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Lee DG, Kim EJ, Kim YH, Cho WC, Cho Y, Han JY, Kim SJ, Park JH, Lee J, Kim E, Jung JY. Mutational analysis of 23 autosomal short tandem repeats based on trio paternity testing in the Korean population. Leg Med (Tokyo) 2024; 69:102447. [PMID: 38640874 DOI: 10.1016/j.legalmed.2024.102447] [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: 01/19/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
This study aimed to estimate A-STR mutation rates in 2,317 Korean parent-child trios by examining 20 Combined DNA Index System (CODIS) core loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045) and three non-CODIS loci (Penta E, Penta D, and SE33). Locus-specific mutation rate estimates varied from 0.00 to 8.63 × 10-3 per generation, with an average mutation rate of 1.62 × 10-3 (95 % CI, 1.39-1.88 × 10-3). We also combined data from previous studies to obtain comprehensive genetic values for the Korean population, and the average mutation rate was 1.59 × 10-3 (95 % CI, 1.38-1.82 × 10-3). Single-step mutations (95.69 %) and double-step mutations (3.35 %) were observed in the mutation pattern analysis, and cases expected to have multi-step mutations (0.96 %) were also observed. Large-sized alleles exhibited more loss mutations than gain mutations, and paternal mutations (62.68 %) were more frequently observed than maternal mutations (19.62 %). The calculated values and features of the 23 A-STRs explored in this study are expected to play a crucial role in establishing criteria for forensic genetic interpretation.
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Affiliation(s)
- Dong Gyu Lee
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea; Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do 16419, Republic of Korea
| | - Eun Jin Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Yoo Hee Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Woo-Cheol Cho
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Yoonjung Cho
- DNA Analysis Division, National Forensic Service Gwangju Institute, 60-15, Nanosandan 5-ro, Nam-myeon, Jangseong-gun, Gwangju 57248, Republic of Korea
| | - Ji Yeon Han
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Su Jin Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Jinmyung Lee
- DNA Analysis Division, National Forensic Service Seoul Institute, 139, Jiyang-ro, Yangcheon-gu, Seoul 08036, Republic of Korea
| | - Eungsoo Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea.
| | - Ju Yeon Jung
- Forensic DNA Section, National Forensic Service Jeju Branch, 221, Cheomdan-ro, Jeju-si, Jeju-do 63309, Republic of Korea; Department of Forensic Medicine, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea.
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Antão-Sousa S, Gusmão L, Modesti NM, Feliziani S, Faustino M, Marcucci V, Sarapura C, Ribeiro J, Carvalho E, Pereira V, Tomas C, de Pancorbo MM, Baeta M, Alghafri R, Almheiri R, Builes JJ, Gouveia N, Burgos G, Pontes MDL, Ibarra A, da Silva CV, Parveen R, Benitez M, Amorim A, Pinto N. Microsatellites' mutation modeling through the analysis of the Y-chromosomal transmission: Results of a GHEP-ISFG collaborative study. Forensic Sci Int Genet 2024; 69:102999. [PMID: 38181588 DOI: 10.1016/j.fsigen.2023.102999] [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: 05/08/2023] [Revised: 10/25/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024]
Abstract
The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) organized a collaborative study on mutations of Y-chromosomal short tandem repeats (Y-STRs). New data from 2225 father-son duos and data from 44 previously published reports, corresponding to 25,729 duos, were collected and analyzed. Marker-specific mutation rates were estimated for 33 Y-STRs. Although highly dependent on the analyzed marker, mutations compatible with the gain or loss of a single repeat were 23.2 times more likely than those involving a greater number of repeats. Longer alleles (relatively to the modal one) showed to be nearly twice more mutable than the shorter ones. Within the subset of longer alleles, the loss of repeats showed to be nearly twice more likely than the gain. Conversely, shorter alleles showed a symmetrical trend, with repeat gains being twofold more frequent than reductions. A positive correlation between the paternal age and the mutation rate was observed, strengthening previous findings. The results of a machine learning approach, via logistic regression analyses, allowed the establishment of algebraic formulas for estimating the probability of mutation depending on paternal age and allele length for DYS389I, DYS393 and DYS627. Algebraic formulas could also be established considering only the allele length as predictor for DYS19, DYS389I, DYS389II-I, DYS390, DYS391, DYS393, DYS437, DYS439, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS576, DYS626 and DYS627 loci. For the remaining Y-STRs, a lack of statistical significance was observed, probably as a consequence of the small effective size of the subsets available, a common difficulty in the modeling of rare events as is the case of mutations. The amount of data used in the different analyses varied widely, depending on how the data were reported in the publications analyzed. This shows a regrettable waste of produced data, due to inadequate communication of the results, supporting an urgent need of publication guidelines for mutation studies.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Nidia M Modesti
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Sofía Feliziani
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Marisa Faustino
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Valeria Marcucci
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Claudia Sarapura
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Almheiri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Juan José Builes
- GENES SAS Laboratory, Medellín, Colombia; Institute of Biology, University of Antioquia, Medellín, Colombia
| | - Nair Gouveia
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Centro, Portugal
| | - German Burgos
- One Health Global Research Group, Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador; Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria de Lurdes Pontes
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Norte, Portugal
| | - Adriana Ibarra
- Laboratorio IDENTIGEN, Universidad de Antioquia, Colombia
| | - Claudia Vieira da Silva
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Sul, Portugal
| | - Rukhsana Parveen
- Forensic Services Laboratory, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Marc Benitez
- Policia de la Generalitat de Catalunya - Mossos d'Esquadra. Unitat Central del Laboratori Biològic, Barcelona, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Centre of Mathematics of the University of Porto, Porto, Portugal.
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