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Sala A, Marino M, Guinudinik A, Marcucci V, Cano H, Rey SV, Bobillo C, Castagnola J, Garrigós-Calivares L, Ginart S, Caputo M, Corach D. Detection of a novel 16.3 variant allele at locus DYS533 in R1b males inhabiting southern South America: A 19-nucleotide insertion explains its origin based on Sanger sequencing results. Forensic Sci Int Genet 2023; 62:102789. [PMID: 36252401 DOI: 10.1016/j.fsigen.2022.102789] [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: 05/31/2022] [Revised: 08/24/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022]
Abstract
We typed 1541 Y-STR haplotypes from reference samples along forensic casework investigations. In three haplotypes, we detected a variant allele designed as 16.3 at locus DYS533. This was confirmed by amplification using two commercial kits. Sanger sequencing revealing a novel motif corresponding to [TATC]12 repeats with a 19-bp insertion in the flanking upstream region. We propose its origin as an insertion at - 9.1 upstream of the repeat motifs. We searched other local databases and found this allele in various geographical areas of Argentina and neighbouring countries. The haplotypes share a common core of 10 Y-STRs (DYS389-I/13; DYS389-II/30; DYS19/14; DYS481/22; DYS438/12; DYS437/16; DYS635/23; DYS392/13; DYS393/13; GATA H4/11) and belong to the R1b haplogroup. This 16.3 allele is restricted to southern South America, which allows us to propose a local and relatively recent origin. The sequence described herein constitutes a novelty that could be considered in future criteria for the nomenclature of STRs based on massively parallel sequencing.
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Affiliation(s)
- Andrea Sala
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina.
| | - Miguel Marino
- Registro Provincial de Huellas Genéticas Digitalizadas, Lab. de Genética Forense-Ministerio Público Fiscal de Mendoza, Argentina
| | - Alejandra Guinudinik
- Servicio de Biología Molecular del Cuerpo de Investigaciones Fiscales, Ministerio Público de Salta, Argentina
| | - Valeria Marcucci
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Hortensia Cano
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Silvia Vannelli Rey
- Laboratorio Regional de Genética Forense, Ministerio Público de Río Negro, Argentina
| | - Cecilia Bobillo
- Laboratorio de Genética Forense, Ministerio Público de La Pampa, Argentina
| | - Josefina Castagnola
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Lucía Garrigós-Calivares
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
| | - Santiago Ginart
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
| | - Daniel Corach
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
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Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 2021; 57:102646. [PMID: 34875492 DOI: 10.1016/j.fsigen.2021.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/31/2022]
Abstract
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases FST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10-70. In a population genetic analysis, El Salvador showed the lowest FST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.
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Affiliation(s)
- Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadísitca, Universitat de Barcelona, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Nury Rivas
- Instituto de Medicina Legal Dr. Roberto Masferrer, San Salvador, El Salvador
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, 27 calle Pnte. No.1329 Colonia Layco, San Salvador, El Salvador
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Simão F, Ribeiro J, Vullo C, Catelli L, Gomes V, Xavier C, Huber G, Bodner M, Quiroz A, Ferreira AP, Carvalho EF, Parson W, Gusmão L. The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture. Genes (Basel) 2021; 12:1788. [PMID: 34828394 PMCID: PMC8625094 DOI: 10.3390/genes12111788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.
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Affiliation(s)
- Filipa Simão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Laura Catelli
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal;
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), 4099-002 Porto, Portugal
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Alfredo Quiroz
- Instituto de Previsión Social, Asunción 100153, Paraguay;
| | - Ana Paula Ferreira
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Elizeu F. Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
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Insights into the Middle Eastern paternal genetic pool in Tunisia: high prevalence of T-M70 haplogroup in an Arab population. Sci Rep 2021; 11:15728. [PMID: 34344940 PMCID: PMC8333252 DOI: 10.1038/s41598-021-95144-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.
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Fan H, Zeng Y, Wu W, Liu H, Xu Q, Du W, Hao H, Liu C, Ren W, Wu W, Chen L, Liu C. The Y-STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics. Electrophoresis 2021; 42:1578-1593. [PMID: 34018209 DOI: 10.1002/elps.202100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/16/2021] [Accepted: 05/15/2021] [Indexed: 11/09/2022]
Abstract
The Y-STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y-STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA-confirmed father-son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off-ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y-STR mutation rate was 4.85 × 10-3 (95% CI, 4.4 × 10-3 -5.4 × 10-3 ). The Spearman correlation analyses indicated that GD values (R2 = 0.6548) and average allele sizes (R2 = 0.5989) have positive correlations with Y-STR mutation rates. Our RM Y-STR set including 8 candidate RM Y-STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father-son pairs. This study also clarified the population structures of CSEH which isolated in population-mixed South China relatively. The strategy, SM Y-STRs for familial searching and RM Y-STRs for individual identification regionally, could be applicable based on enough knowledge of the Y-STR mutability of different populations.
