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Yang TT, Zhang JR, Xie ZH, Ren ZL, Yan JW, Ni M. Nanopore sequencing of forensic short tandem repeats using QNome of Qitan Technology. Electrophoresis 2024. [PMID: 38884206 DOI: 10.1002/elps.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/21/2024] [Accepted: 04/09/2024] [Indexed: 06/18/2024]
Abstract
Devices of nanopore sequencing can be highly portable and of low cost. Thus, nanopore sequencing is promising in in-field forensic applications. Previous investigations have demonstrated that nanopore sequencing is feasible for genotyping forensic short tandem repeats (STRs) by using sequencers of Oxford Nanopore Technologies. Recently, Qitan Technology launched a new portable nanopore sequencer and became the second supplier in the world. Here, for the first time, we assess the QNome (QNome-3841) for its accuracy in nanopore sequencing of STRs and compare with MinION (MinION Mk1B). We profile 54 STRs of 21 unrelated individuals and 2800M standard DNA. The overall accuracy for diploid STRs and haploid STRs were 53.5% (378 of 706) and 82.7% (134 of 162), respectively, by using QNome. The accuracies were remarkably lower than those of MinION (diploid STRs, 84.5%; haploid, 90.7%), with a similar amount of sequencing data and identical bioinformatics analysis. Although it was not reliable for diploid STRs typing by using QNome, the haploid STRs were consistently correctly typed. The majority of errors (58.8%) in QNome-based STR typing were one-repeat deviations of repeat units in the error from true allele, related with homopolymers in repeats of STRs.
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Affiliation(s)
- Ting-Ting Yang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, P. R. China
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, P. R. China
| | - Jia-Rong Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, P. R. China
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, P. R. China
| | - Zi-Han Xie
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
- School of Life Science, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Zi-Lin Ren
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P. R. China
- School of Information Science and Technology, and Institution of Computational Biology, Northeast Normal University, Changchun, P. R. China
| | - Jiang-Wei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, P. R. China
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
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2
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Nayyar A, Ahmed S. Densitometry of STR-PAGE for donor chimerism in acute leukemia's: A simple method for routine use. Pak J Med Sci 2024; 40:875-878. [PMID: 38827851 PMCID: PMC11140357 DOI: 10.12669/pjms.40.5.9216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 06/05/2024] Open
Abstract
Objective To evaluate a PCR based method of polyacrylamide gel electrophoresis of short tandem repeats and its quantification for detecting donor chimerism after haematopoietic stem cell transplantation in acute leukaemias. Methods The descriptive study was conducted at Genetic Resource Centre (GRC) Lab Rawalpindi from Feb 2018 - Nov 2020. A total of twenty patients with acute leukaemias having undergone HSCT were selected and assessed for the analysis of chimerism status. DNA extraction from the whole blood was done by chelex method and short tandem repeats were amplified by using conventional STR- PCR assay. Electrophoresis was carried out and 6% polyacrylamide gels were used for the resultant amplified DNA products and then followed by their densitometry. These patients had undergone HSCT from Pakistan Institute of Medical Science and Armed Forces Bone Marrow Transplant Centre. Results The peaks in the PAGE densitometry represented the donor chimerism in all post transplant samples of the patients. Conclusion Our study showed that densitometry of STR PCR PAGE is a useful and cheaper method for demonstration of donor chimerism in acute leukaemia patients having undergone HSCT. Hence this method can be a valuable option in the monitoring of chimerism status in these patients and therefore helps in preventing graft failure by fast and early treatment strategies for these patients.
