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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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Walia GK, Sharma P, Agarwal T, Lal M, Negandhi H, Prabhakaran D, Khadgawat R, Sachdeva MP, Gupta V. Genetic associations of TMEM154, PRC1 and ZFAND6 loci with type 2 diabetes in an endogamous business community of North India. PLoS One 2023; 18:e0291339. [PMID: 37738238 PMCID: PMC10516421 DOI: 10.1371/journal.pone.0291339] [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: 03/10/2023] [Accepted: 08/27/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND More than 250 loci have been identified by genome-wide scans for type 2 diabetes in different populations. South Asians have a very different manifestation of the diseases and hence role of these loci need to be investigated among Indians with huge burden of cardio-metabolic disorders. Thus the present study aims to validate the recently identified GWAS loci in an endogamous caste population in North India. METHODS 219 T2D cases and 184 controls were recruited from hospitals and genotyped for 15 GWAS loci of T2D. Regression models adjusted for covariates were run to examine the association for T2D and fasting glucose levels. RESULTS We validated three variants for T2D namely, rs11634397 at ZFAND6 (OR = 3.05, 95%CI = 1.02-9.19, p = 0.047) and rs8042680 at PRC1 (OR = 3.67, 95%CI = 1.13-11.93, p = 0.031) showing higher risk and rs6813195 at TMEM154 (OR = 0.28, 95%CI = 0.09-0.90, p = 0.033) showing protective effect. The combined risk of 9 directionally consistent variants was also found to be significantly associated with T2D (OR = 1.91, 95%CI = 1.18-3.08, p = 0.008). One variant rs10842994 at KLHDC5 was validated for 9.15mg/dl decreased fasting glucose levels (SE = -17.25-1.05, p = 0.027). CONCLUSION We confirm the role of ZFAND6, PRC1 and TMEM154 in the pathophysiology of type 2 diabetes among Indians. More efforts are needed with larger sample sizes to validate the diabetes GWAS loci in South Asian populations for wider applicability.
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Affiliation(s)
- Gagandeep Kaur Walia
- Public Health Foundation of India, Gurugram, India
- Centre for Chronic Disease Control, Safdarjung Development Area, New Delhi, India
| | - Pratiksha Sharma
- Indian Institute of Public Health-Delhi, Public Health Foundation of India, Gurugram, India
| | - Tripti Agarwal
- Indian Institute of Public Health-Delhi, Public Health Foundation of India, Gurugram, India
| | - Moti Lal
- Department of Anthropology, University of Delhi, Delhi, India
| | | | - Dorairaj Prabhakaran
- Public Health Foundation of India, Gurugram, India
- Centre for Chronic Disease Control, Safdarjung Development Area, New Delhi, India
| | - Rajesh Khadgawat
- Department of Endocrinology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | | | - Vipin Gupta
- Department of Anthropology, University of Delhi, Delhi, India
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Shruti T, Khanna D, Khan A, Dandpat A, Tiwari M, Singh AG, Mishra A, Shetty A, Birur P, Chaturvedi P. Status and Determinants of Early Detection of Oral Premalignant and Malignant Lesions in India. Cancer Control 2023; 30:10732748231159556. [PMID: 36809192 PMCID: PMC9947682 DOI: 10.1177/10732748231159556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
It has been over four decades since the launch of the National Cancer Control Programme in India, yet the cancer screening rates for oral cancer remain unremarkable. Moreover, India is bracing a large burden of oral cancer with poor survival rates. An effective public health programme implementation relies on a multitude of factors related to cost-effective evidence-based interventions, the healthcare delivery system, public health human resource management, community behaviour, partnership with stakeholders, identifying opportunities and political commitment. In this context, we discuss the various challenges in the early detection of oral premalignant and malignant lesions and potential solutions.
