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Affiliation(s)
- Jithin Sam Varghese
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
- Emory Global Diabetes Research Center of Woodruff Health Sciences Center and Emory University, Atlanta, GA, 30322, USA.
| | | | - Aryeh D Stein
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - K M Venkat Narayan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Emory Global Diabetes Research Center of Woodruff Health Sciences Center and Emory University, Atlanta, GA, 30322, USA
| | - Shivani A Patel
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Emory Global Diabetes Research Center of Woodruff Health Sciences Center and Emory University, Atlanta, GA, 30322, USA
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8
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Welikala A, Desai S, Pratap Singh P, Fernando A, Thangaraj K, van Driem G, Adikari G, Tennekoon K, Chaubey G, Ranasinghe R. The genetic identity of the Vedda: A language isolate of South Asia. Mitochondrion 2024; 76:101884. [PMID: 38626841 DOI: 10.1016/j.mito.2024.101884] [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: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Linguistic data from South Asia identified several language isolates in the subcontinent. The Vedda, an indigenous population of Sri Lanka, are the least studied amongst them. Therefore, to understand the initial peopling of Sri Lanka and the genetic affinity of the Vedda with other populations in Eurasia, we extensively studied the high-resolution autosomal and mitogenomes from the Vedda population of Sri Lanka. Our autosomal analyses suggest a close genetic link of Vedda with the tribal populations of India despite no evidence of close linguistic affinity, thus suggesting a deep genetic link of the Vedda with these populations. The mitogenomic analysis supports this association by pointing to an ancient link with Indian populations. We suggest that the Vedda population is a genetically drifted group with limited gene flow from neighbouring Sinhalese and Sri Lankan Tamil populations. Interestingly, the genetic ancestry sharing of Vedda neglects the isolation-by-distance model. Collectively, the demography of Sri Lanka is unique, where Sinhalese and Sri Lankan Tamil populations excessively admixed, whilst Vedda largely preserved their isolation and deep genetic association with India.
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Affiliation(s)
- Anjana Welikala
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka; Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Shailesh Desai
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Amali Fernando
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, Bern 3012, Switzerland
| | - Gamini Adikari
- Postgraduate Institute of Archaeology, University of Kelaniya, 407, Bauddhalika Mawatha, Colombo 00700, Sri Lanka
| | - Kamani Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India.
| | - Ruwandi Ranasinghe
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
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9
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Holla B, Mahadevan J, Ganesh S, Sud R, Janardhanan M, Balachander S, Strom N, Mattheisen M, Sullivan PF, Huang H, Zandi P, Benegal V, Reddy YJ, Jain S, Purushottam M, Viswanath B. A cross ancestry genetic study of psychiatric disorders from India. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.25.24306377. [PMID: 38712191 PMCID: PMC11071591 DOI: 10.1101/2024.04.25.24306377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Genome-wide association studies across diverse populations may help validate and confirm genetic contributions to risk of disease. We estimated the extent of population stratification as well as the predictive accuracy of polygenic scores (PGS) derived from European samples to a data set from India. We analysed 2685 samples from two data sets, a population neurodevelopmental study (cVEDA) and a hospital-based sample of bipolar affective disorder (BD) and obsessive-compulsive disorder (OCD). Genotyping was conducted using Illumina's Global Screening Array. Population structure was examined with principal component analysis (PCA), uniform manifold approximation and projection (UMAP), support vector machine (SVM) ancestry predictions, and admixture analysis. PGS were calculated from the largest available European discovery GWAS summary statistics for BD, OCD, and externalizing traits using two Bayesian methods that incorporate local linkage disequilibrium structures (PGS-CS-auto) and functional genomic annotations (SBayesRC). Our analyses reveal global and continental PCA overlap with other South Asian populations. Admixture analysis revealed a north-south genetic axis within India (FST 1.6%). The UMAP partially reconstructed the contours of the Indian subcontinent. The Bayesian PGS analyses indicates moderate-to-high predictive power for BD. This was despite the cross-ancestry bias of the discovery GWAS dataset, with the currently available data. However, accuracy for OCD and externalizing traits was much lower. The predictive accuracy was perhaps influenced by the sample size of the discovery GWAS and phenotypic heterogeneity across the syndromes and traits studied. Our study results highlight the accuracy and generalizability of newer PGS models across ancestries. Further research, across diverse populations, would help understand causal mechanisms that contribute to psychiatric syndromes and traits.
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Affiliation(s)
- Bharath Holla
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Suhas Ganesh
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Meghana Janardhanan
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Srinivas Balachander
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Nora Strom
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Manuel Mattheisen
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Dalhousie University, Department of Community Health and Epidemiology & Faculty of Computer Science, Halifax, Nova Scotia, Canada
- University Hospital of Psychiatry and Psychotherapy, University of Bern
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA02114, USA
| | - Peter Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Vivek Benegal
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Yc Janardhan Reddy
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
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10
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Rout M, Tung GK, Singh JR, Mehra NK, Wander GS, Ralhan S, Sanghera DK. Polygenic Risk Score Assessment for Coronary Artery Disease in Asian Indians. J Cardiovasc Transl Res 2024:10.1007/s12265-024-10511-z. [PMID: 38658478 DOI: 10.1007/s12265-024-10511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
We evaluated the performance of various polygenic risk score (PRS) models derived from European (EU), South Asian (SA), and Punjabi Asian Indians (AI) studies on 13,974 subjects from AI ancestry. While all models successfully predicted Coronary artery disease (CAD) risk, the AI, SA, and EU + AI were superior predictors and more transportable than the EU model; the predictive performance in training and test sets was 18% and 22% higher in AI and EU + AI models, respectively than in EU. Comparing individuals with extreme PRS quartiles, the AI and EU + AI captured individuals with high CAD risk showed 2.6 to 4.6 times higher efficiency than the EU. Interestingly, including the clinical risk score did not significantly change the performance of any genetic model. The enrichment of diversity variants in EU PRS improves risk prediction and transportability. Establishing population-specific normative and risk factors and inclusion into genetic models would refine the risk stratification and improve the clinical utility of CAD PRS.
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Affiliation(s)
- Madhusmita Rout
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA
| | - Gurleen Kaur Tung
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA
| | | | | | | | - Sarju Ralhan
- Hero DMC Heart Institute, Ludhiana, Punjab, India
| | - Dharambir K Sanghera
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA.
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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11
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Kerdoncuff E, Skov L, Patterson N, Zhao W, Lueng YY, Schellenberg GD, Smith JA, Dey S, Ganna A, Dey AB, Kardia SL, Lee J, Moorjani P. 50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580575. [PMID: 38405782 PMCID: PMC10888882 DOI: 10.1101/2024.02.15.580575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.
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Affiliation(s)
- Elise Kerdoncuff
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuk Yee Lueng
- Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Gerard D. Schellenberg
- Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Jennifer A. Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - AB Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jinkook Lee
- Department of Economics, and Center for Economic & Social Research, University of Southern California, Los Angeles, California, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
- Center for Computational Biology, University of California, Berkeley, United States of America
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12
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Varghese JS, Ghosh A, Stein A, Narayan KV, Patel S. The association of hypertension among married Indian couples: a nationally representative cross-sectional study. RESEARCH SQUARE 2024:rs.3.rs-3865512. [PMID: 38352475 PMCID: PMC10862969 DOI: 10.21203/rs.3.rs-3865512/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Mounting evidence demonstrates that intimate partners sharing risk factors have similar propensities for chronic conditions such as hypertension. The objective was to study whether spousal hypertension was associated with one's own hypertension status independent of known risk factors, and stratified by socio-demographic subgroups (age, sex, wealth quintile, caste endogamy). Data were from heterosexual married couples (n = 50,023, women: 18-49y, men: 21-54y) who participated in the National Family Health Survey-V (2019-21). Hypertension was defined as self-reported diagnosis of hypertension or average of three blood pressure measurements ≥ 140 systolic or 90 mmHg diastolic BP. Among married adults, the prevalence of hypertension among men (38.8 years [SD: 8.3]) and women (33.9 years [SD: 7.9]) were 29.1% [95%CI: 28.5-29.8] and 20.6% [95%CI: 20.0-21.1] respectively. The prevalence of hypertension among both partners was 8.4% [95%CI: 8.0-8.8]. Women and men were more likely to have hypertension if their spouses had the condition (husband with hypertension: PR = 1.37 [95%CI: 1.30-1.44]; wife with hypertension: PR = 1.32 [95%CI: 1.26-1.38]), after adjusting for known risk factors. Spouse's hypertension status was consistently associated with own status across all socio-demographic subgroups examined. These findings present opportunities to consider married couples as a unit in efforts to diagnose and treat hypertension.
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13
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Abu-Amara H, Zhao W, Li Z, Leung YY, Schellenberg GD, Wang LS, Moorjani P, Dey A, Dey S, Zhou X, Gross AL, Lee J, Kardia SL, Smith JA. Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301482. [PMID: 38293024 PMCID: PMC10827235 DOI: 10.1101/2024.01.18.24301482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The prevalence of dementia among South Asians across India is approximately 7.4% in those 60 years and older, yet little is known about genetic risk factors for dementia in this population. Most known risk loci for Alzheimer's disease (AD) have been identified from studies conducted in European Ancestry (EA) but are unknown in South Asians. Using whole-genome sequence data from 2680 participants from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study of India (LASI-DAD), we performed a gene-based analysis of 84 genes previously associated with AD in EA. We investigated associations with the Hindi Mental State Examination (HMSE) score and factor scores for general cognitive function and five cognitive domains. For each gene, we examined missense/loss-of-function (LoF) variants and brain-specific promoter/enhancer variants, separately, both with and without incorporating additional annotation weights (e.g., deleteriousness, conservation scores) using the variant-Set Test for Association using Annotation infoRmation (STAAR). In the missense/LoF analysis without annotation weights and controlling for age, sex, state/territory, and genetic ancestry, three genes had an association with at least one measure of cognitive function (FDR q<0.1). APOE was associated with four measures of cognitive function, PICALM was associated with HMSE score, and TSPOAP1 was associated with executive function. The most strongly associated variants in each gene were rs429358 (APOE ε4), rs779406084 (PICALM), and rs9913145 (TSPOAP1). rs779406084 is a rare missense mutation that is more prevalent in LASI-DAD than in EA (minor allele frequency=0.075% vs. 0.0015%); the other two are common variants. No genes in the brain-specific promoter/enhancer analysis met criteria for significance. Results with and without annotation weights were similar. Missense/LoF variants in some genes previously associated with AD in EA are associated with measures of cognitive function in South Asians from India. Analyzing genome sequence data allows identification of potential novel causal variants enriched in South Asians.
