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Zhang R, Xue J, Tan M, Chen D, Xiao Y, Liu G, Zheng Y, Wu Q, Liao M, Lv M, Qu S, Liang W. An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis. Genes (Basel) 2023; 14:genes14040865. [PMID: 37107623 PMCID: PMC10137789 DOI: 10.3390/genes14040865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11–81 bp and 123–198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93–100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels.
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Affiliation(s)
- Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
- West China Forensics Center, Sichuan University, No. 16, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Shengqiu Qu
- West China Forensics Center, Sichuan University, No. 16, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
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Sampaio B, Dos Santos Silva AM, de Sá Paiva Leitão Júnior S, de Souza Liberal AT, da Cruz HLA, de Queiroz Balbino V. Allelic frequencies distribution and forensic parameters of 23 autosomal short tandem repeats in the population of the State of Pernambuco, Brazil. Leg Med (Tokyo) 2022; 59:102112. [PMID: 35839577 DOI: 10.1016/j.legalmed.2022.102112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/30/2022] [Accepted: 07/01/2022] [Indexed: 10/31/2022]
Abstract
Located in the Northeast Region, the Pernambuco State is one of the 27 federative units of Brazil. Here, we determined populational data for 23 short tandem repeat (STR) markers - CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, PENTA D, PENTA E and SE33 - of the Pernambuco population. The sample consisted of 767 healthy, adult, unrelated individuals (437 males, 330 females) born and resident in the State of Pernambuco. STRs were amplified using three multiplex kits, according to the availability: PowerPlex® Fusion 6C System (Promega Corporation), PowerPlex® Fusion System (Promega Corporation) and GlobalFiler™ Express (Thermo Fisher Scientific). Allelic frequencies, forensic parameters and Hardy-Weinberg equilibrium determinations were estimated for all the 23 loci. No deviations from the Hardy-Weinberg equilibrium were observed for any of the markers, after Bonferroni correction. We observed that the most and less informative markers were SE33 and TPOX, respectively. The combined power of discrimination (CPD) was 0.99999999999999999999999999999, and the combined power of exclusion (CPE) was 0.99999999997. The cumulative typical paternity index was 37,919,301,869.3021. Interpopulation analyses (Nei's genetic distance) based on the expanded CODIS core loci was performed between the Pernambuco sample and other global populations. Pernambuco was the closest Brazilian population to African group and stayed distant from the Native American group. This work contributed to show that a panel of 23 autosomal STR loci is very informative, being able for forensic applications related in this population.
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Affiliation(s)
- Bruno Sampaio
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil.
| | - Abigail Marcelino Dos Santos Silva
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Sérgio de Sá Paiva Leitão Júnior
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Anna Theresa de Souza Liberal
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Heidi Lacerda Alves da Cruz
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
| | - Valdir de Queiroz Balbino
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco (PE), Brazil
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Neyra Rivera CD, Delgado Ramos E, Díaz Soria F, Quispe Ramírez JS, Ge J, Budowle B. Genetic study with autosomal STR markers in people of the Peruvian jungle for human identification purposes. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2021. [DOI: 10.1080/00085030.2021.1933811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Edgardo Delgado Ramos
- Universidad Nacional Mayor de San Marcos, Ciudad Universitaria Cercado de Lima, Lima, Perú
| | - Fabiola Díaz Soria
- Instituto Nacional de Salud, Centro de Investigación en Enfermedades Tropicales “Máxime Kuczynski”, Iquitos, Perú
| | | | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Ft Worth, TX, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Ft Worth, TX, USA
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Neyra-Rivera CD, Ticona Arenas A, Delgado Ramos E, Velasquez Reinoso MRE, Caceres Rey OA, Budowle B. Population data of 27 Y-chromosome STRS in Aymara population from Peru. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1882571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Andres Ticona Arenas
- Posgrado de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Ciudad Universitaria Cercado de Lima, Lima, Perú
| | - Edgardo Delgado Ramos
- Universidad Nacional Mayor de San Marcos, Ciudad Universitaria Cercado de Lima, Lima, Perú
| | | | | | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
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