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Červenák Z, Červenák F, Baldovič M, Patlevičová A, Masnicová S. Mutational analysis of 16 STR markers in the Slovak population. Ann Hum Biol 2022; 49:248-253. [PMID: 35867540 DOI: 10.1080/03014460.2022.2105397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Short tandem repeats (STRs) are genetic markers frequently used for human identification and paternity testing. They are highly mutable, which may occasionally lead to inconsistencies between the genotypes of parents and their children. As the mutation rates of individual STR markers can vary among populations, population-specific data are of high importance. AIM To investigate the mutation rates of 16 STR markers in the Slovak population. SUBJECTS AND METHODS In this study, we analysed the germline mutation rates of 16 STR markers (TH01, D3S1358, vWA, D21S11, D16S539, D1S1656, D19S433, SE33, D10S1248, D22S1045, D12S391, D8S1179, D2S1338, D2S441, D18S51 and FGA) in the Slovak population. At these loci, we analysed 42 096 allelic transfers and identified 61 mutation events. RESULTS The loci with the highest overall mutation rates were SE33 and FGA, while no mutations were identified in TH01, D19S433 and D22S1045. The average paternal mutation rate was higher than the maternal mutation rate. All but one mutation consisted of gains or losses of a single repeat unit and the overall mutation rate was estimated to be 1.45 x10-3 per meiosis. CONCLUSION This study provides data which can be used to further strengthen the correct paternity index calculations and reliability of paternity testing in Slovakia.
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Affiliation(s)
- Zdenko Červenák
- Faculty of Medicine, Comenius University, Clinical Research Unit, 5. Department of Internal Medicine, Comenius University Science Park, Bratislava, Slovak Republic
| | - Filip Červenák
- Faculty of Natural Sciences, Comenius University, Department of Genetics, Bratislava, Slovak Republic
| | - Marian Baldovič
- Faculty of Natural Sciences, Comenius University, Department of Molecular Biology, Bratislava, Slovak Republic.,GHC GENETICS SK, Bratislava, Slovak Republic
| | - Andrea Patlevičová
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovak Republic.,GHC GENETICS SK, Bratislava, Slovak Republic
| | - Soňa Masnicová
- Department of Criminalistics and Forensic Sciences, Academy of Police Force in Bratislava, Bratislava, Slovak Republic
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Badiye A, Kapoor N, Kumawat RK, Dixit S, Mishra A, Dixit A, Kathane P, Bag S, Thakre V, Kaitholia K, Srivastava A, Chaubey G, Shrivastava P. A study of genomic diversity in populations of Maharashtra, India, inferred from 20 autosomal STR markers. BMC Res Notes 2021; 14:69. [PMID: 33622409 PMCID: PMC7903603 DOI: 10.1186/s13104-021-05485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 02/13/2021] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE This study was planned to evaluate the genetic diversity in the admixed and Teli (a Hindu caste) populations of Maharashtra, India using 20 autosomal Short Tandem Repeat (STR) genetic markers. We further investigated the genetic relatedness of the studied populations with other Indian populations. RESULTS The studied populations showed a wide range of observed heterozygosity viz. 0.690 to 0.918 for the admixed population and 0.696 to 0.942 for the Teli population. This might be due to the multi-directional gene flow. The admixed and Teli populations also showed a high degree polymorphism which ranged from 0.652 to 0.903 and 0.644 to 0.902, respectively. Their combined value of matching probability for all the studied loci was 4.29 × 10-25 and 5.01 × 10-24, respectively. The results of Neighbor-Joining tree and Principal Component Analysis showed that the studied populations clustered with the general populations of Jharkhand, UttarPradesh, Rajasthan and Central Indian States, as well as with the specific populations of Maharashtra (Konkanastha Brahmins) and Tamil Nadu (Kurmans). Overall, the obtained data showed a high degree of forensic efficacy and would be useful for forensic applications as well as genealogical studies.
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Affiliation(s)
- Ashish Badiye
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Neeti Kapoor
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, India
| | - Shivani Dixit
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
| | - Aditi Mishra
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
| | - Akansha Dixit
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P., 284128, India
| | - Prachi Kathane
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Sudeshna Bag
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Vaishnavi Thakre
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
| | - Ankit Srivastava
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P., 284128, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Dept of Zoology, Banaras Hindu University, Varanasi, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India.