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Affiliation(s)
- Hasan Abu-Amara
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Zheng Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
- Center for Computational Biology, University of California, Berkeley, United States of America
| | - A.B. Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sharmitha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alden L. Gross
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jinkook Lee
- Department of Economics, University of Southern California, Los Angeles, California, United States of America
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
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14
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Dokuru DR, Horwitz TB, Freis SM, Stallings MC, Ehringer MA. South Asia: The Missing Diverse in Diversity. Behav Genet 2024; 54:51-62. [PMID: 37917228 PMCID: PMC11129896 DOI: 10.1007/s10519-023-10161-y] [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: 04/23/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
South Asia, making up around 25% of the world's population, encompasses a wide range of individuals with tremendous genetic and environmental diversity. This region, which spans eight countries, is home to over 4500 anthropologically defined groups that speak numerous languages and have an array of religious beliefs and cultures, making it one of the most diverse places in the world. Much of the region's rich genetic diversity and structure is the result of a complex combination of population history, migration patterns, and endogamous practices. Despite the overwhelming size and diversity, South Asians have often been underrepresented in genetic research, making up less than 2% of the participants in genetic studies. This has led to a lack of population specific understanding of genetic disease risks. We aim to raise awareness about underlying genetic diversity in this ancestry group, call attention to the lack of representation of the group, and to highlight strategies for future studies in South Asians.
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Affiliation(s)
- Deepika R Dokuru
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA.
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA.
| | - Tanya B Horwitz
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Samantha M Freis
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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15
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Kumar L, Chowdhari A, Sequeira JJ, Mustak MS, Banerjee M, Thangaraj K. Genetic Affinities and Adaptation of the South-West Coast Populations of India. Genome Biol Evol 2023; 15:evad225. [PMID: 38079532 PMCID: PMC10745260 DOI: 10.1093/gbe/evad225] [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] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Evolutionary event has not only altered the genetic structure of human populations but also associated with social and cultural transformation. South Asian populations were the result of migration and admixture of genetically and culturally diverse groups. Most of the genetic studies pointed to large-scale admixture events between Ancestral North Indian (ANI) and Ancestral South Indian (ASI) groups, also additional layers of recent admixture. In the present study, we have analyzed 213 individuals inhabited in South-west coast India with traditional warriors and feudal lord status and historically associated with migratory events from North/North West India and possible admixture with West Eurasian populations, whose genetic links are still missing. Analysis of autosomal Single Nucleotide Polymorphism (SNP) markers suggests that these groups possibly derived their ancestry from some groups of North West India having additional Middle Eastern genetic components. Higher distribution of West Eurasian mitochondrial haplogroups also points to female-mediated admixture. Estimation of Effective Migration Surface (EEMS) analysis indicates Central India and Godavari basin as a crucial transition zone for population migration from North and North West India to South-west coastal India. Selection screen using 3 distinct outlier-based approaches revealed genetic signatures related to Immunity and protection from Viral infections. Thus, our study suggests that the South-west coastal groups with traditional warriors and feudal lords' status are of a distinct lineage compared to Dravidian and Gangetic plain Indo-Europeans and are remnants of very early migrations from North West India following the Godavari basin to Karnataka and Kerala.
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Affiliation(s)
- Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Anuhya Chowdhari
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Jaison J Sequeira
- Department of Applied Zoology, Mangalore University, Mangalore 574199, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore 574199, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
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16
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Chougule A, Chandrani P, Noronha V, Pange P, Kale S, Nikam A, Nambiar K, Marchande D, Durve A, Gupta V, Jagtap V, Tiwrekar P, Menon N, Joshi A, Kaushal R, Pai T, Patil VM, Dutt A, Banavali SD, Prabhash K. Real-World Evidence of EGFR Targeted Therapy in NSCLC- A Brief Report of Decade Long Single Center Experience. JTO Clin Res Rep 2023; 4:100566. [PMID: 38033811 PMCID: PMC10682910 DOI: 10.1016/j.jtocrr.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 12/02/2023] Open
Abstract
The significance of EGFR targeted therapy in the lung adenocarcinoma is paramount. Several controlled clinical trials have reported considerable survival of EGFR mutation positive patients on receiving the EGFR tyrosine kinase inhibitor (TKI). However, the real-world evidence of benefits of EGFR TKI would be further useful to understand how the designated therapeutic regimen benefits the patients. In this study, we report a decade long real-world evidence of EGFR molecular testing in lung cancer at Tata Memorial Hospital (Mumbai, India). Laboratory and hospital records containing basic demographic details, clinical characteristics, treatment regimen, survival outcome were collected retrospectively. Statistical association and survival analysis were performed using the R programming. The cohort includes 9,053 lung cancer patients tested for EGFR mutations during 2011 to 2019. Baseline T790M and compound mutations were the only mutations observed co-occurring while all other EGFR mutations were mutually exclusive. Furthermore, the baseline T790M were also observed to be associated with TTF1 positivity, smoking and local metastasis. Overall survival of the patients harboring co-occurring compound mutations was significantly lesser than the other EGFR positive patients. Overall, our study suggests that EGFR TKI may provide real-world benefit to the lung cancer patients harboring mutually exclusive EGFR mutations. On the other hand, further systematic study is essential to develop better therapeutic regimen for co-occurring baseline EGFR T790M and other compound mutations.
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Affiliation(s)
- Anuradha Chougule
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Pratik Chandrani
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Centre for Computational Biology, Bioinformatics and Crosstalk Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Vanita Noronha
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Priyanka Pange
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Shrutikaa Kale
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Ankita Nikam
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Kavya Nambiar
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Dipika Marchande
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Arpana Durve
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinod Gupta
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinita Jagtap
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Priyanka Tiwrekar
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Nandini Menon
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Amit Joshi
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Rajeev Kaushal
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Trupti Pai
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Vijay Maruti Patil
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Shripad Dinanath Banavali
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Kumar Prabhash
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
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17
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Srinivas SM, Dhar S, Gowdra A, Saha A, Sundararajan L, Geetha TS, Banerjee R, Malakar R, Sil A, Lakshminarayana Shyam Prasad A. Filaggrin gene polymorphisms in Indian children with atopic dermatitis: A cross-sectional multicentre study. Indian J Dermatol Venereol Leprol 2023; 89:819-827. [PMID: 37067103 DOI: 10.25259/ijdvl_37_2022] [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: 01/09/2022] [Accepted: 10/15/2022] [Indexed: 04/18/2023]
Abstract
Background Filaggrin (FLG) gene encoding the protein filaggrin plays an important role in barrier function of the skin and its alteration is a predisposing factor for atopic dermatitis. FLG gene variants result in absent or decreased filaggrin protein. Worldwide, the prevalence of FLG variants ranges from 14 to 56%. FLG null variants are distinct in each population. Objectives To study the FLG gene polymorphisms in Indian children and attempt a genotype-phenotype correlation in atopic dermatitis. Methods This was a cross-sectional, multicentre study conducted on 75 Indian children. Demographic details, clinical features and identified FLG null variants were recorded. We performed a whole gene sequencing of the entire FLG coding region using next-generation sequencing technology. Results The prevalence of FLG null variants was 34.7%. A total of 20 different FLG loss of function variants in 26 children were documented. Sixteen (80%) variants were novel and four (20%) were previously reported in Asian and European populations. We found a statistically significant association between FLG variants with early age of onset of atopic dermatitis (P = 0.016) and elevated serum IgE levels (P = 0.051). There was no significant difference between atopic dermatitis phenotypes in children having one variant as compared to children harbouring two or more null variants. Limitation Small sample size. Conclusion Our study reports a unique set of FLG variants different from Asian and European populations, with these variants being significantly associated with an early age of onset of atopic dermatitis and elevated serum IgE levels.
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Affiliation(s)
- Sahana M Srinivas
- Department of Pediatric Dermatology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Sandipan Dhar
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | - Aruna Gowdra
- Department of Microbiology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Abhijit Saha
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | | | | | - Raghubir Banerjee
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | - Rajib Malakar
- Department of Pediatric Dermatology, Institute of Child Health, Kolkata, West Bengal, India
| | - Amrita Sil
- Department of Pharmacology, Rampurhat Government Medical College and Hospital, Birbhum, West Bengal, India
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18
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Kumar L, Ahlawat B, Kumar S, Mushrif-Tripathy V, Rai N. Maternal Ancestry of First Parsi Settlers of India Using Ancient Mitogenome. Mitochondrion 2023:S1567-7249(23)00055-7. [PMID: 37379890 DOI: 10.1016/j.mito.2023.06.004] [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: 02/27/2023] [Revised: 06/18/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
The rich cultural and genetic diversity of South Asia emerged from multiple migrations and cultural assimilation of multiple waves of migrants. The Parsi community of North-western India were one of those who migrated from West Eurasia in the aftermath of 7th century CE and assimilated into the local cultural framework. Earlier genetic studies further strengthened this notion with the finding that they harbour both Middle Eastern and South Asian genetic components. Although these studies covered both autosomal and uniparental markers, still maternal ancestry was not covered in depth and with good resolution of mitochondrial markers. Hence in our current study, we have first time generated a complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan and performed detailed phylogenetic analysis to infer their maternal genetic affinity. In our analysis, we found that the Parsi mitogenome with mtDNA haplogroup M3a1+204 shares clade with both Middle Eastern and South Asian modern individuals in both the Maximum Likelihood tree and Bayesian phylogenetic tree. This haplogroup was also prevalent among the medieval Swat valley population of present-day Northern Pakistan and was also observed in two Roopkund A individuals. In the phylogenetic network this sample share haplotype with both South Asian and Middle Eastern samples. So conclusively, the first Parsi settlers' maternal ancestry encompasses both South Asian and Middle Eastern genetic composition.
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Affiliation(s)
- Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India; Department of Anthropology, Panjab University, Chandigarh, 160014, India
| | - Sachin Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Veena Mushrif-Tripathy
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra, 411006, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India.
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19
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Augsburg B, Baquero JP, Gautam S, Rodriguez-Lesmes P. Sanitation and marriage markets in India: Evidence from the Total Sanitation Campaign. JOURNAL OF DEVELOPMENT ECONOMICS 2023; 163:103092. [PMID: 37334279 PMCID: PMC10273184 DOI: 10.1016/j.jdeveco.2023.103092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 06/20/2023]
Abstract
This paper measures the additional value of sanitation within the marriage arrangement. We use data from the Indian human development household survey (IHDS) to model the marital decisions of men and women in rural India and to estimate the marital surplus (the gains from being married). We use the model to demonstrate that the government's Total Sanitation Campaign (TSC) increased marital surplus and changed marriage market outcomes for men and women. Decomposition reveals (i) that sanitation makes it more attractive to be in a marriage for both gender, and (ii) that TSC exposure led to a decrease in the wife's surplus share, implying a redistribution of gains within the marriage.
