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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [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: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Miao X, Gong X, Paul G, Shen Y, Gao J, Li B, Yu H, Chang L, Li S, Liang Z, Yan C, Ma T, Zhang B. Sequenced-based Rwanda population provides insights into demographic history. Electrophoresis 2024; 45:517-527. [PMID: 38100194 DOI: 10.1002/elps.202300161] [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: 07/21/2023] [Revised: 11/22/2023] [Accepted: 11/30/2023] [Indexed: 03/20/2024]
Abstract
Rwanda is known as the heart of Africa, reflecting the history of the world. Colonization and genocide have led to Rwanda's existing genetic structure. Herein, we used massively parallel sequencing to analyze 296 loci in 185 Rwandans and constructed a database for Rwandan forensic data for the first time. We found the following results: First, forensic parameters demonstrated that all loci were highly informative and could be used for forensic identification and paternity tests in Rwandans. Second, we found that the differences in genetic background between Rwandans and other African populations were similar but slight, as indicated by the massively parallel sequencing panel. Rwandans belonged to the African population and were inseparable from populations from neighboring countries. Also, Rwandans were closer to the European and American populations because of colonization, war, and other reasons. There was no scientific basis for racial classification established by colonization. Further research still needs to be carried out on more loci and larger Rwandan samples.
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Affiliation(s)
- Xinyao Miao
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
- Department of Computer Science, City University of Hong Kong, Hong Kong, P. R. China
| | - Xiaojuan Gong
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
- Department of Computer Science, City University of Hong Kong, Hong Kong, P. R. China
| | - Gasana Paul
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
- Department of Biomedical Laboratory Science, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Yuesheng Shen
- School of Life Science, Northwest A&F University, Yanglin, P. R. China
| | - Jiayang Gao
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Bowen Li
- School of Life Science, Sichuan University, Chengdu, P. R. China
| | - Huiyun Yu
- School of Life Science, Northwest A&F University, Yanglin, P. R. China
| | - Liao Chang
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Shengbin Li
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
| | | | - Chunxia Yan
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tao Ma
- MGI Tech Co., Ltd, Shenzhen, P. R. China
| | - Bao Zhang
- College of Forensic Medicine, Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, P. R. China
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Yang C, He M, Liu C, Liu X, Lun M, Su Q, Han X, Liu H, Wang M, Chen L, Liu C. Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application. Electrophoresis 2023; 44:1704-1713. [PMID: 37622566 DOI: 10.1002/elps.202300044] [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: 02/27/2023] [Revised: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresis platform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25 ng. All genotypes were obtained in the presence of 80 ng/µL humic acid, 2000 µmol/L calcium, 3000 µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951 × 10-32 and 1-4.2956 × 10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.
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Affiliation(s)
- Chengliang Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Meiyun He
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Miaoqiang Lun
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Qin Su
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xiaolong Han
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, P. R. China
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Yang SB, Lee JE, Lee HY. Forensic genetic analysis of single-nucleotide polymorphisms and microhaplotypes in Koreans through next-generation sequencing using precision ID identity panel. Genes Genomics 2023; 45:1281-1293. [PMID: 37440105 DOI: 10.1007/s13258-023-01424-3] [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: 05/25/2023] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND Forensic DNA analysis has seen remarkable advancements with the advent of Next Generation Sequencing (NGS). In particular, NGS analysis of single nucleotide polymorphisms (SNPs) offers significant advantages in the analysis of challenging samples compared to conventional STR analysis. OBJECTIVE This study aimed to investigate the SNPs of the Precision ID Identity Panel, a commercially available NGS panel for personal identification, by generating genetic profiles of 298 Koreans and comparing them with other global populations. METHODS A total of 124 SNPs, including 90 autosomal and 34 Y-SNPs, were analyzed using the Precision ID Identity Panel, and forensic parameters, microhaplotypes, and population differences were investigated. RESULTS The NGS data were successfully obtained from 298 Koreans. The analysis of forensic parameters exhibited a low combined match probability of 1.532 × 10- 34, which is comparable to that obtained from commonly used STR analysis. Additionally, the microhaplotype analysis revealed that the use of 16 microhaplotypes provided higher discriminatory power compared to single target SNPs. Furthermore, the adoption of microhaplotype data resulted in an increase of over 20% in expected heterozygosity at five loci. Inter-population analysis showed a close genetic relationship between Koreans and individuals from China and Myanmar in East and Southeast Asia, which are geographically adjacent to Korea. CONCLUSIONS The results of this study show that the Precision ID Identity panel can be a useful alternative where traditional STR typing is not feasible. Also, the data from our study will be useful as a reference for Koreans in forensic investigations and the prosecution of criminal justice.