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Affiliation(s)
- Tulika Shruti
- Departmentof Preventive Oncology,
Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi Bhabha
Cancer Hospital (HBCH), Tata Memorial Centres, Varanasi, India
| | - Divya Khanna
- Departmentof Preventive Oncology,
Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi Bhabha
Cancer Hospital (HBCH), Tata Memorial Centres, Varanasi, India,Divya Khanna, MD, Department of Preventive
Oncology, Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi
Bhabha Cancer Hospital (HBCH), Tata Memorial Centres, Banaras Hindu University,
Campus, Sundar Bagiya Colony, Sundarpur, Varanasi 221005, India.
| | - Aqusa Khan
- Departmentof Preventive Oncology,
Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi Bhabha
Cancer Hospital (HBCH), Tata Memorial Centres, Varanasi, India
| | - Abhishek Dandpat
- Departmentof Preventive Oncology,
Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi Bhabha
Cancer Hospital (HBCH), Tata Memorial Centres, Varanasi, India
| | - Manish Tiwari
- Department of Head and Neck
Oncology, Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi
Bhabha Cancer Hospital (HBCH), Tata Memorial Centres, Varanasi, India
| | - Arjun G. Singh
- Department of Head and Neck
Oncology, Tata Memorial Centre, Mumbai, India
| | - Aseem Mishra
- Department of Head and Neck
Oncology, Mahamana Pandit Madan Mohan Malaviya Cancer Centre (MPMMCC) and Homi
Bhabha Cancer Hospital (HBCH), Tata Memorial Centres, Varanasi, India
| | | | - Praveen Birur
- Department of Oral Medicine and
Radiology, Consultant Biocon Foundation and Integrated Head and Neck Programme,
Mazumdar Shaw Medical Foundation, KLES Institute of Dental
Sciences, Bengaluru, India
| | - Pankaj Chaturvedi
- Department of Surgical Oncology, Homi Bhabha National
Institute, Anushakti Nagar, India,Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
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Song M, Wang X, Zhao C, Qian X, Lang M, Hou Y, Song F. Inference of population structure and admixture proportion from Y chromosomal data of Chinese population. Electrophoresis 2022; 43:2351-2362. [PMID: 35973689 DOI: 10.1002/elps.202200041] [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: 02/18/2022] [Revised: 07/14/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
In the past two decades, Y chromosome data has been generated for human population genetic studies. These Y chromosome datasets were produced with various testing methods and markers, thus difficult to combine them for a comprehensive analysis. In this study, we combine four human Y chromosomal datasets of Han, Tibetan, Hui, and Li ethnic groups. The dataset contains 27 microsatellites and 137 single nucleotide polymorphisms these populations share in common. We assembled a single dataset containing 2439 individuals from 25 nationwide populations in China. A systematic analysis of genetic distance and clustering was performed. To determine the gene flow of the studied population with worldwide populations, we modeled the ancestry informative markers. The reference panel was regarded as a mixture of South Asian (SAS), East Asian (EAS), European (EUR), African (AFR), and American (AMR) populations from 1000 Genomes data of Y chromosome using nonlinear data-fitting. We then calculated the admixture proportion of these four studied populations with 26 worldwide populations. The results showed that the Han and Hui have great genetic affinity, and Hui is the most admixed ethnic group, with 61.53% EAS, 34.65% SAS, 1.91% AFR, 1.56% AMR, and 0.04% EUR ancestry component (the AMR is highly admixed and thus should be ignored). All the other three ethnic groups contained more than 97% EAS ancestry component. The Li is the least admixed population in this study. The combined dataset in this study is the largest of this kind reported to date and proposes reference population data for use in future paternal genetic studies and forensic genealogical identification.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University; Med+Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, P. R. China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Xindi Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Chenxi Zhao
- College of Computer Science, Sichuan University, Chengdu, P. R. China
| | - Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Min Lang