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Affiliation(s)
| | | | - Sanghmitra Gautam
- Department of Economics, Washington University in St Louis, United States of America
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20
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Zhao W, Smith J, Wang Y, Chintalapati M, Ammous F, Yu M, Moorjani P, Ganna A, Gross A, Dey S, Benerjee J, Chatterjee P, Dey A, Lee J, Kardia S. Polygenic Risk Scores for Alzheimer's Disease and General Cognitive Function Are Associated With Measures of Cognition in Older South Asians. J Gerontol A Biol Sci Med Sci 2023; 78:743-752. [PMID: 36782352 PMCID: PMC10172981 DOI: 10.1093/gerona/glad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 02/15/2023] Open
Abstract
Genome-wide association studies (GWAS) conducted in European ancestry (EA) have identified hundreds of single-nucleotide polymorphisms (SNPs) associated with general cognitive function and/or Alzheimer's disease (AD). The association between these SNPs and cognitive function has not been fully evaluated in populations with complex genetic substructure such as South Asians. This study investigated whether SNPs identified in EA GWAS, either individually or as polygenic risk scores (PRSs), were associated with general cognitive function and 5 broad cognitive domains in 932 South Asians from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study in India (LASI-DAD). We found that SNPs identified from AD GWAS were more strongly associated with cognitive function in LASI-DAD than those from a GWAS of general cognitive function. PRSs for general cognitive function and AD explained up to 1.1% of the variability in LASI-DAD cognitive domain scores. Our study represents an important stepping stone toward better characterization of the genetic architecture of cognitive aging in the Indian/South Asian population and highlights the need for further research that may lead to the identification of new variants unique to this population.
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Affiliation(s)
- Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Yi Zhe Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Miao Yu
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Alden Gross
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Joyita Benerjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Prasun Chatterjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Aparajit B Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jinkook Lee
- Department of Economics, University of Southern California, Los Angeles, California, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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21
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Narayan KMV, Varghese JS, Beyh YS, Bhattacharyya S, Khandelwal S, Krishnan GS, Siegel KR, Thomas T, Kurpad AV. A Strategic Research Framework for Defeating Diabetes in India: A 21st-Century Agenda. J Indian Inst Sci 2023; 103:1-22. [PMID: 37362852 PMCID: PMC10029804 DOI: 10.1007/s41745-022-00354-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/14/2022] [Indexed: 03/24/2023]
Abstract
Indian people are at high risk for type 2 diabetes (T2DM) even at younger ages and lower body weights. Already 74 million people in India have the disease, and the proportion of those with T2DM is increasing across all strata of society. Unique aspects, related to lower insulin secretion or function, and higher hepatic fat deposition, accompanied by the rise in overweight (related to lifestyle changes) may all be responsible for this unrelenting epidemic of T2DM. Yet, research to understand the causes, pathophysiology, phenotypes, prevention, treatment, and healthcare delivery of T2DM in India seriously lags behind. There are major opportunities for scientific discovery and technological innovation, which if tapped can generate solutions for T2DM relevant to the country's context and make leading contributions to global science. We analyze the situation of T2DM in India, and present a four-pillar (etiology, precision medicine, implementation research, and health policy) strategic research framework to tackle the challenge. We offer key research questions for each pillar, and identify infrastructure needs. India offers a fertile environment for shifting the paradigm from imprecise late-stage diabetes treatment toward early-stage precision prevention and care. Investing in and leveraging academic and technological infrastructures, across the disciplines of science, engineering, and medicine, can accelerate progress toward a diabetes-free nation.
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Affiliation(s)
- K. M. Venkat Narayan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA 30322 USA
| | - Jithin Sam Varghese
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA 30322 USA
| | - Yara S. Beyh
- Laney Graduate School, Nutrition and Health Sciences Doctoral Program, Emory University, Atlanta, USA
| | | | | | - Gokul S. Krishnan
- Robert Bosch Centre for Data Science and Artificial Intelligence, Indian Institute of Technology Madras, Chennai, India
| | - Karen R. Siegel
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA 30322 USA
| | - Tinku Thomas
- Department of Biostatistics, St. John’s Medical College, Bengaluru, India
| | - Anura V. Kurpad
- Department of Physiology, St. John’s Medical College, Bengaluru, India
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22
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [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: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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23
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De S, Rai D, Tamang S, Sherpa RD, Subba S, Lepcha DT, Govindaraj P, Thangaraj K, Chaubey G, Tamang R. Signatures of high altitude adaptation in Tibeto-Burman tribes of the Darjeeling Hill Region. Am J Hum Biol 2023; 35:e23858. [PMID: 36591954 DOI: 10.1002/ajhb.23858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/23/2022] [Accepted: 12/21/2022] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES The long-term isolation, endogamy practices, and environmental adaptations have shaped the enormous human diversity in India. The genetic and morphological variations in mainland Indians are well studied. However, the data on the Indian Himalayan populations are scattered. Thus, the present study attempts to understand variations in the selected parameter among four Tibeto-Burman speaking ethnic tribal populations from the Darjeeling Hill Region (DHR) in the Eastern Himalaya Biodiversity Hotspot region of India. METHODS A total of 178 healthy male individuals (Lepcha 98, Sherpa 31, Bhutia 27, and Tibetans 22) living at an altitudinal range of 1467-2258 m above the sea level were studied for the 10 parameters namely, weight (kg), height (cm), body mass index (BMI) (kg/m2 ) systolic and diastolic pressure (mm of Hg), pulse rate (per minute), saturation of peripheral oxygen (SPO2 ) (%), hemoglobin (g/dl), hematocrit (HCT) (%), and blood glucose (mg/dl). The data was statistically analyzed using analysis of variance and multiple linear regression methods. RESULTS Our analysis revealed comparatively lower hemoglobin and HCT levels, and higher systolic and diastolic blood pressure in the Sherpas followed by the Tibetans. This may be reflecting the persistence of high-altitude adaptation signatures even in lowlands. Interestingly, the Tibetans differed significantly from other populations in terms of their higher body weight, height, and BMI. CONCLUSION Thus, our study showed the persistence of high altitude signatures in Tibetans and Sherpa inhabited the DHR. Additionally, we also observed significant differences in the anthropometric and physiological parameters among the Tibeto-Burman populations of the DHR.
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Affiliation(s)
- Saptaparni De
- Department of Zoology, University of Calcutta, Kolkata, India
| | - Divya Rai
- Department of Zoology, University of Calcutta, Kolkata, India
| | - Shishir Tamang
- Department of Zoology, University of Calcutta, Kolkata, India
| | | | - Soni Subba
- Department of Zoology, University of Calcutta, Kolkata, India
| | | | | | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Rakesh Tamang
- Department of Zoology, University of Calcutta, Kolkata, India
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24
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Nayanar SK, Mohan A, Shenoy P, Saravanan M, Gopinath V, Deepak Roshan VG. Frequency of EGFR mutations in lung adenocarcinoma patients - A study from tertiary cancer center of South India. J Cancer Res Ther 2023; 19:S712-S718. [PMID: 38384044 DOI: 10.4103/jcrt.jcrt_653_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/31/2022] [Indexed: 02/23/2024]
Abstract
BACKGROUND AND OBJECTIVES Epidermal growth factor receptor (EGFR) mutation analysis has become an important part of the initial workup of non-squamous non-small cell lung cancer (NS-NSCLC) patients. This study is attempted as South Indians population is comprised of ethnic groups with diverse genetic makeup and only very limited data on EGFR mutation is available from south India. A detailed understanding of EGFR mutation profile will help in better planning of treatment strategies and resource allocation. METHODS A retrospective analysis of EGFR mutation frequency in 350 patients diagnosed with adenocarcinoma of lung and its association with pathological characteristics was done. RESULTS Out of 350 cases of pulmonary adenocarcinoma, within an age group ranging from 30 to 86 years. EGFR mutations were identified in 34.8% (n = 122) cases, out of which 35.24% (n = 43) were in non-smoker females (P = 0.001). Of the 14 cases with resistant type of EGFR mutations, nine were in smoker males and the remaining five in non-smoker females. INTERPRETATION AND CONCLUSION Overall EGFR mutation frequency observed in our study was similar to other Indian studies. However, in our study, we observed that mutation in exon 21 was less frequent compared to other studies. A similar slightly increased frequency of rare mutations and double mutations were observed in our study. A detailed study of the molecular epidemiology of lung cancer and its association with different geographical zones of India is needed. This understanding will help in better planning of treatment strategies and resource allocation.
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Affiliation(s)
- Sangeetha K Nayanar
- Division of Oncopathology, Departmentof Clinical Lab Services and Translational Research, Kerala, India
| | - Anju Mohan
- Division of Oncopathology, Departmentof Clinical Lab Services and Translational Research, Kerala, India
| | - Praveen Shenoy
- Department of Clinical Hematology and Medical Oncology, Kerala, India
| | - M Saravanan
- Division of Microbiology, Department of Clinical Lab Services and Translational Research, Kerala, India
| | - Vipin Gopinath
- Division of Genetics and Cytogentics, Department of Clinical Lab Services and Translational Research, Malabar Cancer Centre, Moozhikkara P.O, Thalassery, Kerala, India
| | - V G Deepak Roshan
- Division of Genetics and Cytogentics, Department of Clinical Lab Services and Translational Research, Malabar Cancer Centre, Moozhikkara P.O, Thalassery, Kerala, India
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25
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Kumar S, Voracek M. Effects of caste, birth season, and family income on digit ratios. Am J Hum Biol 2022; 35:e23852. [PMID: 36524699 DOI: 10.1002/ajhb.23852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES The contributions of latitude and ethnicity in the determination of cross-society differences in digit ratios are unclear. In India, different castes (endogamous groups) have been living in the same areas (villages or towns) for the last 1500 years and, therefore, these groups may have different gene pools without a latitude-related difference component. Thus, in the present study, we studied the effect of caste on digit ratios. We also studied the effects of sex, birth season, and family income on digit ratios. METHODS We selected a sample of 301 college students (age: M = 19.9 years, SD = 2.63) in Muzaffarnagar city of western Uttar Pradesh, India, and asked participants for information regarding their birth month, religion, caste, and monthly family income. We measured participants' dorsal and palmar digit lengths (of all fingers, except the thumb, in both hands) using vernier calipers of 0.01 mm accuracy. RESULTS Other backward castes (intermediate castes) had longer digit lengths than general castes (upper castes), scheduled castes (lower castes), and Muslims. However, there was no difference in digit ratios of caste groups (scheduled castes vs. other backward castes vs. general castes vs. Muslims) or specific castes (Chamar-Jatav vs. Jat vs. Pandit-Tyagi). Winter-born women had lower left dorsal 2D:4D and 3D:4D ratios than summer-born women. Family income was related to higher dorsal 2D:4D and 3D:4D ratios among women. Moreover, in dorsal digit ratios, sex difference (men < women) occurred in digit ratios constituting digit 5, whereas, in palmar digit ratios, sex difference occurred in digit ratios constituting digit 2. CONCLUSIONS The present study suggests that endogamy-led genetic difference in ethnic/caste groups is not a determinant, whereas birth season (i.e., the exposure to sunlight) and family income might be determinants of digit ratios. In addition, compared to palmar digit ratios, dorsal digit ratios are better markers of sexual dimorphism.