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Affiliation(s)
- Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Eun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea.
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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Ge J, Crysup B, Peters D, Franco R, Liu M, Wang X, Huang M, Budowle B. MPKin-YSTR: Interpretation of Y chromosome STR haplotypes for missing persons cases. Electrophoresis 2023; 44:1080-1087. [PMID: 37016479 DOI: 10.1002/elps.202200225] [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: 09/16/2022] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/06/2023]
Abstract
Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines for Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with Y-STR haplotypes. Because of the high mutation rate of Y-STRs, there are complex missing person cases in which inconsistent Y-STR haplotypes between true paternal lineage relatives will arise and cases with two or more male references in the same lineage and yet differ in their haplotypes. Therefore, more useful methods are needed for interpreting the Y-STR haplotype data. Computational methods and interpretation guidelines have been developed specifically addressing this issue, either using a mismatch-based counting method or a pedigree likelihood ratio method. In this study, a software program, MPKin-YSTR, was developed by implementing those more sophisticated methods. This software should be able to improve the interpretation of complex cases with Y-STR haplotype evidence. Thus, more biological evidence will be interpreted, which in turn will result in more investigation leads to help solve crimes.
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Affiliation(s)
- Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Dixie Peters
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Romy Franco
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Muyi Liu
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
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Joo SM, Kwon YL, Moon MH, Shin KJ. Genetic investigation of 124 SNPs in a Myanmar population using the Precision ID Identity Panel and the Illumina MiSeq. Leg Med (Tokyo) 2023; 63:102256. [PMID: 37058993 DOI: 10.1016/j.legalmed.2023.102256] [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: 09/19/2022] [Revised: 03/16/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs). The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs, enabled human identification studies on global populations through next-generation sequencing (NGS). However, most previous studies on the panel have used the Ion Torrent platform, and there are few reports on the Southeast Asian population. Here, a total of 96 unrelated males from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter and a custom variant caller, Visual SNP. The sequencing performance evaluated by locus balance and heterozygote balance was comparable to that of the Ion Torrent platform. For 90 autosomal SNPs, the combined match probability (CMP) was 6.994 × 10-34, lower than that of 22 PowerPlex Fusion autosomal STRs (3.130 × 10-26). For 34 Y-SNPs, 14 Y-haplogroups (mostly O2 and O1b) were observed. We found 51 cryptic variations (42 haplotypes) around target SNPs, of which haplotypes corresponding to 33 autosomal SNPs decreased CMP. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations. In conclusion, the Precision ID Identity Panel can be successfully analyzed on the Illumina MiSeq and provides high discrimination power for human identification in the Myanmar population. This study broadened the accessibility of the NGS-based SNP panel by expanding the available NGS platforms and adopting a robust NGS data analysis tool.
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Affiliation(s)
- Su Min Joo
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ye-Lim Kwon
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Mi Hyeon Moon
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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Felkl AB, Avila E, Gastaldo AZ, Lindholz CG, Dorn M, Alho CS. Ancestry resolution of South Brazilians by forensic 165 ancestry-informative SNPs panel. Forensic Sci Int Genet 2023; 64:102838. [PMID: 36736201 DOI: 10.1016/j.fsigen.2023.102838] [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: 08/24/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023]
Abstract
Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10-6). Interpopulation comparisons by FST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation.