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Affiliation(s)
- Ayesha Nayyar
- Ayesha Nayyar, M. Phil, PhD Department of Pathology, Islamic International Medical College, Riphah International University, Islamabad, Pakistan
| | - Suhaib Ahmed
- Suhaib Ahmed, FCPS, PhD Department of Pathology, Islamic International Medical College, Riphah International University, Islamabad, Pakistan
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3
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Guo F, Liu Z, Long G, Zhang B, Liu D, Yu S. Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit. J Forensic Leg Med 2024; 103:102678. [PMID: 38522119 DOI: 10.1016/j.jflm.2024.102678] [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: 11/04/2023] [Revised: 03/05/2024] [Accepted: 03/17/2024] [Indexed: 03/26/2024]
Abstract
Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples. Bioinformatic concordance achieves 99.99% between the ForenSeq Universal Analysis Software (UAS) and the Integrative Genomic Viewer (IGV) inspection. Discordance results from flanking region deletions of rs10776839, rs8078417, rs2831700, and rs1454361. Due to FR variants within amplicons detected by massively parallel sequencing (MPS), the increases in the number of unique alleles, effective alleles (Ae), and observed heterozygosity (Hobs) are 46.81%, 4.51%, and 3.29%, respectively. Twelve FR variants are first reported to dbSNP, such as rs1252699848, rs1665500714, rs1771121532, rs2097285015, rs1851671415, rs2045669877, rs2046758811, rs2044248635, rs1251308240, rs1968822112, rs1981638299, and rs1341756746. All 94 iSNPs from target and amplicon data are in Hardy-Weinberg equilibrium (HWE) and independent within autosomes. As expected, forensic parameters from the amplicon data increase significantly on the combined power of discrimination (CPD = 1 - 3.9876 × 10-38) and the combined power of exclusion (CPE = 1 - 6.6690 × 10-8). Additionally, the power of the system effectiveness (CPD = 1 - 6.7054 × 10-72 and CPE = 1 - 4.4719 × 10-20) with sequence-based 27 autosomal STRs and 94 iSNP amplicons in combination is substantially improved compared to one type of marker alone. In conclusion, we have established a traditional length-based and current sequence-based reference database with 58 STRs and 94 iSNPs in the Northern Han Chinese population. We hope these data can serve as a solid reference and foundation for forensic practice.
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Affiliation(s)
- Fei Guo
- Shenyang Medical College, Shenyang, Liaoning, 110034, PR China; Key Laboratory of Human Ethnic Specificity and Phenomics of Critical Illness in Liaoning Province, Shenyang, Liaoning, 110034, PR China; Key Laboratory of Phenomics in Shenyang City, Shenyang, Liaoning, 110034, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning, 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China.
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4
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Tao R, Dong X, Zhen X, Xia R, Qu Y, Liu S, Zhang S, Li C. Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit. Mol Genet Genomics 2024; 299:9. [PMID: 38374461 DOI: 10.1007/s00438-024-02121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024]
Abstract
Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Minhang Branch of Shanghai Public Security Bureau, Shanghai, 201108, China
| | - Xiaoyuan Zhen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, 100088, China.
| | - Suhua Zhang
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China.
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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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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Sathirapatya T, Worrapitirungsi W, Sukawutthiya P, Noh H, Pitiwararom R, Vongpaisarnsin K. The concordance of length- and sequence-based STRs used in forensic markers with guidance for practice. Forensic Sci Int 2023; 348:111729. [PMID: 37196610 DOI: 10.1016/j.forsciint.2023.111729] [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: 03/28/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Next-generation sequencing (NGS) technology has shed light on every aspect of genetic discoveries, including forensic genetics. The Miseq® FGx Forensic Genetic System (Verogen) is one of the pioneering forensic NGS that provided a complete system from library preparation to data analysis. The system has been validated by several studies and led to a more practical aspect. Short tandem repeat (STR) is a well-established marker that was designed specifically for human individualization. Since NGS provides different data from fragment analysis, a new STR nomenclature is established to make NGS backward compatible with the previous data. In this study, Thai population were used to evaluate the Miseq® FGx Forensic genetic system (Verogen) in practical aspect, including concordance study and forensic population parameters. In summary, we purposed a practical guideline for sequence-based STRs.
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Affiliation(s)
- Tikumphorn Sathirapatya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hasnee Noh
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rachtipan Pitiwararom
- Faculty of Criminology and Justice Administration, Rangsit University, Pathum Thani, Thailand
| | - Kornkiat Vongpaisarnsin
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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7
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Guo F, Liu Z, Long G, Zhang B, Dong X, Liu D, Yu S. High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System. Forensic Sci Int Genet 2023; 65:102879. [PMID: 37150076 DOI: 10.1016/j.fsigen.2023.102879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/16/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp - Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.