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Affiliation(s)
- Sanjay Kumar
- Department of Psychology D.A.V. College Muzaffarnagar Uttar Pradesh India
| | - Martin Voracek
- Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology University of Vienna Vienna Austria
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26
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Pojar T, Langstieh BT, Hemphill BE. An initial investigation of dental morphology variation among three southern Naga ethnic groups of Northeast India. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:184-210. [PMID: 36790681 DOI: 10.1002/ajpa.24605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/29/2022] [Accepted: 07/28/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES This study examines dental morphology trait prevalence among three southern Naga groups and compares them to 10 ethnic groups from other regions of South Asia to accomplish two objectives: assess the biological relationship of these Tibeto-Burman-speakers to speakers of non-Tibeto-Burman languages in other South Asian regions, and determine which traits distinguish northeast Indians from other South Asians. METHODS Dental morphology traits were scored with the Arizona State University Dental Anthropology System. Tooth-trait combinations were evaluated for significant inter-trait correlation and intra-trait correspondence within dental fields. Comparisons were based on simple trait prevalence and with Smith's MMD. Affinities based on the former were accomplished with correspondence analysis and principal components analysis. Affinities based on the latter were undertaken with neighbor-joining cluster analysis and multidimensional scaling. RESULTS After elimination due to inter-trait correlations and uniform prevalence, biodistances based on the remaining 17 tooth-trait combinations identify significant differences between northeast Indians and other South Asian ethnic groups due to high frequencies of shoveling on the maxillary incisors and Cusp 6 on the mandibular molars coupled with low frequencies of Carabelli's trait and Cusp 5 on UM1 and UM2, respectively. CONCLUSIONS Patterns of biodistances obtained from dental morphology are consilient with those obtained from DNA indicating statistically significant differences between northeast Indians from members of ethnic groups of other regions of South Asia. Researchers should explore the sex-specific patterns. Biodistances should not be limited to "key" teeth within dental fields, for in almost every case traits present on mesial and distal teeth yield non-redundant information.
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Affiliation(s)
- Tsiapisa Pojar
- Department of Anthropology, North-Eastern Hill University, Shillong, India
| | | | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, Fairbanks, Alaska, USA
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27
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Tournebize R, Chu G, Moorjani P. Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals. PLoS Genet 2022; 18:e1010243. [PMID: 35737729 PMCID: PMC9223333 DOI: 10.1371/journal.pgen.1010243] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
Founder events play a critical role in shaping genetic diversity, fitness and disease risk in a population. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods require large sample sizes or phased genomes. Thus, we developed ASCEND that measures the correlation in allele sharing between pairs of individuals across the genome to infer the age and strength of founder events. We show that ASCEND can reliably estimate the parameters of founder events under a range of demographic scenarios. We then apply ASCEND to two species with contrasting evolutionary histories: ~460 worldwide human populations and ~40 modern dog breeds. In humans, we find that over half of the analyzed populations have evidence for recent founder events, associated with geographic isolation, modes of sustenance, or cultural practices such as endogamy. Notably, island populations have lower population sizes than continental groups and most hunter-gatherer, nomadic and indigenous groups have evidence of recent founder events. Many present-day groups––including Native Americans, Oceanians and South Asians––have experienced more extreme founder events than Ashkenazi Jews who have high rates of recessive diseases due their known history of founder events. Using ancient genomes, we show that the strength of founder events differs markedly across geographic regions and time––with three major founder events related to the peopling of Americas and a trend in decreasing strength of founder events in Europe following the Neolithic transition and steppe migrations. In dogs, we estimate extreme founder events in most breeds that occurred in the last 25 generations, concordant with the establishment of many dog breeds during the Victorian times. Our analysis highlights a widespread history of founder events in humans and dogs and elucidates some of the demographic and cultural practices related to these events. A founder event occurs when small numbers of ancestral individuals give rise to a large fraction of the population. Founder events reduce genetic variation and increase the risk of recessive diseases. Despite their importance in evolutionary and disease studies, we still only have a limited comprehension of their prevalence and properties in humans and other species, as most existing methods require large sample sizes or phased genomes. Here, we present a flexible method, ASCEND, to infer the timing and the strength of founder events that is suitable for sparse datasets with few samples or limited coverage. ASCEND provides reliable estimates across a wide range of demographic scenarios. By applying it to data from two species (humans and dogs), we document a widespread history of recent founder events in both species and provide insights about the demographic processes related to these events. Our analysis helps to identify groups with strong founder events that should be prioritized for future studies as they offer a unique opportunity for biological discovery and reducing disease burden through mapping of recessive disease-causing genes and pathways, as previously shown in studies of Ashkenazi Jews and Finns.
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Affiliation(s)
- Rémi Tournebize
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RT); (PM)
| | - Gillian Chu
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, California, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RT); (PM)
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28
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Sarohi V, Srivastava S, Basak T. A Comprehensive Outlook on Dilated Cardiomyopathy (DCM): State-Of-The-Art Developments with Special Emphasis on OMICS-Based Approaches. J Cardiovasc Dev Dis 2022; 9:jcdd9060174. [PMID: 35735803 PMCID: PMC9225617 DOI: 10.3390/jcdd9060174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023] Open
Abstract
Dilated cardiomyopathy (DCM) remains an enigmatic cardiovascular disease (CVD) condition characterized by contractile dysfunction of the myocardium due to dilation of the ventricles. DCM is one of the major forms of CVD contributing to heart failure. Dilation of the left or both ventricles with systolic dysfunction, not explained by known causes, is a hallmark of DCM. Progression of DCM leads to heart failure. Genetic and various other factors greatly contribute to the development of DCM, but the etiology has still remained elusive in a large number of cases. A significant number of studies have been carried out to identify the genetic causes of DCM. These candidate-gene studies revealed that mutations in the genes of the fibrous, cytoskeletal, and sarcomeric proteins of cardiomyocytes result in the development of DCM. However, a significant proportion of DCM patients are idiopathic in nature. In this review, we holistically described the symptoms, causes (in adults and newborns), genetic basis, and mechanistic progression of DCM. Further, we also summarized the state-of-the-art diagnosis, available biomarkers, treatments, and ongoing clinical trials of potential drug regimens. DCM-mediated heart failure is on the rise worldwide including in India. The discovery of biomarkers with a better prognostic value is the need of the hour for better management of DCM-mediated heart failure patients. With the advent of next-generation omics-based technologies, it is now possible to probe systems-level alterations in DCM patients pertaining to the identification of novel proteomic and lipidomic biomarkers. Here, we also highlight the onset of a systems-level study in Indian DCM patients by applying state-of-the-art mass-spectrometry-based “clinical proteomics” and “clinical lipidomics”.
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Affiliation(s)
- Vivek Sarohi
- Indian Institute of Technology (IIT)-Mandi, School of Basic Sciences (SBS), Mandi 175075, HP, India; (V.S.); (S.S.)
- BioX Centre, Indian Institute of Technology (IIT)-Mandi, Mandi 175075, HP, India
| | - Shriya Srivastava
- Indian Institute of Technology (IIT)-Mandi, School of Basic Sciences (SBS), Mandi 175075, HP, India; (V.S.); (S.S.)
| | - Trayambak Basak
- Indian Institute of Technology (IIT)-Mandi, School of Basic Sciences (SBS), Mandi 175075, HP, India; (V.S.); (S.S.)
- BioX Centre, Indian Institute of Technology (IIT)-Mandi, Mandi 175075, HP, India
- Correspondence: ; Tel.: +91-1905-267826
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Siddiqui MK, Anjana RM, Dawed AY, Martoeau C, Srinivasan S, Saravanan J, Madanagopal SK, Taylor A, Bell S, Veluchamy A, Pradeepa R, Sattar N, Venkatesan R, Palmer CNA, Pearson ER, Mohan V. Young-onset diabetes in Asian Indians is associated with lower measured and genetically determined beta cell function. Diabetologia 2022; 65:973-983. [PMID: 35247066 PMCID: PMC9076730 DOI: 10.1007/s00125-022-05671-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 01/11/2023]
Abstract
AIMS/HYPOTHESIS South Asians in general, and Asian Indians in particular, have higher risk of type 2 diabetes compared with white Europeans, and a younger age of onset. The reasons for the younger age of onset in relation to obesity, beta cell function and insulin sensitivity are under-explored. METHODS Two cohorts of Asian Indians, the ICMR-INDIAB cohort (Indian Council of Medical Research-India Diabetes Study) and the DMDSC cohort (Dr Mohan's Diabetes Specialties Centre), and one of white Europeans, the ESDC (East Scotland Diabetes Cohort), were used. Using a cross-sectional design, we examined the comparative prevalence of healthy, overweight and obese participants with young-onset diabetes, classified according to their BMI. We explored the role of clinically measured beta cell function in diabetes onset in Asian Indians. Finally, the comparative distribution of a partitioned polygenic score (pPS) for risk of diabetes due to poor beta cell function was examined. Replication of the genetic findings was sought using data from the UK Biobank. RESULTS The prevalence of young-onset diabetes with normal BMI was 9.3% amongst white Europeans and 24-39% amongst Asian Indians. In Asian Indians with young-onset diabetes, after adjustment for family history of type 2 diabetes, sex, insulin sensitivity and HDL-cholesterol, stimulated C-peptide was 492 pmol/ml (IQR 353-616, p<0.0001) lower in lean compared with obese individuals. Asian Indians in our study, and South Asians from the UK Biobank, had a higher number of risk alleles than white Europeans. After weighting the pPS for beta cell function, Asian Indians have lower genetically determined beta cell function than white Europeans (p<0.0001). The pPS was associated with age of diagnosis in Asian Indians but not in white Europeans. The pPS explained 2% of the variation in clinically measured beta cell function, and 1.2%, 0.97%, and 0.36% of variance in age of diabetes amongst Asian Indians with normal BMI, or classified as overweight and obese BMI, respectively. CONCLUSIONS/INTERPRETATION The prevalence of lean BMI in young-onset diabetes is over two times higher in Asian Indians compared with white Europeans. This phenotype of lean, young-onset diabetes appears driven in part by lower beta cell function. We demonstrate that Asian Indians with diabetes also have lower genetically determined beta cell function.