- Law School, Sichuan University, Chengdu, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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Ikram MS, Mehmood T, Rakha A, Akhtar S, Khan MIM, Al-Qahtani WS, Safhi FA, Hadi S, Wang CC, Adnan A. Genetic diversity and forensic application of Y-filer STRs in four major ethnic groups of Pakistan. BMC Genomics 2022; 23:788. [PMID: 36451116 PMCID: PMC9714238 DOI: 10.1186/s12864-022-09028-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: 06/12/2022] [Accepted: 09/14/2022] [Indexed: 12/05/2022] Open
Abstract
17 Y-chromosomal STRs which are part of the Yfiler Amplification Kit were investigated in 493 unrelated Pakistani individuals belonging to the Punjabi, Sindhi, Baloch, and Pathan ethnic groups. We have assessed the forensic parameters and population genetic structure for each group. Among the 493 unrelated individuals from four ethnic groups (128 Baloch, 122 Pathan, 108 Punjabi, and 135 Sindhi), 82 haplotypes were observed with haplotype diversity (HD) of 0.9906 in Baloch, 102 haplotypes with HD value of 0.9957 in Pathans, 80 haplotypes with HD value of 0.9924 in Punjabi, and 105 haplotypes with HD value of 0.9945 in the Sindhi population. The overall gene diversity for Baloch, Pathan, Punjabi, and Sindhi populations was 0.6367, 0.6479, 0.6657, and 0.6112, respectively. The results had shown us that Pakistani populations do not have a unique set of genes but share the genetic affinity with regional (Central Asia and Northern India) populations. The observed low gene diversity (heterozygosity) values may be because of endogamy trends and this observation is equally supported by the results of forensic parameters which are mostly static across 4 combinations (minimal STRs, extended 11 Y-STRs, Powerplex 12 Y System, and Yfiler 17 Y-STRs) of STRs in these four populations.
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Affiliation(s)
- Muhammad Salman Ikram
- grid.12955.3a0000 0001 2264 7233Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China ,grid.412782.a0000 0004 0609 4693Institute of Chemistry, University of Sargodha, Sargodha, 40100 Punjab Pakistan
| | - Tahir Mehmood
- grid.412782.a0000 0004 0609 4693Institute of Chemistry, University of Sargodha, Sargodha, 40100 Punjab Pakistan ,grid.11173.350000 0001 0670 519XCentre for Applied and Molecular Biology (CAMB), University of the Punjab, Lahore, 53700 Punjab Pakistan
| | - Allah Rakha
- grid.412956.d0000 0004 0609 0537Department of Forensic Sciences, University of Health Sciences, Lahore, 54600 Pakistan
| | - Sareen Akhtar
- grid.412956.d0000 0004 0609 0537Department of Forensic Sciences, University of Health Sciences, Lahore, 54600 Pakistan
| | | | - Wedad Saeed Al-Qahtani
- grid.472319.a0000 0001 0708 9739Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh, 11452 Kingdom of Saudi Arabia
| | - Fatmah Ahmed Safhi
- grid.449346.80000 0004 0501 7602Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671 Saudi Arabia
| | - Sibte Hadi
- grid.472319.a0000 0001 0708 9739Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh, 11452 Kingdom of Saudi Arabia
| | - Chuan-Chao Wang
- grid.12955.3a0000 0001 2264 7233Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Atif Adnan
- grid.12955.3a0000 0001 2264 7233Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China ,grid.472319.a0000 0001 0708 9739Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh, 11452 Kingdom of Saudi Arabia
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Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq. BMC Genomics 2022; 23:763. [DOI: 10.1186/s12864-022-09005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/09/2022] [Indexed: 11/23/2022] Open
Abstract
Abstract
Background
The Kurds as an ethnic group are believed to be a combination of earlier Indo-European tribes who migrated and inhabited a mountainous area thousands of years ago. However, as it is difficult to describe the precise history of their origin, it is necessary to investigate their population relationship with other geographical and ethnic groups.
Results
Seventeen Short Tandem Repeat markers on the Y chromosome (Y-STR) included in the AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, USA) were used to type DNA samples from the Sorani (Central) Kurdish population in Sulaymaniyah province. One hundred fifty-seven haplotypes were obtained from 162 unrelated male individuals. The highest and lowest gene diversities were DYS385a/b (GD = 0.848) and DYS392 (GD = 0.392), respectively. The haplotypes were used to predict the most likely haplogroups in the Sulaymaniyah population.
