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Lendoye E, Mombo LE, N'Negue Ep Mezui-Mbeng MA, Komba OM, Ngoungou EB, Ovono Abessolo F, Djoba Siawaya JF, Alt-Mörbe J. Allelic frequencies of 22 short tandem repeats loci and tri-allelic patterns of Penta D and TPOX identified in Gabonese population. Sci Rep 2023; 13:19938. [PMID: 37968412 PMCID: PMC10651885 DOI: 10.1038/s41598-023-47395-z] [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: 06/09/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023] Open
Abstract
Short tandem repeats (STRs) are repeating DNA sequences used in forensic human identity testing and the diagnosis of aneuploidies. Many STRs like Penta D and TPOX are used routinely for paternity tests, but these tests are not widely used in sub-Saharan Africa. In this study we recruited individuals from Gabonese families seeking a paternity test. After DNA extraction from buccal swabs, we genotyped samples using a panel of 22 STRs. A total of 115 unrelated subjects from 39 families were included. Allele frequencies of the 22 STR loci were determined in unrelated Gabonese subjects. The most polymorphic loci were D21S11 (16 alleles) and FGA (17 alleles), while D3S1358 and TH01 loci were less polymorphic, with five alleles each. Deviation from Hardy-Weinberg equilibrium was observed for TPOX, D3S1358, CSFPO and D7S820 loci. We reported tri-allelic patterns that indicate aneuploidies at a combined frequency of 4% (4/115) with 3% for Penta D (1/35) and 3% for TPOX (3/102). Furthermore, we identified a new tri-allelic genotype 5-8-16 for the Penta D locus located on chromosome 21 in a healthy subject. In addition, we observed three tri-allelic variants of TPOX, located on chromosome 2, in healthy subjects, namely 8-10-11, 8-9-10, and 8-8-10. Our study revealed unsuspected polymorphic variations in Penta D and TPOX for the first time in Gabon, raising several questions about chromosomal disorders. Further population genetics studies are needed in Gabon to better characterize these variations, both qualitatively and quantitative.
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Affiliation(s)
- Elisabeth Lendoye
- DNA-LAB Gabon Clinic, Libreville, Gabon.
- Chemistry-Biochemistry Service, Department of Fundamental and Mixed Sciences, Faculty of Medicine, University of Health Sciences, Libreville, Gabon.
- Laboratory Service, Mother, and Child University Hospital - Jeanne Ebori Foundation, Libreville, Gabon.
| | - Landry Erick Mombo
- Laboratory of Molecular and Cellular Biology (LABMC), University of Sciences and Technology of Masuku (USTM), Franceville, Gabon
| | - Marie-Andree N'Negue Ep Mezui-Mbeng
- DNA-LAB Gabon Clinic, Libreville, Gabon
- Chemistry-Biochemistry Service, Department of Fundamental and Mixed Sciences, Faculty of Medicine, University of Health Sciences, Libreville, Gabon
| | - Opheelia Makoyo Komba
- Gynaecology-Obstetric and IVF Service, Mother, and Child Teaching Hospital - Jeanne Ebori Foundation, Libreville, Gabon
- Epidemiology, Biostatistics and Medical Informatic Service, Department of Fundamental and Mixed Sciences, Faculty of Medicine, University of Health Sciences, Libreville, Gabon
| | | | - Felix Ovono Abessolo
- Chemistry-Biochemistry Service, Department of Fundamental and Mixed Sciences, Faculty of Medicine, University of Health Sciences, Libreville, Gabon
| | - Joel Fleury Djoba Siawaya
- Laboratory Service, Mother, and Child University Hospital - Jeanne Ebori Foundation, Libreville, Gabon
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Flores M, Ly C, Ho E, Ceberio N, Felix K, Thorner HM, Guardado M, Paunovich M, Godek C, Kalaydjian C, Rohlfs R. Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554311. [PMID: 37745566 PMCID: PMC10515773 DOI: 10.1101/2023.08.25.554311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 244 human groups. We find higher false inclusion rates for mixtures with more contributors, and for groups with lower genetic diversity. Even for two-contributor mixtures where one contributor is known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 56 out of 244 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.