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Affiliation(s)
- Moneeza K. Siddiqui
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ranjit Mohan Anjana
- grid.410867.c0000 0004 1805 2183Dr Mohan’s Diabetes Specialities Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Adem Y. Dawed
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Cyrielle Martoeau
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Sundararajan Srinivasan
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Jebarani Saravanan
- grid.410867.c0000 0004 1805 2183Dr Mohan’s Diabetes Specialities Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Sathish K. Madanagopal
- grid.410867.c0000 0004 1805 2183Dr Mohan’s Diabetes Specialities Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Alasdair Taylor
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Samira Bell
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Abirami Veluchamy
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Rajendra Pradeepa
- grid.410867.c0000 0004 1805 2183Dr Mohan’s Diabetes Specialities Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Naveed Sattar
- grid.8756.c0000 0001 2193 314XInstitute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Radha Venkatesan
- grid.410867.c0000 0004 1805 2183Dr Mohan’s Diabetes Specialities Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Colin N. A. Palmer
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ewan R. Pearson
- grid.8241.f0000 0004 0397 2876National Institute for Health Research Global Health Unit for Diabetes Outcomes Research, Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Viswanathan Mohan
- grid.410867.c0000 0004 1805 2183Dr Mohan’s Diabetes Specialities Centre and Madras Diabetes Research Foundation, Chennai, India
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Venkatesan V, Lopez-Alvarenga JC, Arya R, Ramu D, Koshy T, Ravichandran U, Ponnala AR, Sharma SK, Lodha S, Sharma KK, Shaik MV, Resendez RG, Venugopal P, R P, Saju N, Ezeilo JA, Bejar C, Wander GS, Ralhan S, Singh JR, Mehra NK, Vadlamudi RR, Almeida M, Mummidi S, Natesan C, Blangero J, Medicherla KM, Thanikachalam S, Panchatcharam TS, Kandregula DK, Gupta R, Sanghera DK, Duggirala R, Paul SFD. Burden of Type 2 Diabetes and Associated Cardiometabolic Traits and Their Heritability Estimates in Endogamous Ethnic Groups of India: Findings From the INDIGENIUS Consortium. Front Endocrinol (Lausanne) 2022; 13:847692. [PMID: 35498404 PMCID: PMC9048207 DOI: 10.3389/fendo.2022.847692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/21/2022] [Indexed: 01/14/2023] Open
Abstract
To assess the burden of type 2 diabetes (T2D) and its genetic profile in endogamous populations of India given the paucity of data, we aimed to determine the prevalence of T2D and estimate its heritability using family-based cohorts from three distinct Endogamous Ethnic Groups (EEGs) representing Northern (Rajasthan [Agarwals: AG]) and Southern (Tamil Nadu [Chettiars: CH] and Andhra Pradesh [Reddys: RE]) states of India. For comparison, family-based data collected previously from another North Indian Punjabi Sikh (SI) EEG was used. In addition, we examined various T2D-related cardiometabolic traits and determined their heritabilities. These studies were conducted as part of the Indian Diabetes Genetic Studies in collaboration with US (INDIGENIUS) Consortium. The pedigree, demographic, phenotypic, covariate data and samples were collected from the CH, AG, and RE EEGs. The status of T2D was defined by ADA guidelines (fasting glucose ≥ 126 mg/dl or HbA1c ≥ 6.5% and/or use of diabetes medication/history). The prevalence of T2D in CH (N = 517, families = 21, mean age = 47y, mean BMI = 27), AG (N = 530, Families = 25, mean age = 43y, mean BMI = 27), and RE (N = 500, Families = 22, mean age = 46y, mean BMI = 27) was found to be 33%, 37%, and 36%, respectively, Also, the study participants from these EEGs were found to be at increased cardiometabolic risk (e.g., obesity and prediabetes). Similar characteristics for the SI EEG (N = 1,260, Families = 324, Age = 51y, BMI = 27, T2D = 75%) were obtained previously. We used the variance components approach to carry out genetic analyses after adjusting for covariate effects. The heritability (h2) estimates of T2D in the CH, RE, SI, and AG were found to be 30%, 46%, 54%, and 82% respectively, and statistically significant (P ≤ 0.05). Other T2D related traits (e.g., BMI, lipids, blood pressure) in AG, CH, and RE EEGs exhibited strong additive genetic influences (h2 range: 17% [triglycerides/AG and hs-CRP/RE] - 86% [glucose/non-T2D/AG]). Our findings highlight the high burden of T2D in Indian EEGs with significant and differential additive genetic influences on T2D and related traits.
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Affiliation(s)
- Vettriselvi Venkatesan
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - Juan Carlos Lopez-Alvarenga
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Rector Arya
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Deepika Ramu
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - Teena Koshy
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - Umarani Ravichandran
- Department of Medicine, Rajah Muthiah Medical College Hospital, Annamalai University, Chidambaram, India
| | - Amaresh Reddy Ponnala
- Department of Endocrinology, Krishna Institute of Medical Sciences (KIMS) Hospital, Nellore, India
| | | | - Sailesh Lodha
- Departments of Preventive Cardiology, Internal Medicine and Endocrinology, Eternal Heart Care Centre and Research Institute, Mount Sinai New York Affiliate, Jaipur, India
| | - Krishna K. Sharma
- Department of Pharmacology, Lal Bahadur Shastri College of Pharmacy, Rajasthan University of Health Sciences, Jaipur, India
| | - Mahaboob Vali Shaik
- Department of Endocrinology, Narayana Medical College and Hospital, Nellore, India
| | - Roy G. Resendez
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Priyanka Venugopal
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - Parthasarathy R
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - Noelta Saju
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - Juliet A. Ezeilo
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Cynthia Bejar
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Gurpreet S. Wander
- Hero Dayanand Medical College (DMC) Heart Institute, Dayanand Medical College and Hospital, Ludhaina, India
| | - Sarju Ralhan
- Hero Dayanand Medical College (DMC) Heart Institute, Dayanand Medical College and Hospital, Ludhaina, India
| | - Jai Rup Singh
- Honorary or Emeritus Faculty, Central University of Punjab, Bathinda, India
| | - Narinder K. Mehra
- Honorary or Emeritus Faculty, All India Institute of Medical Sciences and Research, New Delhi, India
| | | | - Marcio Almeida
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Srinivas Mummidi
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Chidambaram Natesan
- Department of Medicine, Rajah Muthiah Medical College Hospital, Annamalai University, Chidambaram, India
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | | | - Sadagopan Thanikachalam
- Department of Cardiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | | | | | - Rajeev Gupta
- Departments of Preventive Cardiology, Internal Medicine and Endocrinology, Eternal Heart Care Centre and Research Institute, Mount Sinai New York Affiliate, Jaipur, India
| | - Dharambir K. Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Solomon F. D. Paul
- Department of Human Genetics, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
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Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan. Sci Rep 2022; 12:1027. [PMID: 35046511 PMCID: PMC8770644 DOI: 10.1038/s41598-022-05076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.
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Shaki D, Eskin-Schwartz M, Hadar N, Bosin E, Carmon L, Refetoff S, Hershkovitz E, Birk OS, Haim A. TSHB R75G is a founder variant and prevalent cause of low or undetectable TSH in Indian Jews. Eur Thyroid J 2022; 11:e210072. [PMID: 34981755 PMCID: PMC9142811 DOI: 10.1530/etj-21-0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/26/2021] [Indexed: 11/11/2022] Open
Abstract
Objective Bi-allelic loss-of-function mutations in TSHB, encoding the beta subunit of thyroid-stimulating hormone (TSH), cause congenital hypothyroidism. Homozygosity for the TSHB p.R75G variant, previously described in South Asian individuals, does not alter TSH function but abrogates its detection by some immune detection-based platforms, leading to erroneous diagnosis of hyperthyroidism. We set out to identify and determine the carrier rate of the p.R75G variant among clinically euthyroid Bene Israel Indian Jews, to examine the possible founder origin of this variant worldwide, and to determine the phenotypic effects of its heterozygosity. Design Molecular genetic studies of Bene Israel Jews and comparative studies with South Asian cohort. Methods TSHB p.R75G variant tested by Sanger sequencing and restriction fragment length polymorphism (RFLP). Haplotype analysis in the vicinity of the TSHB gene performed using SNP arrays. Results Clinically euthyroid individuals with low or undetectable TSH levels from three apparently unrelated Israeli Jewish families of Bene Israel ethnicity, originating from the Mumbai region of India, were found heterozygous or homozygous for the p.R75G TSHB variant. Extremely high carrier rate of p.R75G TSHB in Bene Israel Indian Jews (~4%) was observed. A haplotype block of 239.7 kB in the vicinity of TSHB shared by Bene Israel and individuals of South Asian origin was detected. Conclusions Our findings highlight the high prevalence of the R75G TSHB variant in euthyroid Bene Israel Indian Jews, demonstrate that heterozygosity of this variant can cause erroneous detection of subnormal TSH levels, and show that R75G TSHB is an ancient founder variant, delineating shared ancestry of its carriers.