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Affiliation(s)
- Aline Brugnera Felkl
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - André Zoratto Gastaldo
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Márcio Dorn
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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Yin Y, Zhang P, Xing Y. A New Computational Deconvolution Algorithm for the Analysis of Forensic DNA Mixtures with SNP Markers. Genes (Basel) 2022; 13:genes13050884. [PMID: 35627269 PMCID: PMC9141285 DOI: 10.3390/genes13050884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) support robust analysis on degraded DNA samples. However, the development of a systematic method to interpret the profiles derived from the mixtures is less studied, and it remains a challenge due to the bi-allelic nature of SNP markers. To improve the discriminating power of SNPs, this study explored bioinformatic strategies to analyze mixtures. Then, computer-generated mixtures were produced using real-world massively parallel sequencing (MPS) data from the single samples processed with the Precision ID Identity Panel. Moreover, the values of the frequency of major allele reads (FMAR) were calculated and applied as key parameters to deconvolve the two-person mixtures and estimate mixture ratios. Four custom R language scripts (three for autosomes and one for Y chromosome) were designed with the K-means clustering method as a core algorithm. Finally, the method was validated with real-world mixtures. The results indicated that the deconvolution accuracy for evenly balanced mixtures was 100% or close to 100%, which was the same as the deconvolution accuracy of inferring the genotypes of the major contributor of unevenly balanced mixtures. Meanwhile, the accuracy of inferring the genotypes of the minor contributor decreased as its proportion in the mixture decreased. Moreover, the estimated mixture ratio was almost equal to the actual ratio between 1:1 and 1:6. The method proposed in this study provides a new paradigm for mixture interpretation, especially for inferring contributor profiles of evenly balanced mixtures and the major contributor profile of unevenly balanced mixtures.
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Affiliation(s)
- Yu Yin
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; (Y.Y.); (P.Z.)
| | - Peng Zhang
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; (Y.Y.); (P.Z.)
- Public Security Bureau of Chongqing Nanchan District, #11 Jinshan Avenue, Nanchang District, Chongqing 408499, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; (Y.Y.); (P.Z.)
- Correspondence:
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Avila E, Speransa PA, Lindholz CG, Kahmann A, Alho CS. Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits. Forensic Sci Int Genet 2021; 57:102650. [PMID: 34972071 DOI: 10.1016/j.fsigen.2021.102650] [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: 10/22/2021] [Accepted: 12/01/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages. PURPOSE This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population. METHODS A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters. RESULTS The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population. CONCLUSIONS The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.
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Affiliation(s)
- Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Pietro Augusto Speransa
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Alessandro Kahmann
- National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, RS, Brazil.
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
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11
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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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12
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Dash HR, Avila E, Jena SR, Kaitholia K, Agarwal R, Alho CS, Srivastava A, Singh AK. Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing. Int J Legal Med 2021; 136:465-473. [PMID: 34748086 DOI: 10.1007/s00414-021-02742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis-based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10-37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.
| | - Eduardo Avila
- Pontifical Catholic University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Soumya Ranjan Jena
- Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | | | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
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13
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An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data. Genes (Basel) 2021; 12:genes12111739. [PMID: 34828345 PMCID: PMC8618049 DOI: 10.3390/genes12111739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.
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14
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Relevance aggregation for neural networks interpretability and knowledge discovery on tabular data. Inf Sci (N Y) 2021. [DOI: 10.1016/j.ins.2021.01.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Liu Y, Jin X, Mei S, Lan Q, Fang Y, Liu C, Zhu B. A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies. Electrophoresis 2020; 41:2036-2046. [DOI: 10.1002/elps.202000128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/10/2020] [Accepted: 08/23/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yanfang Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- College of Forensic Medicine Xi'an Jiaotong University Health Science Center Shaanxi P. R. China
| | - Shuyan Mei
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Qiong Lan
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Yating Fang
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Chao Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Bofeng Zhu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
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16
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Cavalheiro CP, Avila E, Gastaldo AZ, Graebin P, Motta CHA, Rodenbusch R, Alho CS. Uniparental disomy of chromosome 21: A statistical approach and application in paternity tests. Forensic Sci Int Genet 2020; 49:102368. [PMID: 32911454 DOI: 10.1016/j.fsigen.2020.102368] [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: 02/05/2020] [Revised: 06/30/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022]
Abstract
Considering the overall frequency of paternity investigation cases including mutational events, there is a real possibility that at least a fraction of all inconsistencies reported in paternity cases are caused not by polymerase slippage mutations, but to chromosomic abnormalities, as Uniparental Disomy (UPD). We report here the investigation of a trio paternity case (mother, child and alleged father), with observed inconsistencies that can alternatively be explained by occurrence of maternal uniparental isodisomy of chromosome 21 (miUPD21). A total of 350 short tandem repeat (STR) and single nucleotide polymorphism (SNP) markers were tested, statistically suggesting true biological linkage within the trio. Additionally, we propose miUPD21 explains, with significantly greater probability, the occurrence of detected inconsistencies, when compared to alternative hypothesis of multiple and simultaneous slippage mutations. Similar cases could have their statistical conclusions improved or even altered by including unusual chromosomal segregation patterns in the hypothesis formulation, as well as in mathematical calculations. Such reports of allelic inconsistencies being explained by chromosomal alterations are common in clinical genetics, and such situations might have impact on forensic investigation.