Conclusion
Haplogroup prediction indicated predominance (28%) of subclade J2 (44/157) in the Sorani Kurds, northeast of Iraq. The pairwise genetic distance results showed that the Kurdish group clustered along with Asian populations, whereas the furthest countries were Europeans and Africans.
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He G, Adnan A, Al-Qahtani WS, Safhi FA, Yeh HY, Hadi S, Wang CC, Wang M, Liu C, Yao J. Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.939659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.
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Adnan A, Rakha A, Lazim H, Nazir S, Al-Qahtani WS, Abdullah Alwaili M, Hadi S, Wang CC. Are Roma People Descended from the Punjab Region of Pakistan: A Y-Chromosomal Perspective. Genes (Basel) 2022; 13:genes13030532. [PMID: 35328085 PMCID: PMC8951058 DOI: 10.3390/genes13030532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/01/2023] Open
Abstract
Gypsies are a separate ethnic group living in Pakistan and some other countries as well. They are mostly known as ‘Roma’ and ‘untouchables’. They have different types of lifestyles as compared to other common people, as they always keep migrating from one place to another. They do not have proper houses; they live in tent houses and most probably work on daily wages to earn their living. Gypsies cannot be specified according to the place of residence and can only be classified according to their migration route. Previous historical and linguistic research showed the north Indian origin of Roma people. The present study collected 285 unrelated Roma individuals living in Punjab and typed with the Goldeneye Y20 system. Allelic frequencies ranged between 0.0035 and 0.5266, with haplotype diversity (HD) of 0.9999 and discrimination capacity (DC) of 0.8790. Gene diversity (GD) ranged from 0.6489 (DYS391) to 0.9764 (DYS391) (DY385ab). A total of 223 unique alleles were observed. Interestingly, the haplogroup R accounted for 40.56% and J for 22.06%. In MDS analysis, Pakistani Roma formed a close cluster with Roma from Constanta, Romania. The migration pattern of the Roma population from Pakistan, India and Europe was inferred using coalescence theory in the Migrate-n program. Overlapping Y-STR data were used to test different migration models. These migration models showed us the dominant gene flow from Pakistan to India and Europe to Pakistan. The results of our study showed that Y STRs provided substantially stronger discriminatory power in the Pakistani Roma population.
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Affiliation(s)
- Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361000, China
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh 11452, Saudi Arabia; (W.S.A.-Q.); (S.H.)
- Correspondence: (A.A.); (C.-C.W.)
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan; (A.R.); (S.N.)
| | - Hayder Lazim
- Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk L39 4QP, UK;
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan; (A.R.); (S.N.)
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh 11452, Saudi Arabia; (W.S.A.-Q.); (S.H.)
| | - Maha Abdullah Alwaili
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 84428, Saudi Arabia;
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh 11452, Saudi Arabia; (W.S.A.-Q.); (S.H.)
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361000, China
- Correspondence: (A.A.); (C.-C.W.)