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Affiliation(s)
- David Shaki
- Pediatric Endocrinology Unit, Saban Pediatric Medical Center for Israel, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marina Eskin-Schwartz
- Genetics Institute at Soroka University Medical Center and the Morris Kahn Laboratory of Human Genetics, National Center for Rare Diseases, at the Faculty of Health Sciences and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Noam Hadar
- Genetics Institute at Soroka University Medical Center and the Morris Kahn Laboratory of Human Genetics, National Center for Rare Diseases, at the Faculty of Health Sciences and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Emily Bosin
- Endocrinology Lab, Soroka University Medical Center, Beer Sheva, Israel
| | - Lior Carmon
- Pediatric Endocrinology Unit, Saban Pediatric Medical Center for Israel, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Samuel Refetoff
- Departments of Medicine and Pediatrics and the Committee on Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Eli Hershkovitz
- Pediatric Endocrinology Unit, Saban Pediatric Medical Center for Israel, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad S Birk
- Genetics Institute at Soroka University Medical Center and the Morris Kahn Laboratory of Human Genetics, National Center for Rare Diseases, at the Faculty of Health Sciences and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alon Haim
- Pediatric Endocrinology Unit, Saban Pediatric Medical Center for Israel, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Mughal MR, DeGiorgio M. Properties and unbiased estimation of F- and D-statistics in samples containing related and inbred individuals. Genetics 2022; 220:iyab090. [PMID: 34849832 PMCID: PMC8733448 DOI: 10.1093/genetics/iyab090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/26/2021] [Indexed: 11/14/2022] Open
Abstract
The Patterson F- and D-statistics are commonly used measures for quantifying population relationships and for testing hypotheses about demographic history. These statistics make use of allele frequency information across populations to infer different aspects of population history, such as population structure and introgression events. Inclusion of related or inbred individuals can bias such statistics, which may often lead to the filtering of such individuals. Here, we derive statistical properties of the F- and D-statistics, including their biases due to the inclusion of related or inbred individuals, their variances, and their corresponding mean squared errors. Moreover, for those statistics that are biased, we develop unbiased estimators and evaluate the variances of these new quantities. Comparisons of the new unbiased statistics to the originals demonstrates that our newly derived statistics often have lower error across a wide population parameter space. Furthermore, we apply these unbiased estimators using several global human populations with the inclusion of related individuals to highlight their application on an empirical dataset. Finally, we implement these unbiased estimators in open-source software package funbiased for easy application by the scientific community.
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Affiliation(s)
- Mehreen R Mughal
- Bioinformatics and Genomics at the Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, PA 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida
Atlantic University, Boca Raton, FL 33431, USA
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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [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] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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Digumarthi UK, Prakash R. A Cross-Sectional Evaluation of Self-Perceived Orthodontic Treatment Needs Amongst Tribal Adolescent With Remote Access to Orthodontic Treatment Using a Simplified Malocclusion Index. JOURNAL OF INDIAN ORTHODONTIC SOCIETY 2021. [DOI: 10.1177/03015742211056251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Self-perceived orthodontic treatment need is strongly influenced by what is perceived to be the esthetic norm amongst a community, and reluctance toward treatment amongst adolescents with clinically ascertained malocclusion may often be due to readily remediable factors. Of particular interest is the prevalence of malocclusion amongst such communities as a probable indicator of the role of diet and genetics in establishing a predominant clinical phenotype that may also play a role in the construct of what is perceived as the esthetic norm amongst the community, thereby influencing the self-perceived need for treatment. Studies aimed at evaluating the association between self-perceived esthetics, and self-perceived treatment need have not been performed amongst a population with no prior exposure to orthodontic treatment Objectives: The purpose of this study was to evaluate the self-perceived orthodontic treatment need amongst the tribal adolescents belonging to regions with remote access to orthodontic treatment by way of a verbally assigned index and to also identify the reasons of reluctance toward treatment to better understand how to make orthodontic treatment readily accessible to such populations. Participants, Materials, and Methods: The agency areas of Paderu located at 18.0833°N 82.667°E and Parvathipuram located at 18°46'N 83°25'E are 2 revenue districts of Visakhapatnam and Vizianagaram, respectively, in the state of Andhra Pradesh, India, that are home to various tribal populations with remote access to orthodontic treatment. A total of 2,016 school-going tribal adolescents of the Paderu revenue division and 819 tribal adolescents of the Parvathipuram revenue division were examined to ascertain the prevalence of malocclusion. Necessary consent and permissions were obtained from the tribal authorities, the school authorities, parents, and the institutional ethical clearance committee. The screening was done utilizing natural daylight in compliance with infection prevention and control protocol. Clinical examination aimed at categorizing the observed occlusion into either ideal occlusion or one of the three classes of Angle’s class I, II, and III malocclusions. The Simplified Malocclusion Index For Layperson Evaluation (SMILE) was verbally assigned in the vernacular language while interacting with each child and the findings made note of for calculation of relevant scores related to their orthodontic awareness, self-esteem as related to self-perceived esthetics, and their self-perceived need for treatment. Reasons for reluctance to undergo treatment were noted down if expressed. An initial group of 31 adolescents categorized as presenting with clinical malocclusion were randomly picked up and assigned the SMILE index a second time to assess the reliability of the index by way of Cohen’s kappa statistic. Results: The initial test group of 31 individuals assigned the SMILE twice showed a Cohen’s kappa of 0.93 validating almost perfect intraoperator agreement. The SMILE index revealed that 80.95% of the adolescents of Paderu revenue division had orthodontic awareness and 79.51% had self-perceived esthetics but only 15.97% felt a need for orthodontic treatment. Pearson’s Chi squared statistical analysis indicated a gender bias related to the self-perceived need for orthodontic treatment ( X 2 [1, N = 1,371] = 19.71, P < .001). The Index assigned to the Parvathipuram division revealed that 77.04% had orthodontic awareness and 78.38 had self-perceived esthetics but only 6.95% felt the need for orthodontic treatment. Pearson’s Chi squared statistical analysis indicated a gender bias related to the self-perceived need for orthodontic treatment ( X 2 [1, N = 764] = 4.95, P = .02). Conclusion: The self-perceived need for orthodontic treatment is often based on the self-perceived esthetics of an individual or the self-esteem as influenced by the perceived esthetic norm of the community. Orthodontic treatment of adolescents with borderline malocclusion derangements requires careful ascertaining of the actual perceived need of the patient to enable the rendering of a justifiable orthodontic treatment with the complete trust of the young patient. This helps build community trust in regions where orthodontic treatment has not yet made in roads and may help ensure higher end of treatment satisfaction levels.
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Affiliation(s)
- Uday Kumar Digumarthi
- Department of Orthodontics, Anil Neerukonda Institute of Dental Sciences, Visakhapatnam, Andhra Pradesh, India
- Shri Lalitha’s Superspecialty Dental Hospital, Dabagardens, Visakhapatnam, Andhra Pradesh, India
| | - R. Prakash
- Department of Orthodontics, Anil Neerukonda Institute of Dental Sciences, Visakhapatnam, Andhra Pradesh, India
- Department, Prosthodontics, Anil Neerukonda Institute of Dental Sciences, Andhra Pradesh, India
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Sirak KA, Fernandes DM, Lipson M, Mallick S, Mah M, Olalde I, Ringbauer H, Rohland N, Hadden CS, Harney É, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Patterson N, Pinhasi R, Thompson JC, Van Gerven D, Reich D. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat Commun 2021; 12:7283. [PMID: 34907168 PMCID: PMC8671435 DOI: 10.1038/s41467-021-27356-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022] Open
Abstract
Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.
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Affiliation(s)
- Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA.
- Earth Institute and School of Archaeology, University College Dublin, Dublin, 4, Ireland.
| | - Daniel M Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin, 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Harald Ringbauer
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Carla S Hadden
- Center for Applied Isotope Studies, University of Georgia, Athens, GA, 30602, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Anthropology, University of California, Santa Cruz, CA, 95064, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Ron Pinhasi
- Earth Institute and School of Archaeology, University College Dublin, Dublin, 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Jessica C Thompson
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA
- Department of Anthropology, Yale University, New Haven, CT, 06511, USA
- Yale Peabody Museum of Natural History, New Haven, CT, 06511, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
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Dash HR, Avila E, Jena SR, Kaitholia K, Agarwal R, Alho CS, Srivastava A, Singh AK. Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing. Int J Legal Med 2021; 136:465-473. [PMID: 34748086 DOI: 10.1007/s00414-021-02742-5] [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] [Received: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis-based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10-37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.
| | - Eduardo Avila
- Pontifical Catholic University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Soumya Ranjan Jena
- Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | | | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
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Rabbind Singh A, Gupta R, Shukla M, Jain A, Shukla D. Association of VEGFA promoter polymorphisms rs699947 and rs35569394 with diabetic retinopathy among North-Central Indian subjects: a case-control study. Ophthalmic Genet 2021; 43:80-87. [PMID: 34693874 DOI: 10.1080/13816810.2021.1992786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Diabetes mellitus type 2 is often described as the global pandemic of the 21st century with India emerging as its capital. Microvascular complications such as retinopathy associated with diabetes are a serious world health problem, leading to the already existing burden of blindness. The aim of this study was to determine whether VEGF gene polymorphisms rs35569394 and rs699947 are associated with DR in North Indians. MATERIALS AND METHODS North Indian subjects, diabetic controls with no retinopathy (DR I, n = 51), subjects with diabetes with mild-moderate retinal changes (DR II, n = 50), and subjects with diabetes with severe retinopathy with/without retinal neovascularization (DR III, n = 55) were recruited for this study. Genotyping of the VEGF gene I/D polymorphism was done by PCR and C/A polymorphism by PCR-RFLP method. RESULTS DD-genotype was 2.73 times over expressed among DR III category (p = .02; OR: 2.73; 95% CI: 1.20-6.19) as compared to DR I category among male subgroup. C-allele (rs699947) had 1.66-times more exposure among DR III as compared to DR I (C vs. A allele; p = .063; OR: 1.66; 95% CI: 0.97-2.84), probably due to high linkage disequilibrium between both the polymorphisms. CONCLUSIONS Results of our study support the hypothesis that D-allele and DD-genotype of rs35569394 have deleterious effect on the progression of DR. C-allele had skewed frequency towards DR III subjects owing to strong linkage disequilibrium between C-allele (rs699947) and D-allele (rs35569394).
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Affiliation(s)
| | - Rahul Gupta
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, India
| | - Manish Shukla
- Department of Exercise Physiology, Lakshmibai National Institute of Physical Education, Gwalior, India
| | - Anupreeti Jain
- Retina-Vitreous service, Ratan Jyoti Netralaya, Gwalior, India
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Shetty A, Bhat R, Babu B, Hegde MN, Shetty C, Shetty P, Latha Senthilkumar P. Occurrence and Morphology of MB2 Canals in Maxillary First Molars in an Indian Subpopulation: A Cone Beam Computed Tomography Study. JOURNAL OF HEALTH AND ALLIED SCIENCES NU 2021. [DOI: 10.1055/s-0041-1736268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Introduction Molars have been known to display varied morphologies. Maxillary first molar is the tooth with the largest volume and most complex root and root canal anatomy; also, possibly the most treated and least understood posterior tooth. The present study aimed to investigate the occurrence and morphology of MB2 canals in maxillary first molars in an Indian subpopulation (Dakshina kannada) using cone beam CT (CBCT) imaging.