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Sosiawan A, Yudianto A, Furqoni AH, Nzilibili SMM, Nuraini I. Full-sibling allelic frequency and sharing among Madurese: STR technique by 12 locus and the sex-typing amelogenin gene. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2019. [DOI: 10.1186/s41935-019-0143-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Yadav B, Balayan A, Dogra TD, Raina A. Genetic Ancestry of Delhi Population Inferred from Autosomal Short Tandem Repeats: Genetic Diversity Analysis. INT J HUM GENET 2018. [DOI: 10.1080/09723757.2017.1421440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bhuvnesh Yadav
- Amity School of Applied Sciences, Amity University, Gurgaon, Haryana
| | - Ajay Balayan
- DNA Fingerprinting Laboratory, Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, New Delhi, India
| | - T. D. Dogra
- Shree Guru Gobind Singh Tricentenary University, Budhera, Gurgaon, Haryana, India
| | - Anupuma Raina
- DNA Fingerprinting Laboratory, Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, New Delhi, India
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Mohd Yussup SS, Marzukhi M, Md-Zain BM, Mamat K, Mohd Yusof FZ. Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines. Evol Bioinform Online 2017; 13:1176934317735318. [PMID: 29085238 PMCID: PMC5648092 DOI: 10.1177/1176934317735318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 08/23/2017] [Indexed: 12/02/2022] Open
Abstract
The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.
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Affiliation(s)
| | - Marlia Marzukhi
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Malaysia
| | - Badrul Munir Md-Zain
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Kamaruddin Mamat
- Faculty of Computer and Mathematical Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Malaysia
| | - Farida Zuraina Mohd Yusof
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Malaysia.,Integrative Pharmacogenomics Institute (iPROMISE), Bandar Puncak Alam, Malaysia
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Correlation between microsatellite discrepancy scores and transplant outcome after haemopoietic SCT for pediatric ALL. Bone Marrow Transplant 2015; 50:363-6. [PMID: 25581412 DOI: 10.1038/bmt.2014.282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 10/19/2014] [Accepted: 11/05/2014] [Indexed: 11/09/2022]
Abstract
Microsatellite analyses show that self-reported ethnicity often correlates poorly with true genetic ancestry. As unknown ancestral differences could potentially have an impact on transplant outcome, we developed an average allele length discrepancy (AALD) score to assess allele length discrepancy between donor/recipient (D/R) using microsatellites analysed routinely in post-transplant chimeric assessment. This was then compared with outcome in a homogeneously treated cohort of pediatric patients undergoing high-resolution sibling or matched unrelated donor transplantation for acute lymphoblastic leukemia (ALL). AALD scores formed a numeric continuum ranging from 0 to 1.4 (median 0.76) for sibling pairs and 0.8-2.17 (median 1.6) for high-resolution matched unrelated donor (HR-MUD) pairs. There was a trend for worse OS with increasing AALD score, which reached statistical significance above a threshold of 1.7 for OS. Patients whose transplants had an AALD score of ⩾1.8 had a risk of non-relapse mortality 4.9 times greater (P=0.025) and relapse risk three times greater (P=0.058) than those scoring <1.8. This approach will now be explored in a Centre International for Blood and Marrow Transplantation Research (CIBMTR) study of 750 D/R pairs across all disease groups; if confirmed, it has the potential to improve donor selection for patients with multiple prospective donors.
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Fazeli Z, Vallian S. Molecular phylogenetic study of the Iranians based on polymorphic markers. Gene 2013; 512:123-6. [PMID: 23073556 DOI: 10.1016/j.gene.2012.09.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 06/05/2012] [Accepted: 09/11/2012] [Indexed: 11/25/2022]
Abstract
The application of polymorphic markers in construction of phylogenetic trees has been documented. Five polymorphic markers located in the PAH gene region including PAH-BglII, PAH-PvuII(A), PAH-EcoRI, PAH-MspI and PAH-STR were selected for analysis of phylogenetic relationships of the Iranians with 15 other populations of the world. The lowest genetic distance was observed between the Iranians and populations residing in Adygei (an ethnic group of the Russian Caucasus), Russia and Druze (a Middle Eastern group). However, East Asian populations including Han, Japanese and Cambodians, Khmer or the Oceanians (Melanesian, Nasioi) showed high genetic distance with the Iranians. The data suggested that the Iranians might have relatively close evolutionary history with the populations residing in Russia rather than East Asian populations. This study provided the first new molecular insight into the evolutionary history of the Iranian population.