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Affiliation(s)
- Maria Flores
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
- University of California, Los Angeles; Department of Molecular, Cell and Developmental Biology; Los Angeles, CA, 90095, USA
| | - Cara Ly
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Evan Ho
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Niquo Ceberio
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Kamillah Felix
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Hannah Mariko Thorner
- George Washington University; Department of Forensic Sciences - Forensic Molecular Biology; Washington, DC, 20007, USA
| | - Miguel Guardado
- University of California, San Francisco; Biological and Medical Informatics Graduate Program; San Francisco CA, 94143, USA
| | - Matt Paunovich
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Chris Godek
- San Francisco State University; Department of Mathematics; San Francisco, CA, 94132, USA
| | - Carina Kalaydjian
- San Francisco State University; Department of Mathematics; San Francisco, CA, 94132, USA
| | - Rori Rohlfs
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
- University of Oregon; Department of Data Science; Eugene, OR, 97403, USA
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Genetic Polymorphism of 24 Autosomal STR in the Population of Rwanda. Biochem Genet 2021; 60:80-93. [PMID: 34100175 DOI: 10.1007/s10528-021-10067-6] [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: 01/15/2020] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Rwanda is one of the smallest countries of Africa, where forensic genetic studies are rarely being conducted and very few DNA databases have been developed. Short tandem repeats (STRs) polymorphisms were investigated in 505 unrelated Rwandese by using the HUMDNA TYPING (Yanhuang) Kit. The following STRs were targeted: D3S1358, D13S317, D7S820, D16S539, SE33, D10S1248, D5S818, D21S11, TPOX, D1S1656, D6S1043, D19S433, D22S1045, D8S1179, Penta E, D2S441, D12S391, D2S1338, vWA, Penta D, TH01, D18S51, CSF1PO and FGA. The purpose of this study was to elucidate the genetic diversity and explore the potential of applying these 24 STR in 505 Rwandan population in forensics. A total of 360 alleles, with corresponding allele frequencies in the range from 0.001 to 0.442, were found in the Rwandan population. SE33 presented the highest polymorphism (PIC=0.921) among these 24 loci, whereas D13S317 presented the lowest one (PIC=0.671). No deviation from the Hardy-Weinberg equilibrium was observed for any of the 24 loci. The forensic parameters, including the combined power of discrimination (PD and the combined exclusion power, have demonstrated that this panel of 24 STRs is highly informative and useful for forensic applications such as individuals' identification and paternity tests. Additionally, the genetic distances between Rwanda population and other 24 published populations were calculated based on 8 overlapping loci with the polygenetic tree revealing significant clusters in the populations associated with their geographic locations and their historical relationship.
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Borosky A, Rotondo M, Eppel S, Gusmão L, Vullo C. Allele frequency data for 23 aSTR for different ethnic groups from Republic of Zimbabwe. Int J Legal Med 2021; 135:1753-1765. [PMID: 33559001 DOI: 10.1007/s00414-021-02514-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
In order to determine the population allele frequencies of autosomal STR markers of forensic interest in the Zimbabwean population, we analyzed a sample of 478 individuals from 19 different ethnic groups using the PowerPlex® Fusion 6C Kit (Promega Corp, Madison, Wisconsin). The data obtained were compared among the different Zimbabwean ethnic groups as well as with several African populations to establish whether significant differences exist among them. No significant differences were found among the ethnic groups in Zimbabwe. Statistically significant differences were observed between allele frequencies in Zimbabwe and some other African populations, although FST with neighboring Bantu populations from South and Southeast regions were low (below 0.005 in most single locus comparisons).
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Affiliation(s)
| | - Martina Rotondo
- Forensic Genetics Laboratory, Argentine Forensic Anthropology Team, Córdoba, Argentina
| | - Shari Eppel
- Department of Anthropology, University of Cape Town, Cape Town, South Africa
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, 20550-900, Brazil
| | - Carlos Vullo
- LIDMO, EME1, Independencia 644,4A, Córdoba, Argentina.
- Forensic Genetics Laboratory, Argentine Forensic Anthropology Team, Córdoba, Argentina.
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Tau T, Wally A, Fanie TP, Ngono GL, Mpoloka SW, Davison S, D'Amato ME. Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci. Sci Rep 2017; 7:6768. [PMID: 28754995 PMCID: PMC5533702 DOI: 10.1038/s41598-017-06365-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/14/2017] [Indexed: 11/09/2022] Open
Abstract
Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10-19. CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0.9999582029 and 0.9999922652 respectively. CMP ranged from 6.28 × 10-19 (Khoisan Tuu) to 1,02 × 10-18 (Northwest district). Using pairwise genetic distances (FST), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and TESS, ethno-linguistics were found to have a greater influence on population structure than geography. FCA showed clustering between Bantu and Khoisan, and within the Bantu. This Bantu sub-structuring was not seen with STRUCTURE and TESS, which detected clustering only between Bantu and Khoisan. The patterns of population structure revealed highlight the need for regional reference databases that include ethno-linguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications.