Materials and Methods A total of 330 maxillary molars were placed on “U-” shaped modelling wax template, mimicking the natural arch and digitally scanned, of which 196 scans met the inclusion criteria and were analyzed for unusual root canal anatomy by CBCT. To analyze the occurrence and morphology of the canals, the acquired data was examined by two endodontists and discussed till an agreement was reached.
Results The results were subjected to descriptive analysis. The majority of patients 103 (52.6%) teeth showed the presence of MB2 canals. As much as 83.5% of teeth depicted Vertucci's type II morphology, and 16.5% teeth presented with Vertucci's type IV morphology.
Conclusion CBCT overcomes the limitations of conventional radiography. However, the decision to use CBCT in the management of endodontic problems must be based on a case-by-case basis and only when sufficient diagnostic information is not obtained from diagnostic tests.
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Affiliation(s)
- Aditya Shetty
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
| | - Raksha Bhat
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
| | - Bessy Babu
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
| | - Mithra N. Hegde
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
| | - Chitharanjan Shetty
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
| | - Preethesh Shetty
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
| | - Priyanka Latha Senthilkumar
- Department of Conservative Dentistry and Endodontics, AB Shetty Memorial Institute of Dental Sciences, Nitte (deemed to be) University, Mangalore, India
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Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis. Biochem Genet 2021; 60:987-1006. [PMID: 34661819 DOI: 10.1007/s10528-021-10141-z] [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: 04/10/2021] [Accepted: 10/07/2021] [Indexed: 10/20/2022]
Abstract
The Iranian gene pool is seen as an important human genetic resource for investigating the region connecting Mesopotamia and the Iranian plateau. The main objective of this study was to explore gene flow in nine Iranian ethnic/subpopulation groups (402 samples) by examining mtDNA HVS2 sequence variations. This then allowed us to detect mtDNA HVS2 sequence mutations in two independent thalassemia and cystic fibrosis patient sample groups. The patient groups did not explicitly belong to any of the aforementioned nine subpopulations. Across all subpopulations, the haplogroups B4a1c3a, H2a2a1, N10b, H2a2a2, and J1 were seen to be predominant. High haplogroup diversities along with admixture of the exotic groups were observed in this study. The Arab subpopulation was shown to be independent from the others. It was revealed that there is a far distant relationship between Arab and Azeri groups. The thalassemia patient group, represented an almost random sample of most Iranian ethnic groups, and revealed few significant differences (P < 0.05) in their HVS2 sequence. It turned out that the IVS II-I (G → A) mutation in the thalassemia β-globin gene was highly significant. Since the thalassemia patients in the present study represent many unique haplotypes, we can begin to comprehend the importance of mtDNA with this disease and the necessity for more studies in this context.
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Mamtani M, Jaisinghani MT, Jaiswal SG, Pipal KV, Patel AA, Kulkarni H. Genetic association of anthropometric traits with type 2 diabetes in ethnically endogamous Sindhi families. PLoS One 2021; 16:e0257390. [PMID: 34506595 PMCID: PMC8432747 DOI: 10.1371/journal.pone.0257390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 08/31/2021] [Indexed: 12/20/2022] Open
Abstract
Background Ethnically endogamous populations can shed light on the genetics of type 2 diabetes. Such studies are lacking in India. We conducted this study to determine the genetic and environmental contributions of anthropometric traits to type 2 diabetes risk in the Sindhi families in central India. Methods We conducted a family study in Indian Sindhi families with at least one case of type 2 diabetes. Variance components methods were used to quantify the genetic association of 18 anthropometric traits with eight type 2 diabetes related traits. Univariate and bivariate polygenic models were used to determine the heritability, genetic and environmental correlation of anthropometric traits with type 2 diabetes related traits. Results We included 1,152 individuals from 112 phenotyped families. The ascertainment-bias corrected prevalence of type 2 diabetes was 35%. Waist circumference, hip circumference and the biceps, triceps, subscapular and medial calf skinfold thicknesses were polygenically and significantly associated with type 2 diabetes. The range of heritability of the anthropometric traits and type 2 diabetes related traits was 0.27–0.73 and 0.00–0.39, respectively. Heritability of type 2 diabetes as a discrete trait was 0.35. Heritability curves demonstrated a substantial local influence of type 2 diabetes related traits. Bivariate trait analyses showed that biceps and abdominal skinfold thickness and all waist-containing indexes were strongly genetically correlated with type 2 diabetes. Conclusions In this first study of Sindhi families, we found evidence for genetic and environmental concordance of anthropometric traits with type 2 diabetes. Future studies need to probe into the genetics of type 2 diabetes in this population.
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Affiliation(s)
- Manju Mamtani
- Lata Medical Research Foundation, Nagpur, India
- M&H Research, LLC, San Antonio, Texas, United States of America
- * E-mail:
| | | | | | | | | | - Hemant Kulkarni
- Lata Medical Research Foundation, Nagpur, India
- M&H Research, LLC, San Antonio, Texas, United States of America
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Kumar L, Farias K, Prakash S, Mishra A, Mustak MS, Rai N, Thangaraj K. Dissecting the genetic history of the Roman Catholic populations of West Coast India. Hum Genet 2021; 140:1487-1498. [PMID: 34424406 DOI: 10.1007/s00439-021-02346-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
Migration and admixture history of populations have always been curious and an interesting theme. The West Coast of India harbours a rich diversity, bestowing various ethno-linguistic groups, with many of them having well-documented history of migrations. The Roman Catholic is one such distinct group, whose origin was much debated. While some historians and anthropologists relating them to ancient group of Gaud Saraswat Brahmins, others relating them for being members of the Jews Lost Tribes in the first Century migration to India. Historical records suggests that this community was later forcibly converted to Christianity by the Portuguese in Goa during the Sixteenth Century. Till date, no genetic study was done on this group to infer their origin and genetic affinity. Hence, we analysed 110 Roman Catholics from three different locations of West Coast of India including Goa, Kumta and Mangalore using both uniparental and autosomal markers to understand their genetic history. We found that the Roman Catholics have close affinity with the Indo-European linguistic groups, particularly Brahmins. Additionally, we detected genetic signal of Jews in the linkage disequilibrium-based admixture analysis, which was absent in other Indo-European populations, who are inhabited in the same geographical regions. Haplotype-based analysis suggests that the Roman Catholics consist of South Asian-specific ancestry and showed high drift. Ancestry-specific historical population size estimation points to a possible bottleneck around the time of Goan inquisition (fifteenth century). Analysis of the Roman Catholics data along with ancient DNA data of Neolithic and bronze age revealed that the Roman Catholics fits well in a basic model of ancient ancestral composition, typical of most of the Indo-European caste groups of India. Mitochondrial DNA (mtDNA) analysis suggests that most of the Roman Catholics have aboriginal Indian maternal genetic ancestry; while the Y chromosomal DNA analysis indicates high frequency of R1a lineage, which is predominant in groups with higher ancestral North Indian (ANI) component. Therefore, we conclude that the Roman Catholics of Goa, Kumta and Mangalore regions are the remnants of very early lineages of Brahmin community of India, having Indo-Europeans genetic affinity along with cryptic Jewish admixture, which needs to be explored further.
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Affiliation(s)
- Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Kranti Farias
- Canadian Institute for Jewish Research, Montreal, Canada
| | - Satya Prakash
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Anshuman Mishra
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, 590 53, Ulrika, Sweden
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, 574199, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Uttar Pradesh, 53 University Road, Lucknow, 226007, India.
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India.
- DBT-Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, 500007, India.
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Nath S, Shrivastava P, Kumawat RK, Dixit S, Chaubey G. Genomic polymorphism in tribal population of Tripura: Signifying their closer affinity with the Nepalese and Tibetan populations. Ann Hum Biol 2021; 48:360-368. [PMID: 34340604 DOI: 10.1080/03014460.2021.1957148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND India is the second most populous country in the world, which is aligned into various community segments. AIM To evaluate the genetic diversity of the tribal population of Tripura, we carried out this study. SUBJECTS AND METHODS 15 autosomal STR markers were used for investigation of genomic diversity, inter- and intra- population relationships among the studied population, and other reported neighbouring tribal and caste populations. RESULTS Results indicated that the tribals of Tripura share their closer genetic affinity with the Trans-Himalayan (Nepalese, Bhutanese and Tibetan) populations. Locus D18S51 was found as the most discriminatory among all the studied loci with uppermost discrimination power (PD = 0.964) and lowest matching probability (Pm = 0.036) in the study. All the evaluated loci herein are useful, having the maximum value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999746), combined paternity index (CPI = 3 × 105) and combined matching probability (CPm = 2.12 × 1 0 -7). CONCLUSION Population genetic analysis showed that the studied population has genetic relatedness with the compared Nepalese and Tibetan populations i.e., Kathmandu, Tibet, Newar, and Gorkhas, followed by eastern and central Indian populations.
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Affiliation(s)
- Subhankar Nath
- DNA Typing Division, State Forensic Science Laboratory, Narsingarh, Agartala, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, India
| | - Shivani Dixit
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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Sengupta D, Banerjee S, Mukhopadhyay P, Mitra R, Chaudhuri T, Sarkar A, Bhattacharjee G, Nath S, Roychoudhury S, Bhattacharjee S, Sengupta M. A comprehensive meta-analysis and a case-control study give insights into genetic susceptibility of lung cancer and subgroups. Sci Rep 2021; 11:14572. [PMID: 34272429 PMCID: PMC8285487 DOI: 10.1038/s41598-021-92275-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Reports of genetic association of polymorphisms with lung cancer in the Indian subcontinent are often conflicting. To summarise and replicate published evidence for association with lung cancer and its subgroups. We performed a meta-analysis of candidate associations on lung cancer, its histological subtypes and smoking status in the Indian subcontinent following PRISMA guidelines. Multiple testing corrections were done by the Benjamini-Hochberg method through assessment of significance at a false discovery rate of 10%. We genotyped and investigated rs1048943/CYP1A1 in a case-control sample from eastern India, followed by its global meta-analysis using a similar protocol. Meta-analysis of 18 variants of 11 genes reported in 39 studies (7630 cases and 8169 controls) showed significant association of rs1048943/CYP1A1 [2.07(1.49-2.87)] and rs4646903/CYP1A1 [1.48(1.93-1.95)] with overall lung cancer risk at 10% FDR, while nominal association (p < 0.05) was observed for del1/GSTT1, del2/GSTM1, rs1695/GSTP1 and rs17037102/ DKK2. Subtype analysis showed a significant association of del1/GSTT1 with adenocarcinoma, rs4646903/CYP1A1 with squamous carcinoma, and rs1048943/CYP1A1 with both. Association of rs4646903/CYP1A1 in smokers and effect modification by meta-regression analysis was observed. Genotyping of rs1048943/CYP1A1 that presented significant heterogeneity (p < 0.1) revealed an association with adenocarcinoma among eastern Indian smokers, while a global meta-analysis in 10458 cases and 10871 controls showed association with lung cancer and its subgroups. This study identified the susceptibility loci for lung cancer and its covariate-subgroups.