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Affiliation(s)
- Zahra Fazeli
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Islamic Republic of Iran; Department of Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
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Abstract
The forensic genetics field is generating extensive population data on polymorphism of short tandem repeats (STR) markers in globally distributed samples. In this study we explored and quantified the informative power of these datasets to address issues related to human evolution and diversity, by using two online resources: an allele frequency dataset representing 141 populations summing up to almost 26 thousand individuals; a genotype dataset consisting of 42 populations and more than 11 thousand individuals. We show that the genetic relationships between populations based on forensic STRs are best explained by geography, as observed when analysing other worldwide datasets generated specifically to study human diversity. However, the global level of genetic differentiation between populations (as measured by a fixation index) is about half the value estimated with those other datasets, which contain a much higher number of markers but much less individuals. We suggest that the main factor explaining this difference is an ascertainment bias in forensics data resulting from the choice of markers for individual identification. We show that this choice results in average low variance of heterozygosity across world regions, and hence in low differentiation among populations. Thus, the forensic genetic markers currently produced for the purpose of individual assignment and identification allow the detection of the patterns of neutral genetic structure that characterize the human population but they do underestimate the levels of this genetic structure compared to the datasets of STRs (or other kinds of markers) generated specifically to study the diversity of human populations.
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Affiliation(s)
- Nuno M. Silva
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Universidade do Porto, Porto, Portugal
| | - Luísa Pereira
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Universidade do Porto, Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Estella S. Poloni
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
- * E-mail:
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9
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Korzebor A, Derakhshandeh-Peykar P, Meshkani M, Hoseini A, Rafati M, Purhoseini M, Ghaffari SR. Heterozygosity assessment of five STR loci located at 5q13 region for preimplantation genetic diagnosis of spinal muscular atrophy. Mol Biol Rep 2012; 40:67-72. [PMID: 23132709 DOI: 10.1007/s11033-012-2011-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 10/01/2012] [Indexed: 11/25/2022]
Abstract
Preimplantation genetic diagnosis (PGD) has been considered as an alternative to prenatal diagnosis for prevention of genetic disorders while avoiding the subsequent termination of pregnancy. However, the limited amount of template DNA available in a single diploid cell used for PGD leads to number of problems including an increased incidence of detectable contamination; amplification failure and allele drop out. Due to their highly polymorphic and amplifiable characteristics, short tandem repeat (STR) analysis has been proposed as a mean to overcome these limitations. Heterozygosity of the applied STRs is of paramount importance in their informativity, and should therefore be studied in any certain population. Here, for the first time, we report on the heterozygosity analysis of five STR markers (D5S1408, D5S1417, D5S610, D5S629 and D5S637) flanking to SMA gene region, to examine their applicability in the PGD for SMA disease. We have also investigated other statistical features of these markers and found that all of the five studied STRs were informative and four meet the Hardy-Weinberg equilibrium for the studied population. Furthermore, our results propose that similar approaches can be used for the PGD of other single gene disorders.
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Affiliation(s)
- Asghar Korzebor
- Department of Medical Genetics, Tehran University of Medical Sciences, 21, Shabahang Building, 26, Dr Gharib Street, Keshavarz Blvd, 1419783517 Tehran, Iran
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10
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Fazeli Z, Vallian S. Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers. Mol Biol Rep 2012; 39:11187-99. [PMID: 23065267 DOI: 10.1007/s11033-012-2028-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 10/02/2012] [Indexed: 11/29/2022]
Abstract
The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.
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Affiliation(s)
- Zahra Fazeli
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Islamic Republic of Iran
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11
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Ghang HY, Han YJ, Jeong SJ, Bhak J, Lee SH, Kim TH, Kim CH, Kim SS, Al-Mulla F, Youn CH, Yoo HS, The HUGO Pan-Asian SNP Consortium THUGOPASNPC. How Many SNPs Should Be Used for the Human Phylogeny of Highly Related Ethnicities? A Case of Pan Asian 63 Ethnicities. Genomics Inform 2011. [DOI: 10.5808/gi.2011.9.4.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Utter F, Seeb J. A perspective on positive relationships between genetic diversity and abundance in fishes. Mol Ecol 2010; 19:4831-3. [PMID: 21050291 DOI: 10.1111/j.1365-294x.2010.04823.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Given over 90 combined years in academic and professional activities related to genetics and fishery management (FU 57, JS 36-see Waples et al. 2008), we are pleased to provide an invited perspective generated by the interesting and useful article of McCusker & Bentzen (2010). These authors reaffirm the apparent signature of neutrality of mitochondrial and microsatellite markers through an exhaustive analysis of archived genotypic data for 105 marine and freshwater fishes. They note that their conclusions are consistent with earlier and less comprehensive analyses and that they do not exclude the operation of some selective activity (e.g. genetic 'draft'), which may be overwhelmed by N(e) -related stochastic processes. Here, we provide a complementary focus, recalling relevant issues related to neutrality and selection in applications of molecular variations in fishery management.