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Al Zahmi F, Habuza T, Awawdeh R, Elshekhali H, Lee M, Salamin N, Sajid R, Kiran D, Nihalani S, Smetanina D, Talako T, Neidl-Van Gorkom K, Zaki N, Loney T, Statsenko Y. Ethnicity-Specific Features of COVID-19 Among Arabs, Africans, South Asians, East Asians, and Caucasians in the United Arab Emirates. Front Cell Infect Microbiol 2022; 11:773141. [PMID: 35368452 PMCID: PMC8967254 DOI: 10.3389/fcimb.2021.773141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/22/2021] [Indexed: 01/08/2023] Open
Abstract
BackgroundDubai (United Arab Emirates; UAE) has a multi-national population which makes it exceptionally interesting study sample because of its unique demographic factors.ObjectiveTo stratify the risk factors for the multinational society of the UAE.MethodsA retrospective chart review of 560 patients sequentially admitted to inpatient care with laboratory confirmed COVID-19 was conducted. We studied patients’ demographics, clinical features, laboratory results, disease severity, and outcomes. The parameters were compared across different ethnic groups using tree-based estimators to rank the ethnicity-specific disease features. We trained ML classification algorithms to build a model of ethnic specificity of COVID-19 based on clinical presentation and laboratory findings on admission.ResultsOut of 560 patients, 43.6% were South Asians, 26.4% Middle Easterns, 16.8% East Asians, 10.7% Caucasians, and 2.5% are under others. UAE nationals represented half of the Middle Eastern patients, and 13% of the entire cohort. Hypertension was the most common comorbidity in COVID-19 patients. Subjective complaint of fever and cough were the chief presenting symptoms. Two-thirds of the patients had either a mild disease or were asymptomatic. Only 20% of the entire cohort needed oxygen therapy, and 12% needed ICU admission. Forty patients (~7%) needed invasive ventilation and fifteen patients died (2.7%). We observed differences in disease severity among different ethnic groups. Caucasian or East-Asian COVID-19 patients tended to have a more severe disease despite a lower risk profile. In contrast to this, Middle Eastern COVID-19 patients had a higher risk factor profile, but they did not differ markedly in disease severity from the other ethnic groups. There was no noticeable difference between the Middle Eastern subethnicities—Arabs and Africans—in disease severity (p = 0.81). However, there were disparities in the SOFA score, D-dimer (p = 0.015), fibrinogen (p = 0.007), and background diseases (hypertension, p = 0.003; diabetes and smoking, p = 0.045) between the subethnicities.ConclusionWe observed variations in disease severity among different ethnic groups. The high accuracy (average AUC = 0.9586) of the ethnicity classification model based on the laboratory and clinical findings suggests the presence of ethnic-specific disease features. Larger studies are needed to explore the role of ethnicity in COVID-19 disease features.
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Affiliation(s)
- Fatmah Al Zahmi
- Mediclinic Parkview Hospital, Dubai, United Arab Emirates
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- *Correspondence: Fatmah Al Zahmi, ; Yauhen Statsenko, ;
| | - Tetiana Habuza
- College of Information Technology, United Arab Emirates University, Al Ain, United Arab Emirates
- Big Data Analytics Center, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Rasha Awawdeh
- Mediclinic Parkview Hospital, Dubai, United Arab Emirates
| | | | - Martin Lee
- Mediclinic Parkview Hospital, Dubai, United Arab Emirates
| | - Nassim Salamin
- Mediclinic Parkview Hospital, Dubai, United Arab Emirates
| | - Ruhina Sajid
- Mediclinic Parkview Hospital, Dubai, United Arab Emirates
| | - Dhanya Kiran
- Mediclinic Parkview Hospital, Dubai, United Arab Emirates
| | | | - Darya Smetanina
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Tatsiana Talako
- Belarusian Medical Academy of Postgraduate Education, Minsk, Belarus
- Minsk Scientific and Practical Center for Surgery, Transplantology and Hematology, Minsk, Belarus
| | - Klaus Neidl-Van Gorkom
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Nazar Zaki
- College of Information Technology, United Arab Emirates University, Al Ain, United Arab Emirates
- Big Data Analytics Center, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Yauhen Statsenko
- Big Data Analytics Center, United Arab Emirates University, Al Ain, United Arab Emirates
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- *Correspondence: Fatmah Al Zahmi, ; Yauhen Statsenko, ;
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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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11
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Babić Jordamović N, Kojović T, Dogan S, Bešić L, Salihefendić L, Konjhodžić R, Škaro V, Projić P, Hadžiavdić V, Ašić A, Marjanović D. Haplogroup Prediction Using Y-Chromosomal Short Tandem Repeats in the General Population of Bosnia and Herzegovina. Front Genet 2021; 12:671467. [PMID: 34178033 PMCID: PMC8226213 DOI: 10.3389/fgene.2021.671467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
Abstract
Human Y-chromosomal haplogroups are an important tool used in population genetics and forensic genetics. A conventional method used for Y haplogroup assignment is based on a set of Y-single nucleotide polymorphism (SNP) markers deployed, which exploits the low mutation rate nature of these markers. Y chromosome haplogroups can be successfully predicted from Y-short tandem repeat (STR) markers using different software packages, and this method gained much attention recently due to its labor-, time-, and cost-effectiveness. The present study was based on the analysis of a total of 480 adult male buccal swab samples collected from different regions of Bosnia and Herzegovina. Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. The results revealed the existence of 14 different haplogroups, with I2a, R1a, and E1b1b being the most prevalent with frequencies of 43.13, 14.79, and 14.58%, respectively. Compared to the previously published studies on Bosnian-Herzegovinian population based on Y-SNP and Y-STR data, this study represents an upgrade of molecular genetic data with a significantly larger number of samples, thus offering more accurate results and higher probability of detecting rare haplogroups.