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Affiliation(s)
- Debmalya Sengupta
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Souradeep Banerjee
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Pramiti Mukhopadhyay
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Dr., San Antonio, TX-78229, USA
| | - Ritabrata Mitra
- Department of CHEST, IPGME&R, 244 A.J.C. Bose Road, Kolkata, 700020, India
| | - Tamohan Chaudhuri
- Saroj Gupta Cancer Centre and Research Institute, Mahatma Gandhi Road, Thakurpukur, Kolkata, 700063, India
| | - Abhijit Sarkar
- Saroj Gupta Cancer Centre and Research Institute, Mahatma Gandhi Road, Thakurpukur, Kolkata, 700063, India
| | - Gautam Bhattacharjee
- Saroj Gupta Cancer Centre and Research Institute, Mahatma Gandhi Road, Thakurpukur, Kolkata, 700063, India
| | - Somsubhra Nath
- Saroj Gupta Cancer Centre and Research Institute, Mahatma Gandhi Road, Thakurpukur, Kolkata, 700063, India
| | - Susanta Roychoudhury
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Samsiddhi Bhattacharjee
- National Institute of Biomedical Genomics, Near Netaji Subhas Sanatorium Post Office, Kalyani, West Bengal, 741251, India.
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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45
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Jablonski NG. The evolution of human skin pigmentation involved the interactions of genetic, environmental, and cultural variables. Pigment Cell Melanoma Res 2021; 34:707-729. [PMID: 33825328 PMCID: PMC8359960 DOI: 10.1111/pcmr.12976] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
The primary biological role of human skin pigmentation is as a mediator of penetration of ultraviolet radiation (UVR) into the deep layers of skin and the cutaneous circulation. Since the origin of Homo sapiens, dark, protective constitutive pigmentation and strong tanning abilities have been favored under conditions of high UVR and represent the baseline condition for modern humans. The evolution of partly depigmented skin and variable tanning abilities has occurred multiple times in prehistory, as populations have dispersed into environments with lower and more seasonal UVR regimes, with unique complements of genes and cultural practices. The evolution of extremes of dark pigmentation and depigmentation has been rare and occurred only under conditions of extremely high or low environmental UVR, promoted by positive selection on variant pigmentation genes followed by limited gene flow. Over time, the evolution of human skin pigmentation has been influenced by the nature and course of human dispersals and modifications of cultural practices, which have modified the nature and actions of skin pigmentation genes. Throughout most of prehistory and history, the evolution of human skin pigmentation has been a contingent and non-deterministic process.
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Affiliation(s)
- Nina G. Jablonski
- Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkPAUSA
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46
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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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47
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Complete mitogenomes document substantial genetic contribution from the Eurasian Steppe into northern Pakistani Indo-Iranian speakers. Eur J Hum Genet 2021; 29:1008-1018. [PMID: 33637889 DOI: 10.1038/s41431-021-00829-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/26/2022] Open
Abstract
To elucidate whether Bronze Age population dispersals from the Eurasian Steppe to South Asia contributed to the gene pool of Indo-Iranian-speaking groups, we analyzed 19,568 mitochondrial DNA (mtDNA) sequences from northern Pakistani and surrounding populations, including 213 newly generated mitochondrial genomes (mitogenomes) from Iranian and Dardic groups, both speakers from the ancient Indo-Iranian branch in northern Pakistan. Our results showed that 23% of mtDNA lineages with west Eurasian origin arose in situ in northern Pakistan since ~5000 years ago (kya), a time depth very close to the documented Indo-European dispersals into South Asia during the Bronze Age. Together with ancient mitogenomes from western Eurasia since the Neolithic, we identified five haplogroups (~8.4% of maternal gene pool) with roots in the Steppe region and subbranches arising (age ~5-2 kya old) in northern Pakistan as genetic legacies of Indo-Iranian speakers. Some of these haplogroups, such as W3a1b that have been found in the ancient samples from the late Bronze Age to the Iron Age period individuals of Swat Valley northern Pakistan, even have sub-lineages (age ~4 kya old) in the southern subcontinent, consistent with the southward spread of Indo-Iranian languages. By showing that substantial genetic components of Indo-Iranian speakers in northern Pakistan can be traced to Bronze Age in the Steppe region, our study suggests a demographic link with the spread of Indo-Iranian languages, and further highlights the corridor role of northern Pakistan in the southward dispersal of Indo-Iranian-speaking groups.
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48
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Yelmen B, Marnetto D, Molinaro L, Flores R, Mondal M, Pagani L. Improving Selection Detection with Population Branch Statistic on Admixed Populations. Genome Biol Evol 2021; 13:6151747. [PMID: 33638983 PMCID: PMC8046333 DOI: 10.1093/gbe/evab039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.
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Affiliation(s)
- Burak Yelmen
- Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Ludovica Molinaro
- Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | | | - Luca Pagani
- Institute of Genomics, University of Tartu, Estonia.,Department of Biology, University of Padova, Italy
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49
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Nizamuddin S, Dubey S, Singh S, Sharma S, Machha P, Thangaraj K. CYP2C9 Variations and Their Pharmacogenetic Implications Among Diverse South Asian Populations. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:135-147. [PMID: 33536773 PMCID: PMC7850565 DOI: 10.2147/pgpm.s272015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/01/2020] [Indexed: 11/23/2022]
Abstract
Introduction Allelic frequency distribution of drug metabolizing enzyme genes among populations is important to identify risk groups for adverse drug reaction and to select representative populations for clinical trials. Although India emerged as an important hub for clinical trials, information about the pharmacogenetic diversity for this region is still lacking. Here, we investigated genetic diversity of cytochrome-P450-2C9 (CYP2C9) gene which metabolizes wide range of drugs and is highly expressed in the human liver. Methods In total, 1278 individuals from 36 diverse Indian populations, 210 individuals from in-house data-repository and 489 other South Asian samples from the 1000 Genomes Project were selected. Variants observed in CYP2C9 gene were subjected to various statistical analyses. Results High frequency of CYP2C9*3 (~13%) and CYP2C9*3/*3 (~1%) was observed among South Asians, compared to 21 populations living outside the Indian subcontinent. The allelic/genotypic frequency does not correlate with geographical location or linguistic affiliation, except populations speaking Tibeto-Burmans language, who have lower frequency of CYP2C9*3 and CYP2C9*3/*3. Since, South Asians practice strict endogamy, presence of unique mutation and high frequency of homozygous genotypes not surprising. CYP2C9*3 has been associated with therapeutic response.The effect of CYP2C9*3/*3 is more pronounced compared to heterozygous and wild type homozygous genotypes as evident in many in vitro studies. As South Asians have high frequency, it would be interesting to explore potential of CYP2C9*3 as a marker for personalized therapy. Our study revealed several rare functional variants, which form eight novel and rare haplotypes of CYP2C9 (CYP2C9*63–*70). Of which, CYP2C9*64, *65, *66, *68, *69 and *70 haplotypes are South Asian-specific. Conclusion Overall, we find high genetic heterogeneity within South Asians and identified South Asian-specific putative functional CYP2C9 haplotypes. High frequency of CYP2C9*3 and CYP2C9*3/*3 was observed in South Asian populations. Taken together, current study greatly enriches the knowledge of naturally occurring CYP2C9 variants and its diversity in South Asia, which are relevant to further CYP2C9-related functional research and for personalized medicine.
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Affiliation(s)
- Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,German Cancer Consortium (DKTK) c/o Zentrale Klinische Forschung (ZKF), University Medical Center, Freiburg, Germany
| | - Shivendra Dubey
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Saurav Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Pratheusa Machha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,AcSIR (Academy of Scientific and Innovative Research), CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,AcSIR (Academy of Scientific and Innovative Research), CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,DBT-Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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50
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Bianco E, Laval G, Font-Porterias N, García-Fernández C, Dobon B, Sabido-Vera R, Sukarova Stefanovska E, Kučinskas V, Makukh H, Pamjav H, Quintana-Murci L, Netea MG, Bertranpetit J, Calafell F, Comas D. Recent Common Origin, Reduced Population Size, and Marked Admixture Have Shaped European Roma Genomes. Mol Biol Evol 2020; 37:3175-3187. [PMID: 32589725 DOI: 10.1093/molbev/msaa156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Roma Diaspora-traditionally known as Gypsies-remains among the least explored population migratory events in historical times. It involved the migration of Roma ancestors out-of-India through the plateaus of Western Asia ultimately reaching Europe. The demographic effects of the Diaspora-bottlenecks, endogamy, and gene flow-might have left marked molecular traces in the Roma genomes. Here, we analyze the whole-genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. Our analyses revealed a strong, early founder effect followed by a drastic reduction of ∼44% in effective population size. The Roma common ancestors split from the Punjabi population, from Northwest India, some generations before the Diaspora started, <2,000 years ago. The initial bottleneck and subsequent endogamy are revealed by the occurrence of extensive runs of homozygosity and identity-by-descent segments in all Roma populations. Furthermore, we provide evidence of gene flow from Armenian and Anatolian groups in present-day Roma, although the primary contribution to Roma gene pool comes from non-Roma Europeans, which accounts for >50% of their genomes. The linguistic and historical differentiation of Roma in migrant groups is confirmed by the differential proportion, but not a differential source, of European admixture in the Roma groups, which shows a westward cline. In the present study, we found that despite the strong admixture Roma had in their diaspora, the signature of the initial bottleneck and the subsequent endogamy is still present in Roma genomes.
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Affiliation(s)
- Erica Bianco
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Guillaume Laval
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, UMR 2000, CNRS, Institut Pasteur, Paris, France
| | - Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Carla García-Fernández
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Begoña Dobon
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rubén Sabido-Vera
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Emilija Sukarova Stefanovska
- Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Science and Arts, Skopje, Macedonia
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Halyna Makukh
- Institute of Hereditary Pathology of the Ukrainian Academy of Medical Sciences, Lviv, Ukraine
| | - Horolma Pamjav
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, UMR 2000, CNRS, Institut Pasteur, Paris, France.,Chair Human Genomics and Evolution, Collège de France, Paris, France
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences 12 Institute (LIMES), University of Bonn, Bonn, Germany
| | - Jaume Bertranpetit
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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