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Liu YY, Bright JA, Taylor D, Kruijver M, Buckleton J. Estimation of population specific values of theta for sequence-based STR profiles. Forensic Sci Int Genet 2024; 68:102973. [PMID: 37913640 DOI: 10.1016/j.fsigen.2023.102973] [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: 06/05/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
We describe the estimation of θ (theta) values from autosomal STR sequencing data for five metapopulations. The data were compiled from 20 publications and included 39 datasets comprising a total of 7005 samples. The estimates are suitable for use within the calculation of match probabilities in forensic casework. We also have constructed a phylogenetic tree using this data that aligns with our understanding of human evolution.
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Affiliation(s)
- Yao-Yuan Liu
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand.
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Duncan Taylor
- Forensic Science SA, PO Box 2790, Adelaide, SA 5000, Australia; School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Maarten Kruijver
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - John Buckleton
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand; Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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2
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Riman S, Ghemrawi M, Borsuk LA, Mahfouz R, Walsh S, Vallone PM. Sequence-based allelic variations and frequencies for 22 autosomal STR loci in the Lebanese population. Forensic Sci Int Genet 2023; 65:102872. [PMID: 37068444 DOI: 10.1016/j.fsigen.2023.102872] [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: 12/22/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/19/2023]
Abstract
This is the first study that characterizes the sequence-based allelic variations of 22 autosomal Short Tandem Repeat (aSTR) loci in a population dataset collected from Lebanon. Genomic DNA extracts from 195 unrelated Lebanese individuals were amplified with PowerSeq 46GY System Prototype. Targeted amplicons were subjected to DNA library preparation and sequenced on the Verogen MiSeq FGx Sequencing System. Raw FASTQ data files were processed by STRait Razor v3. Sequence strings were annotated according to the considerations of the DNA Commission of the International Society for Forensic Genetics (ISFG) and tabulated herein with their respective allelic frequencies and GeneBank accession and version numbers. The sequenced Lebanese dataset resulted in 429 distinct allelic sequences as compared to the 236 alleles identified by length only. The increase in the number of alleles was observed at 18 out of 22 aSTR loci and was attributed to the sequence variations residing in both the STR repeat motifs and flanking regions. The study uncovered 25 novel aSTR allelic sequences across 12 loci for which GenBank records did not previously exist in the STRSeq BioProject, PRJNA380127. For a concordance check, the length-based allelic calls derived from the full sequences were compared to those genotyped using capillary electrophoresis (CE) methods. Population genetic parameters relevant to the evaluation of forensic DNA evidence were assessed for the sequence-based data and compared to the parameters generated from the length-based information. Using the sequence-based data, Analysis of MOlecular VAriance (AMOVA), genetic distances, and population genetic structure were evaluated for 1231 individuals sampled from the Lebanese and four U.S. populations (African American, Asian, Caucasian, and Hispanic). The results were tabulated and visualized in a population tree, multidimensional scaling scatter plots, and bar plots. This newly established sequence-based database for the Lebanese population can be beneficial for extending NGS applicability to casework or paternity testing and assessing the strength of evidence for NGS-STR profiles. The described novel sequence variants at certain loci can further help in the effort to characterize the sequence diversity of STR markers from different populations around the world.
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Affiliation(s)
- Sarah Riman
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Mirna Ghemrawi
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, Miami, FL 33199, USA
| | - Lisa A Borsuk
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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Allelic diversity and forensic estimations of the Beijing Hans: Comparative data on sequence-based and length-based STRs. Forensic Sci Int Genet 2020; 51:102424. [PMID: 33248347 DOI: 10.1016/j.fsigen.2020.102424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/25/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022]
Abstract
Short tandem repeat (STR) profiling is routinely used in forensic genetics. At present, STR analysis is mainly performed by capillary electrophoresis (CE). However, due to limitations associated with the CE method, STR genotyping has been limited to length polymorphisms only. Because next generation sequencing (NGS) is capable of providing full resolution STR data at the sequence variation level, the individual identification capability of forensic STR loci could be significantly improved. Here we present sequence-based STR data for the Beijing Han population in which 291 individuals were screened for 23 commonly used forensic STRs using the SeqTypeR24 CASE kit on an Ion PGM platform. In total, 234 length-based alleles and 356 sequence-based alleles, which included 22 novel core repeat sequences, were observed. The sequence-based matching probability and power of discrimination were superior to the length-based numbers for 16 loci bearing micro-variant alleles. Combined matching probability reached 8.2 × 10-29 for 23 STR loci at the sequence level. This was two orders of magnitude higher than the parameters at length level and provides a data base for sequence-based STR casework applications.