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Affiliation(s)
- Tiroyamodimo Tau
- University of the Western Cape, Department of Biotechnology, Forensic DNA Laboratory, Private Bag X17, 7535, Bellville, Cape Town, South Africa
| | - Anthony Wally
- Botswana Police Service, Forensic Science Laboratory, Private Bag 0400, Gaborone, Botswana
| | | | - Goitseone Lorato Ngono
- Botswana Police Service, Forensic Science Laboratory, Private Bag 0400, Gaborone, Botswana
| | - Sununguko Wata Mpoloka
- University of Botswana, Biological Sciences Department, Private Bag 00704, Gaborone, Botswana
| | - Sean Davison
- University of the Western Cape, Department of Biotechnology, Forensic DNA Laboratory, Private Bag X17, 7535, Bellville, Cape Town, South Africa
| | - María Eugenia D'Amato
- University of the Western Cape, Department of Biotechnology, Forensic DNA Laboratory, Private Bag X17, 7535, Bellville, Cape Town, South Africa.
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Castrì L, Tofanelli S, Garagnani P, Bini C, Fosella X, Pelotti S, Paoli G, Pettener D, Luiselli D. mtDNA variability in two Bantu-speaking populations (Shona and Hutu) from Eastern Africa: implications for peopling and migration patterns in sub-Saharan Africa. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 140:302-11. [PMID: 19425093 DOI: 10.1002/ajpa.21070] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu-speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu-speaking populations. Moreover, by comparing our data with those from other Niger-Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub-Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu-speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu-speaking populations, but also between Bantu and non-Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu-speakers, with strong interactions between the different lines of Bantu-speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages.
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Affiliation(s)
- Loredana Castrì
- Dipartimento di Biologia Evoluzionistica Sperimentale, Unità di Antropologia, Università di Bologna, I-40126 Bologna, Italy
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de Assis Poiares L, de Sá Osorio P, Spanhol FA, Coltre SC, Rodenbusch R, Gusmão L, Largura A, Sandrini F, da Silva CMD. Allele frequencies of 15 STRs in a representative sample of the Brazilian population. Forensic Sci Int Genet 2009; 4:e61-3. [PMID: 20129458 DOI: 10.1016/j.fsigen.2009.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 03/26/2009] [Accepted: 05/22/2009] [Indexed: 11/30/2022]
Abstract
Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a sample of 12,030 individuals undergoing paternity testing. This sample includes individuals from all States in Brazil, combined according to the current country division into five regions (North, Northeast, Central West, Southeast, and South). The most polymorphic loci were D2S1338 and D18S51. All the analysed loci meet Hardy-Weinberg equilibrium expectations. Combined power of discrimination and combined power of exclusion for the 15 tested STR loci were 0.999999999999990 and 0.9999992, respectively. Comparative analysis between populations from different Brazilian macroregions as well as between Brazil and other relevant populations are presented.
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Affiliation(s)
- Lilian de Assis Poiares
- Laboratório Alvaro, Centro de Análises e Pesquisas Clínicas, Rua General Osório, 3212, Bairro Centro, Cascavel, Paraná, Brazil
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Gomes V, Sánchez-Diz P, Alves C, Gomes I, Amorim A, Carracedo Á, Gusmão L. Population data defined by 15 autosomal STR loci in Karamoja population (Uganda) using AmpF/STR Identifiler kit. Forensic Sci Int Genet 2009; 3:e55-8. [DOI: 10.1016/j.fsigen.2008.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 06/13/2008] [Indexed: 10/21/2022]
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9
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Gusmão L, Sánchez-Diz P, Gomes I, Alves C, Carracedo Á, João Prata M, Amorim A. Genetic analysis of autosomal and Y-specific STRs in the Karimojong population from Uganda. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.09.129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Shepard EM, Herrera RJ. Genetic encapsulation among Near Eastern populations. J Hum Genet 2006; 51:467-476. [PMID: 16557342 DOI: 10.1007/s10038-006-0387-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2005] [Accepted: 01/26/2006] [Indexed: 11/29/2022]
Abstract
This report aims to genetically characterize the relationships between geographically targeted human populations covering an expanse from east sub-Saharan Africa northeastward into northern India with an emphasis on the Near East. A number of parameters of population genetics interest were examined based on allele frequencies from 15 forensic autosomal STR markers [D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA]. The phylogenetic analyses generated from genetic profiles of 885 individuals indicate that populations west of and including Iran have experienced substantial gene flow. Accordingly, our findings delineate a region of genetic homogeneity concentrated within the Near East with increasing genetic differentiation moving south into Africa and further east into Asia. We suggest that the Saharan desert, the Hindu Kush mountain range and perhaps to a lesser extent, the deserts of Iran may have acted as southern, eastern and northern geographical barriers, respectively, forming a genetic enclosure that allows limited gene flow outside the Near East. The biparental genetic landscape supports a picture of close contact between the Arab and Persian populations, perhaps beginning during the initial settlement of Asia from Africa extending to recent times.