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Affiliation(s)
- Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Xinyu Dong
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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10
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Aguilar-Velázquez JA, Duran-Salazar MÁ, Córdoba-Mercado MF, Coronado-Avila CE, Salas-Salas O, Martinez-Cortés G, Casals F, Calafell F, Ramos-González B, Rangel-Villalobos H. Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico). Mol Biol Rep 2022; 49:7601-7609. [PMID: 35657453 DOI: 10.1007/s11033-022-07575-y] [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: 10/26/2021] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND STR allele frequency databases from populations are necessary to take full advantage of the increased power of discrimination offered by massively parallel sequencing (MPS) platforms. MATERIAL AND METHODS For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 105 Mestizo (admixed) individuals from Monterrey City (Northeast, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit. RESULTS Most of the STR markers were in Hardy Weinberg equilibrium, with a few exceptions. We found 346 different length-based alleles for these 58 STRs; nevertheless, they became 528 alleles when the sequence was assessed. The combined power of discrimination from autosomal STRs (aSTRs) was -virtually- 100% in both length and sequence-based alleles, while the power of exclusion was 99.9999999976065 and 99.9999999999494%, respectively. Haplotypes based on X-STRs and Y-STRs showed 100% of discriminatory capacity. CONCLUSIONS These results provide -for the first time- forensic genomic population data from Mexico necessary for interpretation in kinship and criminal analyses.
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Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.,Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Miguel Ángel Duran-Salazar
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.,Programa de Doctorado en Biociencias, Centro Universitario de los Altos, Universidad de uadalajara, Tepatitlán de Morelos, Jalisco, Mexico
| | - Miranda Fabiola Córdoba-Mercado
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico
| | - Carolina Elena Coronado-Avila
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico
| | - Orlando Salas-Salas
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico
| | - Gabriela Martinez-Cortés
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico
| | - Ferrán Casals
- Servei de Genómica, Universitat Pampeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Benito Ramos-González
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico.
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.
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11
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Sequence polymorphisms of forensic Y-STRs revealed by a 68-plex in-house massively parallel sequencing panel. Forensic Sci Int Genet 2022; 59:102727. [DOI: 10.1016/j.fsigen.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/03/2022] [Accepted: 05/23/2022] [Indexed: 11/20/2022]
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12
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Graffelman J, Weir BS. The transitivity of the Hardy-Weinberg law. Forensic Sci Int Genet 2022; 58:102680. [PMID: 35313226 PMCID: PMC10693928 DOI: 10.1016/j.fsigen.2022.102680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/27/2022]
Abstract
The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in genetic data analysis is explored, using high-quality autosomal microsatellite databases from the US National Institute of Standards and Technology. We address the reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit. Equilibrium test results obtained with the original and reduced polymorphisms are generally observed to be coherent, in particular when results obtained with length-based and sequence-based microsatellites are compared. We exploit the transitivity principle in order to identify disequilibrium-related alleles, and show its usefulness for detecting population substructure and genotyping problems that relate to null alleles and allele imbalance.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Carrer Jordi Girona, 1-3, 08034, Barcelona, Spain; Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America.