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Affiliation(s)
- Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ying Zeng
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Weiwei Wu
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Honglei Hao
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Wenyan Ren
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Weibin Wu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Guangzhou Forensic Science Institute, Guangzhou, P. R. China
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6
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Luo C, Duan L, Li Y, Xie Q, Wang L, Ru K, Nazir S, Jawad M, Zhao Y, Wang F, Du Z, Peng D, Wen SQ, Qiu P, Fan H. Insights From Y-STRs: Forensic Characteristics, Genetic Affinities, and Linguistic Classifications of Guangdong Hakka and She Groups. Front Genet 2021; 12:676917. [PMID: 34108995 PMCID: PMC8181459 DOI: 10.3389/fgene.2021.676917] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Guangdong province is situated in the south of China with a population size of 113.46 million. Hakka is officially recognized as a branch of Han Chinese, and She is the official minority group in mainland China. There are approximately 25 million Hakka people who mainly live in the East and North regions of China, while there are only 0.7 million She people. The genetic characterization and forensic parameters of these two groups are poorly defined (She) or still need to be explored (Hakka). In this study, we have genotyped 475 unrelated Guangdong males (260 Hakka and 215 She) with Promega PowerPlex® Y23 System. A total of 176 and 155 different alleles were observed across all 23 Y-STRs for Guangdong Hakka (with a range of allele frequencies from 0.0038 to 0.7423) and Guangdong She (0.0047–0.8605), respectively. The gene diversity ranged from 0.4877 to 0.9671 (Guangdong Hakka) and 0.3277–0.9526 (Guangdong She), while the haplotype diversities were 0.9994 and 0.9939 for Guangdong Hakka and Guangdong She, with discrimination capacity values of 0.8885 and 0.5674, respectively. With reference to geographical and linguistic scales, the phylogenetic analyses showed us that Guangdong Hakka has a close relationship with Southern Han, and the genetic pool of Guangdong Hakka was influenced by surrounding Han populations. The predominant haplogroups of the Guangdong She group were O2-M122 and O2a2a1a2-M7, while Guangdong She clustered with other Tibeto-Burman language-speaking populations (Guizhou Tujia and Hunan Tujia), which shows us that the Guangdong She group is one of the branches of Tibeto-Burman populations and the Huonie dialect of She languages may be a branch of Tibeto-Burman language families.
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Affiliation(s)
- Chunfang Luo
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Lizhong Duan
- Beijing Municipal Public Security Bureau, Beijing, China
| | - Yanning Li
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Lingxiang Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Yifeng Zhao
- Nanjing Zhenghong Judicial Identification Institute, Nanjing, China
| | - Fenfen Wang
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Zhengming Du
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Dehua Peng
- Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Institute of Archaeological Science, Fudan University, Shanghai, China.,School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
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Ibrahim M, Salih A. The Y chromosome ancestry marker R1b1b2: a surrogate of the SARS-CoV-2 population affinity. Hum Genome Var 2021; 8:11. [PMID: 33602939 PMCID: PMC7890103 DOI: 10.1038/s41439-021-00141-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 11/09/2022] Open
Abstract
Individual and population susceptibilities to disease remain a murky area of investigation, clouded by past bias based on ideological differences and wars. The current SARS-CoV-2 pandemic, the largest in living memory, brought this matter to forefront as the disparity in disease burden became apparent. A timeline analysis of the pandemic revealed the presence of country clusters that display a marked preponderance of disease among populations carrying the ancestry marker R1b1b2, notably associated with both infection and mortality. This marker is a relic of past human expansions from western Asia and subsequently Europe and the rest of the world, which may have been accompanied by peculiar biological events rendering these populations vulnerable to SARS-CoV-2.
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Affiliation(s)
- Muntaser Ibrahim
- Institute of Endemic Diseases, University of Khartoum, Medical Campus Qasser Street, Khartoum, Sudan.