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Affiliation(s)
- Fred Utter
- University of Washington, School of Aquatic & Fishery Sciences, Box 355820, Seattle, WA 98195, USA.
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Novokmet N, Marjanović D, Skaro V, Projić P, Lauc G, Grahovac B, Ostojić S, Kapović M, Rudan P. Genetic polymorphisms of 15 STR loci in the population of the island of Cres (Croatia). Ann Hum Biol 2010; 38:12-21. [PMID: 20446818 DOI: 10.3109/03014461003789127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The population of the island of Cres presents one of the few persisting Eastern Adriatic isolates and is thereby suitable for human population differentiation analyses. AIM The aim of this study was to analyse the genetic structure of the island of Cres with respect to its eight sub-populations and to compare the genetic variation of the island of Cres with other Eastern Adriatic islands and the Croatian mainland. SUBJECTS AND METHODS Fifteen AmpFlSTR identifiler loci were analysed in a sample group of 122 unrelated autochthonous individuals from the island of Cres, Croatia. RESULTS Analysis of STR polymorphisms revealed genetic homogeneity among sub-populations of the island of Cres and small but significant levels of genetic heterogeneity among geographically distant Eastern Adriatic islands. CONCLUSION Despite a considerable degree of genetic homogeneity among the studied Eastern Adriatic islands, small but significant differentiation between distant islands indicates geographic sub-structuring which follows the isolation by distance model. This study is supportive of the notion that STR markers are useful for genetic differentiation between larger and geographically more distant regions.
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Scliar MO, Vaintraub MT, Vaintraub PMV, Fonseca CG. Brief communication: Admixture analysis with forensic microsatellites in Minas Gerais, Brazil: the ongoing evolution of the capital and of an African-derived community. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 139:591-5. [PMID: 19350638 DOI: 10.1002/ajpa.21046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report the estimated allele frequencies for 13 and 14 microsatellite loci in two populations of Minas Gerais, Brazil as follows: Belo Horizonte (the capital) and Marinhos (an African-derived community). Analysis of the African, Amerindian, and European genetic contributions to both populations, together with historical information, revealed distinct differences between the two populations. Estimates for Belo Horizonte revealed a higher-European (66%) than African (32%) contribution, and a minimal Amerindian contribution. These results are consistent with the peopling of the city mainly by people from the Minas Gerais hinterland, a people highly admixed but with more European ancestry. Estimates for Marinhos confirmed the high-African component of the population. However, a temporal analysis of two datasets-CURRENT (representing the population living in Marinhos today) and ORIGINAL (representing families, who have lived in Marinhos since the onset of the 20th century),-identified a diminishing of the population's African ancestry from 92% in the ORIGINAL group to 67% in the CURRENT group. This change is here interpreted as a consequence of the growing migration into the village of people with more European ancestry and subsequent admixture with the local population.
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Affiliation(s)
- Marília O Scliar
- Departamento de Biologia Geral, ICB, Universidade Federal de Minas Gerais. Caixa Postal 486, 31270-910 Belo Horizonte, MG, Brazil.