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Affiliation(s)
- Erica M Shepard
- Department of Biological Sciences, Florida International University, University Park, OE 304, Miami, FL, 33199, USA
- Counterterrorism Forensic Science Research Unit, FBI Academy, Bldg. 12, Quantico, VA, 22135, USA
| | - Rene J Herrera
- Department of Biological Sciences, Florida International University, University Park, OE 304, Miami, FL, 33199, USA.
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Barnholtz-Sloan JS, Chakraborty R, Sellers TA, Schwartz AG. Examining population stratification via individual ancestry estimates versus self-reported race. Cancer Epidemiol Biomarkers Prev 2005; 14:1545-51. [PMID: 15941970 DOI: 10.1158/1055-9965.epi-04-0832] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Population stratification has the potential to affect the results of genetic marker studies. Estimating individual ancestry provides a continuous measure to assess population structure in case-control studies of complex disease, instead of using self-reported racial groups. We estimate individual ancestry using the Federal Bureau of Investigation CODIS Core short tandem repeat set of 13 loci using two different analysis methods in a case-control study of early-onset lung cancer. Individual ancestry proportions were estimated for "European" and "West African" groups using published allele frequencies. The majority of Caucasian, non-Hispanics had >50% European ancestry, whereas the majority of African Americans had <20% European ancestry, regardless of ancestry estimation method, although significant overlap by self-reported race and ancestry also existed. When we further investigated the effect of ancestry and self-reported race on the frequency of a lung cancer risk genotype, we found that the frequency of the GSTM1 null genotype varies by individual European ancestry and case-control status within self-reported race (particularly for African Americans). Genetic risk models showed that adjusting for individual European ancestry provided a better fit to the data compared with the model with no group adjustment or adjustment for self-reported race. This study suggests that significant population substructure differences exist that self-reported race alone does not capture and that individual ancestry may be confounded with disease status and/or a candidate gene risk genotype.
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Affiliation(s)
- Jill S Barnholtz-Sloan
- Cancer Prevention and Control Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, USA.
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Carpio Y, Sainz de la Peña MV, Santiesteban M, Amaro F, Ferreira R, Lleonart R. Genetic structure of a Cuban population based on nine short tandem repeat loci. Int J Legal Med 2005; 119:137-41. [PMID: 15711979 DOI: 10.1007/s00414-005-0522-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 01/07/2005] [Indexed: 10/25/2022]
Abstract
Cuba is a multiethnic and multiracial society. Here we describe the genetic variation of a sample of the Cuban population, which include the three most common racial groups, Caucasians, Negroids and Mestizos, by means of a set of nine microsatellites (HUMTH01, HUMTPOX, HUMCFS1PO, HUMVWA, HUMFESFPS, HUMF13A, HUMF13B, HUMLPL and HUMHPRTB). The analysis presented here indicates that these STR loci are highly informative for forensic purposes. The genetic data on the major racial groups is in good agreement with current demographic tendencies and with historic events that took place during the formation of the Cuban population.
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Affiliation(s)
- Yamila Carpio
- Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana 10600, Cuba
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Calzada P, Suárez I, García S, Barrot C, Sánchez C, Ortega M, Mas J, Huguet E, Corbella J, Gené M. The Fang population of Equatorial Guinea characterised by 15 STR-PCR polymorphisms. Int J Legal Med 2004; 119:107-10. [PMID: 15565295 DOI: 10.1007/s00414-004-0505-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Accepted: 10/14/2004] [Indexed: 11/25/2022]
Abstract
Allele frequencies for 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, HUMVWA31A, HUMTPOX, D18S51, D3S1358, HUMTHO1, D13S317, D16S539, D2S1338, D5S818 and HUMFGA) were analysed in the Fang population of Bioko Island, Equatorial Guinea. No deviation from Hardy-Weinberg equilibrium was found for all loci. Statistical parameters demonstrated the forensic utility of the analysed systems.
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Affiliation(s)
- P Calzada
- University Hospital of Bellvitge, L'Hospitalet de Llobregat, Spain
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