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America
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13
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Dash HR, Vajpayee K, Shukla R, Srivastava A, Shrivastava P, Das S. Sequence-based assessment of expediency of tri-, tetra-, and penta-nucleotides repeat autosomal STR markers in the central Indian population using Next Generation Sequencing (NGS). Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.100983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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14
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Dash HR, Vajpayee K, Srivastava A, Das S. Prevalence and characterisation of size and sequence-based microvariant alleles at nine autosomal STR markers in the Central Indian population. Ann Hum Biol 2021; 48:614-620. [PMID: 34818952 DOI: 10.1080/03014460.2021.2010804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Though microvariant alleles are widely reported in global populations, they are not well characterised to date. AIM To study the prevalence and characterisation of size and sequence-based microvariant alleles. SUBJECTS AND METHODS Next Generation Sequencing (NGS) was used to sequence microvariant alleles at nine autosomal STR markers in 138 samples. RESULTS After sequencing 31 STR markers using Precision ID GlobalFilerTM NGS STR panel v2, only nine markers, i.e. D12S391, D19S433, D1S1656, D21S11, D2S441, D7S820, FGA, Penta D, and TH01 showed the prevalence of microvariant alleles. Occurrence of microvariant alleles was positively correlated with Total Possible Alleles (p < 0.005), Power of Discrimination (p < 0.01), Polymorphic Information Content (p < 0.01), and Power of Exclusion (p < 0.05) and negatively correlated with the Matching Probability (p < 0.01). The average allele frequency of the microvariant alleles was found to be significantly less than the allele frequency value of the complete alleles (p = 0.88). Further, sequencing of these microvariant alleles reveals the deletion of nucleotides from the start, end, or middle of the repeat unit is responsible for the generation of a microvariant allele. CONCLUSIONS Prevalence of microvariant alleles is rare in nature and is limited to 9 STR loci out of 31 STR loci tested in the central Indian population. The occurrence of microvariant alleles in a locus increases its forensic and paternity application.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | - Kamayani Vajpayee
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.,School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India
| | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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15
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Dash HR, Kaitholia K, Kumawat RK, Singh AK, Shrivastava P, Chaubey G, Das S. Sequence variations, flanking region mutations, and allele frequency at 31 autosomal STRs in the central Indian population by next generation sequencing (NGS). Sci Rep 2021; 11:23238. [PMID: 34853383 PMCID: PMC8636586 DOI: 10.1038/s41598-021-02690-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/18/2021] [Indexed: 02/05/2023] Open
Abstract
Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India.
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, Madhya Pradesh, 769001, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 470001, India
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16
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Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing. Int J Legal Med 2021; 136:447-464. [PMID: 34741666 DOI: 10.1007/s00414-021-02738-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods.
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17
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Hulaniuk ML, Corach D, Trinks J, Caputo M. A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension. Lett Appl Microbiol 2021; 73:308-317. [PMID: 34048079 DOI: 10.1111/lam.13515] [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: 02/12/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/28/2022]
Abstract
Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.
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Affiliation(s)
- M L Hulaniuk
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - D Corach
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,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, Buenos Aires, Argentina
| | - J Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Caputo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,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, Buenos Aires, Argentina
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18
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Li H, Zhang C, Song G, Ma K, Cao Y, Zhao X, Yang Q, Xie J. Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population. Mol Genet Genomic Med 2021; 9:e1626. [PMID: 33630413 PMCID: PMC8123751 DOI: 10.1002/mgg3.1626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/17/2021] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Massively parallel sequencing (MPS) is a promising supplementary method for forensic casework in short tandem repeats (STRs) genotyping, owing to several advantageous features in comparison to traditional capillary electrophoresis (CE). However, the application of MPS in casework requires accessible datasets from the worldwide population to enrich the allele frequencies of sequence-based STR genotypes. METHODS In this study, we report the characterization of sequence-based allele frequencies of 58 STRs from a Tibetan population comprising 120 unrelated individuals using the ForenSeq™ DNA Signature Prep Kit. A concordance study evaluating MPS and CE allele data was performed to ensure that MPS is compatible with current CE-based forensic databases. The diversity of observed alleles, allele frequencies, and forensic parameters per locus by length (LB), sequence without flanking region (RSB), and sequence with flanking region (FSB) were analyzed and compared. RESULTS The concordance study demonstrated a concordance rate exceeding 99%. The combined random match probability (RMP) for the 26 A-STRs was 2.04 × 10-29 , 1.93 × 10-31 , and 9.56 × 10-33 for LB, RSB, and FSB, respectively. Similar trends were observed in other forensic parameters resulting from the increase in the number of unique alleles available. A total of 111 and 113 unique haplotypes in the Y-STR loci were observed when using length-based and sequence-based alleles, respectively. In addition, we identified 35 novel alleles at 25 loci and 25 polymorphisms in the flanking regions at 17 STRs. CONCLUSIONS Our data suggest that MPS- and CE-derived alleles are compatible. MPS-based analysis of the STR data substantially increased the allele diversity and improved the forensic parameters, which clearly demonstrated the advantages of MPS in comparison to CE. With more pooled data and larger-scale validation, MPS could play a valuable role in forensic genetics and might be an additional tool for routine casework.