| | - Abdalhameed Salih
- Institute of Endemic Diseases, University of Khartoum, Medical Campus Qasser Street, Khartoum, Sudan
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Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, Balaresque P. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters. Forensic Sci Int Genet 2020; 48:102342. [PMID: 32818722 DOI: 10.1016/j.fsigen.2020.102342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022]
Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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Affiliation(s)
- Caroline Bouakaze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Franklin Delehelle
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; REVA Unit, UMR 5505 - CNRS & Université de Toulouse, Institut de Recherche en Informatique de Toulouse, 31400 Toulouse, France
| | - Nancy Saenz-Oyhéréguy
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Andreia Moreira
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Stéphanie Schiavinato
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Solène Delon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Cesar Fortes-Lima
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Morgane Gibert
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Louis Bujan
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Eric Huyghe
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Gil Bellis
- INED Institut National d'Etudes Démographiques, 133 Boulevard Davout, 75980 Paris cedex 20, France
| | - Rosario Calderon
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Candela Lucia Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Efren Avendaño-Tamayo
- Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia, Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Instituto de Biología, Universidad de Antioquia Medellín Colombia, Colombia
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, GenPoB Research Group, Instituto de Investigaciones, Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | | | - Jacques Charioni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Andres Ruiz-Linares
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jean-Michel Dugoujon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Thèves
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Mollereau-Manaute
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Camille Noûs
- Laboratoire Cogitamous, CNRS & Université Toulouse III, 31000 Toulouse, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400 Toulouse, France
| | - Turi King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of Western Cape, Cape Town, South Africa
| | - Patricia Balaresque
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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9
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Ambrosio IB, Braganholi DF, Orlando LBM, Andrekenas NC, da Mota Pontes I, da Silva DA, Astolfi-Filho S, de Carvalho EF, Cicarelli RMB, Gusmão L. Mutational data and population profiling of 23 Y-STRs in three Brazilian populations. Forensic Sci Int Genet 2020; 48:102348. [PMID: 32707472 DOI: 10.1016/j.fsigen.2020.102348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 11/18/2022]
Abstract
Y-chromosomal STRs are important markers in forensic genetics, due to some peculiar characteristics. The absence of recombination makes them a useful tool to infer kinship in complex cases involving distant paternal relatives, or to infer paternal bio-geographic ancestry. The presence of a single copy, being transmitted from father to son, allow tracing mutational events in Y-STRs without ambiguity. For the statistical interpretation of forensic evidences based on Y-STR profiles, it is necessary to have estimates on both mutation rates and haplotype frequencies. In this work, 407 father-son duos from São Paulo and Rio de Janeiro states and 204 unrelated individuals from Manaus were analyzed. Haplotype frequencies and mutation rates for the Y-STRs from the PowerPlex Y23 commercial kit were estimated. Thirty-six mutations were observed in 15 of the 22 Y-STRs analyzed, for an average mutation rate of 3.84 × 10-3 (95 % CI 2.69 × 10-3 to 5.32 × 10-3). All mutations in GAAA repeats occurred in alleles with 13 or more uninterrupted units. Mutations in GATA repeats were observed in alleles with 9-17 uninterrupted units. An analysis carried out in different father's age groups showed an increase of 2.48 times the mutation rate in the age group of 40-50 years, when compared to the 20-30 age group, in agreement with the described for autosomal STRs. A high haplotype diversity was found in the three Brazilian populations. Pairwise genetic distance analysis (FST) showed no significant differences between the three populations in this study, which were also close to populations with strong European influence. The highest distances among the Brazilian populations were with São Gabriel da Cachoeira, which has a high Native American ancestry.
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Affiliation(s)
- Isabela Brunelli Ambrosio
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil.
| | - Danilo Faustino Braganholi
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil
| | - Larissa Barros Muniz Orlando
- Laboratório de Genética Forense, do Instituto de Criminalística "Lorena do Santos Baptista" da Polícia Civil do Estado do Amazonas, Manaus, AM, Brazil
| | - Natalia Carolina Andrekenas
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil
| | - Isabel da Mota Pontes
- Laboratório de Diagnóstico Molecular, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | - Dayse Aparecida da Silva
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Spartaco Astolfi-Filho
- Laboratório de Diagnóstico Molecular, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | | | - Regina Maria Barretto Cicarelli
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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10
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Schaan AP, Gusmão L, Jannuzzi J, Modesto A, Amador M, Marques D, Rabenhorst SH, Montenegro R, Lopes T, Yoshioka FK, Pinto G, Santos S, Costa L, Silbiger V, Ribeiro-Dos-Santos Â. New insights on intercontinental origins of paternal lineages in Northeast Brazil. BMC Evol Biol 2020; 20:15. [PMID: 31996123 PMCID: PMC6990597 DOI: 10.1186/s12862-020-1579-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022] Open
Abstract
Background The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states. Results Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, FST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions. Conclusions We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.
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Affiliation(s)
- Ana Paula Schaan
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Antonio Modesto
- Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil
| | - Marcos Amador
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Diego Marques
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Silvia Helena Rabenhorst
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Raquel Montenegro
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Thayson Lopes
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - France Keiko Yoshioka
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Giovanny Pinto
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Lorenna Costa
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Vivian Silbiger
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil. .,Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil.
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