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Alfonso-Sánchez MA, Pérez-Miranda AM, Herrera RJ. Autosomal microsatellite variability of the Arrernte people of Australia. Am J Hum Biol 2007; 20:91-9. [PMID: 17957762 DOI: 10.1002/ajhb.20685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The genomic diversity of the Arrernte people of Australia or caterpillar people was investigated utilizing 13 autosomal short tandem repeat (STR) markers. Significant departures from Hardy-Weinberg equilibrium were detected at the D18S51, TPOX and CSF1PO loci, which persisted after applying the Bonferroni correction. Gene diversity values oscillate between 0.6302 (CSF1PO) and 0.8731 (D21S11). Observed heterozygosity (Ho) ranges from 0.2632 (D18S51) to 0.8333 (vWA) and is lower than the expected heterozygosity (He) for 12 of the 13 loci analyzed. The genetic relationships of the Arrernte with Middle Eastern, East Asian, South Asian and Indian populations were analyzed by distance-based methods, including Neighbor-Joining trees and nonmetric multidimensional scaling. In addition, the genetic contribution of the populations included in the analysis to the Arrernte gene pool was estimated utilizing weighted least square coefficients. Although the Arrernte population exhibits a remarkable level of genetic differentiation, results of the phylogeographic analyses based on autosomal microsatellite data suggest a certain degree of genetic relatedness between the Arrernte tribe of Australia and populations from the Indian subcontinent. In contrast, the STR diversity analyses failed to detect substantial East Asian contribution to the genetic background of the Arrernte group.
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Affiliation(s)
- M A Alfonso-Sánchez
- Molecular Biology and Human Diversity Laboratory, Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Demographic changes and marker properties affect detection of human population differentiation. BMC Genet 2007; 8:21. [PMID: 17498298 PMCID: PMC1876243 DOI: 10.1186/1471-2156-8-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 05/11/2007] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese) using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats). RESULTS Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African) while both successfully distinguished Hmong from Thai and Chinese. CONCLUSION Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.
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Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh. BMC Genet 2007; 8:12. [PMID: 17417972 PMCID: PMC1855350 DOI: 10.1186/1471-2156-8-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Accepted: 04/07/2007] [Indexed: 11/12/2022] Open
Abstract
Background India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp). It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. Results We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst – 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians. Conclusion The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and both upper caste and Muslim populations are genetically closer to the Caucasians.
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Tripathi G, Dharmani P, Khan F, Sharma RK, Pandirikkal Baburajan V, Agrawal S. High prevalence of ACE DD genotype among north Indian end stage renal disease patients. BMC Nephrol 2006; 7:15. [PMID: 17042963 PMCID: PMC1626448 DOI: 10.1186/1471-2369-7-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Accepted: 10/17/2006] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The Renin-Angiotensin system (RAS) is a key regulator of both blood pressure and kidney functions and their interaction. In such a situation, genetic variability in the genes of different components of RAS is likely to contribute for its heterogeneous association in the renal disease patients. Angiotensin converting enzyme-1 (ACE-1) is an important component of RAS which determines the vasoactive peptide Angiotensin-II. METHODS In the present study, we have investigated 127 ESRD patients and 150 normal healthy controls from north India to deduce the association between ACE gene polymorphism and ESRD. The inclusion criteria for patients included a constantly elevated serum creatinine level above normal range (ranging from 3.4 to 15.8) and further the patients were recommended for renal transplantation. A total of 150 normal healthy controls were also genotyped for ACE I/D polymorphism. The criterion of defining control sample as normal was totally based on the absence of any kidney disease determined from the serum creatinin level. Genotyping of ACE I/D were assayed by polymerase chain reaction (PCR) based DNA amplification using specific flanking primers Based on the method described elsewhere. RESULTS The difference of DD and II genotypes was found highly significant among the two groups (p = 0.025; OR = 3.524; 95% CI = 1.54-8.07). The combined genotype DD v/s ID+II comparison validated that DD genotype is a high risk genotype for ESRD (p = 0.001; OR = 5.74; 95% CI limit = 3.4-8.5). However, no correlation was obtained for different biochemical parameters of lipid profile and renal function among DD and non DD genotype. Interestingly, approximately 87% of the DD ESRD patients were found hypertensive in comparison to the 65% patients of non DD genotype CONCLUSION Based on these observations we conclude that ACE DD genotype implicate a strong possible role in the hypertensive state and in renal damage among north Indians. The study will help in predetermining the timing, type and doses of anti-hypertensive therapy for ESRD patients.
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Affiliation(s)
- Gaurav Tripathi
- Department of Medical Genetics, Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow (UP) 226014, India
| | - Poonam Dharmani
- Department of Medical Genetics, Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow (UP) 226014, India
| | - Faisal Khan
- Department of Medical Genetics, Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow (UP) 226014, India
| | - RK Sharma
- Department of Nephrology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow (UP) 226014, India
| | - Vinod Pandirikkal Baburajan
- Department of Nephrology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow (UP) 226014, India
| | - Suraksha Agrawal
- Department of Medical Genetics, Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow (UP) 226014, India
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