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Affiliation(s)
- Hui Li
- Department of Forensic MedicineSchool of Basic Medical SciencesFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Crime Scene EvidenceShanghai Research Institute of Criminal Science and TechnologyShanghai Municipal Public Security BureauShanghaiChina
| | - Cheng Zhang
- Center for Material EvidenceTibet Autonomous Region Public SecurityLhasa, TibetChina
| | - Guoqing Song
- Laboratory of Forensic Evidence and Science TechnologyXianyang Municipal Public Security BureauXianyangShaanxiChina
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene EvidenceShanghai Research Institute of Criminal Science and TechnologyShanghai Municipal Public Security BureauShanghaiChina
| | - Yu Cao
- Shanghai Key Laboratory of Crime Scene EvidenceShanghai Research Institute of Criminal Science and TechnologyShanghai Municipal Public Security BureauShanghaiChina
| | - Xueying Zhao
- National Demonstration Center for Experimental Biology EducationSchool of Life SciencesFudan UniversityShanghaiChina
| | - Qinrui Yang
- Department of Forensic MedicineSchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Jianhui Xie
- Department of Forensic MedicineSchool of Basic Medical SciencesFudan UniversityShanghaiChina
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19
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Shen X, Li R, Li H, Gao Y, Chen H, Qu N, Peng D, Wu R, Sun H. Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing. Genes (Basel) 2021; 12:genes12030454. [PMID: 33810139 PMCID: PMC8004970 DOI: 10.3390/genes12030454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/05/2021] [Accepted: 03/20/2021] [Indexed: 01/04/2023] Open
Abstract
Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology.
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Affiliation(s)
- Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yu Gao
- Department of Obstetrics, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China;
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ning Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Riga Wu
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
- Correspondence: (R.W.); (H.S.)
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Correspondence: (R.W.); (H.S.)
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20
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King JL, Woerner AE, Mandape SN, Kapema KB, Moura-Neto RS, Silva R, Budowle B. STRait Razor Online: An enhanced user interface to facilitate interpretation of MPS data. Forensic Sci Int Genet 2021; 52:102463. [PMID: 33493821 DOI: 10.1016/j.fsigen.2021.102463] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/06/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
Since 2013, STRait Razor has enabled analysis of massively parallel sequencing (MPS) data from various marker systems such as short tandem repeats, single nucleotide polymorphisms, insertion/deletions, and mitochondrial DNA. In this paper, STRait Razor Online (SRO), available at https://www.unthsc.edu/straitrazor, is introduced as an interactive, Shiny-based user interface for primary analysis of MPS data and secondary analysis of STRait Razor haplotype pileups. This software can be accessed from any common browser via desktop, tablet, or smartphone device. SRO is available also as a standalone application and open-source R script available at https://github.com/ExpectationsManaged/STRaitRazorOnline. The local application is capable of batch processing of both fastq files and primary analysis output. Processed batches generate individual report folders and summary reports at the locus- and haplotype-level in a matter of minutes. For example, the processing of data from ∼700 samples generated with the ForenSeq Signature Preparation Kit from allsequences.txt to a final table can be performed in ∼40 min whereas the Excel-based workbooks can take 35-60 h to compile a subset of the tables generated by SRO. To facilitate analysis of single-source, reference samples, a preliminary triaging system was implemented that calls potential alleles and flags loci suspected of severe heterozygote imbalance. When compared to published, manually curated data sets, 98.72 % of software-assigned allele calls without manual interpretation were consistent with curated data sets, 0.99 % loci were presented to the user for interpretation due to heterozygote imbalance, and the remaining 0.29 % of loci were inconsistent due to the analytical thresholds used across the studies.
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Affiliation(s)
- Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - Sammed N Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - Kapema Bupe Kapema
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | | | - Rosane Silva
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
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