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Affiliation(s)
- C P Cavalheiro
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil.
| | - E Avila
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil; Polícia Federal, Setor Técnico Científico, Porto Alegre, RS, Brazil
| | - A Z Gastaldo
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
| | - P Graebin
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
| | - C H A Motta
- Instituto de Medicina Social e Criminalística de São Paulo, São Paulo, SP, Brazil
| | - R Rodenbusch
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - C S Alho
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
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17
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Miao X, Shen Y, Gong X, Yu H, Li B, Chang L, Wang Y, Fan J, Liang Z, Tan B, Li S, Zhang B. A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. Int J Legal Med 2020; 135:709-718. [PMID: 32851473 DOI: 10.1007/s00414-020-02403-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/21/2020] [Indexed: 01/23/2023]
Abstract
The MiSeq® FGX Forensic system and the HID-Ion AmpliSeq Panel were previously developed for massively parallel sequencing (MPS) for forensic casework. Among the three major sequencing platforms, BGISEQ-500TM, which is based on multiple PCRs, is still lacking in forensics. Here, a novel forensic panel was constructed to detect 186 single-nucleotide polymorphisms (SNPs) and 123 short tandem repeats (STRs) with MPS technology on the BGISEQ-500™ platform. First, the library preparation, sequencing process, and data analysis were performed, focusing on the average depth of coverage and heterozygote balance. We calculated the allelic frequencies and forensic parameters of STR and SNP loci in 73 unrelated Chinese Han individuals. In addition, performance was evaluated with accuracy, uniformity, sensitivity, PCR inhibitor, repeatability and reproducibility, mixtures, degraded samples, case-type samples, and pedigree analyses. The results showed that 100% accurate and concordant genotypes can be obtained, and the loci with an abundance in the interquartile range accounted for 92.90% of the total, suggesting reliable uniformity in this panel. We obtained a locus detection rate that was higher than 98.78% from 78 pg of input DNA, and the optimal amount was 1.25-10 ng. The maximum concentrations of hematin and humic acid were 200 and 100 μM, respectively (the ratios of detected loci were 96.52% and 92.41%), in this panel. As a mixture, compared with those of SNPs, minor-contributor alleles of STRs could be detected at higher levels. For the degraded sample, the ratio of detected loci was 98.41%, and most profiles from case-type samples were not significantly different in abundance in our studies. As a whole, this panel showed high-performance, reliable, robust, repeatable, and reproducible results, which are sufficient for paternity testing, individual identification, and use for potentially degraded samples in forensic science.
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Affiliation(s)
- Xinyao Miao
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yuesheng Shen
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Xiaojuan Gong
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
- School of Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Huiyun Yu
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Bowen Li
- School of Life Science, Sichuan University, Chengdu, People's Republic of China
| | - Liao Chang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yinan Wang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jingna Fan
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zuhuan Liang
- Forensic Genomics International, The Beijing Genomics Institute (BGI), Shenzhen, People's Republic of China
| | - Bowen Tan
- School of Computer Science, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Shengbin Li
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Bao Zhang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
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18
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Analysis of 124 SNP loci included in HID Ampliseq identity panel in a small population of Rio de Janeiro, Brazil. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Brazilian forensic casework analysis through MPS applications: Statistical weight-of-evidence and biological nature of criminal samples as an influence factor in quality metrics. Forensic Sci Int 2019; 303:109938. [DOI: 10.1016/j.forsciint.2019.109938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 12/18/2022]
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20
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Avila E, Graebin P, Chemale G, Freitas J, Kahmann A, Alho CS. Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. Forensic Sci Int Genet 2019; 42:154-164. [PMID: 31325893 DOI: 10.1016/j.fsigen.2019.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.
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Affiliation(s)
- E Avila
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil; Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil.
| | - P Graebin
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - G Chemale
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil
| | - J Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brasília, DF, Brazil
| | - A Kahmann
- Instituto de Matemática, Estatística e Física, Universidade Federal de Rio Grande, Rio Grande, Brazil
| | - C S Alho
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil
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