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5
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DNA typing from skeletal remains: a comparison between capillary electrophoresis and massively parallel sequencing platforms. Int J Legal Med 2020; 134:2029-2035. [DOI: 10.1007/s00414-020-02327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
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Butler JM, Willis S. Interpol review of forensic biology and forensic DNA typing 2016-2019. Forensic Sci Int Synerg 2020; 2:352-367. [PMID: 33385135 PMCID: PMC7770417 DOI: 10.1016/j.fsisyn.2019.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/23/2022]
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.
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High polymorphism detected by massively parallel sequencing of autosomal STRs using old blood samples from a Chinese Han population. Sci Rep 2019; 9:18959. [PMID: 31831766 PMCID: PMC6908607 DOI: 10.1038/s41598-019-55282-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/31/2019] [Indexed: 12/02/2022] Open
Abstract
The development of massively parallel sequencing (MPS) has quickly changed forensic short tandem repeat (STR) genotyping. By providing detailed sequence information, MPS technology may be used as an alternative or additional method to overcome the limitations of capillary electrophoresis-based STR profiling. Most current NGS processes are labour-intensive with regard to library preparation and require high-quality DNA template. In this study, a 16-plex STR typing system (SeqType®R16) was used to achieve direct library preparation without DNA extraction and adaptor ligation. The efficiency of this system was tested in 601 individuals, including 593 old blood samples from the Chinese Han population and eight positive controls. It took approximately 4 hours for library preparation, including blood direct multiplex PCR (1.5 hours), mixing of the product (15 minutes), single tube purification (2 hours) and quantification (15 minutes). The results showed that MPS presented a broader allele range and higher discrimination power. Except for FGA and D19S433, the allele number almost doubled or more than doubled at all complex STR loci and simple STR loci, including D13S317, D16S539, D5S818, and D7S820. The range of discrimination power increased from 0.8008–0.9572 to 0.8401–0.9753, and the culminated matching probability decreased from 1.7 × 10−15 to 1.1 × 10−17.
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Hamester FIR, da Silva DS, Leboute APM, Motta CHA, Alho CS. Slippage mutation rates in 15 autosomal short tandem repeat loci for forensic purposes in a Southeastern Brazilian population. Electrophoresis 2019; 40:2873-2876. [PMID: 31442316 DOI: 10.1002/elps.201800491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/24/2019] [Accepted: 08/13/2019] [Indexed: 11/06/2022]
Abstract
Well-defined estimates of mutation rates in highly polymorphic tetranucleotide STR loci are a prerequisite for human identification in genetics laboratory routines useful for civil and criminal investigations. Studying 15 autosomal STR loci of forensic interest (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPOX, and vWA), we detected 193 slippage mutations (189 one-step and four two-step mutations) in 148 875 parent-child allelic transfers from 5171 paternity cases with true biological relationship (15 096 individuals; 4754 trios and 417 duos; 9925 meiosis) from the state of São Paulo, a very representative population of Brazil. The overall mutation rate was 1.3 × 10-3 and the highest rates were observed at loci vWA (2.8 × 10-3 ), FGA and D18S51 (2.7 × 10-3 for both), while loci TH01 and TPOX did not present any mutations. The mean slippage mutation rate of paternal origin (1.8 × 10-3 ) was six times higher than that observed for maternal origin (0.3 × 10-3 ).
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Affiliation(s)
- Fernanda Irma Remus Hamester
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Laboratório de Genética Humana e Molecular - Genética Forense, Porto Alegre, RS, Brazil.,Instituto-Geral de Perícias do Estado do Rio Grande do Sul (IGP-RS), Divisão de Genética Forense, Porto Alegre, RS, Brazil
| | - Débora Santos da Silva
- Instituto de Medicina Social e Criminologia (IMESC), Núcleo de Perícias Laboratoriais, São Paulo, SP, Brazil
| | - Ana Paula Magalhães Leboute
- Instituto-Geral de Perícias do Estado do Rio Grande do Sul (IGP-RS), Divisão de Genética Forense, Porto Alegre, RS, Brazil
| | - Carlos Henrique Ares Motta
- Instituto de Medicina Social e Criminologia (IMESC), Núcleo de Perícias Laboratoriais, São Paulo, SP, Brazil
| | - Clarice Sampaio Alho
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Laboratório de Genética Humana e Molecular - Genética Forense, Porto Alegre, RS, Brazil
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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