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Affiliation(s)
- Naida Babić Jordamović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Tamara Kojović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Serkan Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Lana Salihefendić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | | | - Vedrana Škaro
- Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.,DNA Laboratory, Genos Ltd., Zagreb, Croatia
| | - Petar Projić
- Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.,DNA Laboratory, Genos Ltd., Zagreb, Croatia
| | - Vesna Hadžiavdić
- Department of Biology, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Adna Ašić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
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12
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Rubab A, Shafique M, Javed F, Saleem S, Zahra FT, McNevin D, Shahid AA. Population genetic portrait of Pakistani Lahore-Christians based on 32 STR loci. Sci Rep 2020; 10:18960. [PMID: 33144642 PMCID: PMC7609739 DOI: 10.1038/s41598-020-76016-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFℓSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples. A total of 147 alleles were observed in 15 loci and allele 11 at the TPOX locus was the most frequent with frequency value (0.464). The data revealed that the Christian population has unique genetic characteristics with respect to a few unusual alleles and their frequencies relative to the other Pakistani population. Significant deviations from Hardy–Weinberg equilibrium were found at two loci (D13S317, D18S51) after Boneferroni’s correction (p ≤ 0.003). The combined power of discrimination, combined power of exclusion and cumulative probability of matching were 0.999999999999999978430815060354, 0.999995039393942 and 2.15692 × 10−17, respectively. On the bases of genetic distances, PCA, phylogenetic and structure analysis Lahore-Christians appeared genetically more associated to south Asian particularly Indian populations like Tamil, Karnataka, Kerala and Andhra Pradesh than rest of global populations.
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Affiliation(s)
- Aqsa Rubab
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Muhammad Shafique
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.
| | - Faqeeha Javed
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Samia Saleem
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Fatima Tuz Zahra
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Dennis McNevin
- Centre for Forensic Science, University of Technology Sydney, Ultimo, Australia
| | - Ahmad Ali Shahid
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
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13
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Mahal DG. Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population. Mol Genet Genomics 2020; 296:67-78. [PMID: 32978661 DOI: 10.1007/s00438-020-01725-2] [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: 07/11/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
The ancient geographical origins of Brahmins-a prominent ethnic group in the Indian subcontinent-have remained controversial for a long time. This study employed the AMOVA (analysis of molecular variance) test to evaluate genetic affinities of this group with thirty populations of Central Asia and Europe. A domestic comparison was performed with fifty non-Brahmin groups in India. The results showed that Brahmins had genetic affinities with several foreign populations and also shared their genetic heritage with several domestic non-Brahmin groups. The study identified the deep ancient origins of Brahmins by tracing their Y-chromosome haplogroups and genetic markers on the Y-DNA phylogenetic tree. It was confirmed that the progenitors of this group emerged from at least 12 different geographic regions of the world. The study concluded that about 83% of the Brahmins in the dataset belonged to four major haplogroups, of which two emerged from Central Asia, one from the Fertile Crescent, and one was of an indigenous Indian origin.
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Affiliation(s)
- David G Mahal
- DGM Associates, Pacific Palisades, CA, USA. .,Institut Avrio de Geneve, Geneva, Switzerland.
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