1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Mandape SN, Budowle B, Mittelman K, Mittelman D. Dense single nucleotide polymorphism testing revolutionizes scope and degree of certainty for source attribution in forensic investigations. Croat Med J 2024; 65:249-260. [PMID: 38868971 PMCID: PMC11157251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/06/2024] [Indexed: 06/14/2024] Open
Abstract
The field of forensic DNA analysis has experienced significant advancements over the years, such as the advent of DNA fingerprinting, the introduction of the polymerase chain reaction for increased sensitivity, the shift to a primary genetic marker system based on short tandem repeats, and implementation of national DNA databases. Now, the forensics field is poised for another revolution with the advent of dense single nucleotide polymorphisms (SNPs) testing. SNP testing holds the potential to significantly enhance source attribution in forensic cases, particularly those involving low-quantity or low-quality samples. When coupled with genetic genealogy and kinship analysis, it can resolve countless active cases as well as cold cases and cases of unidentified human remains, which are hindered by the limitations of existing forensic capabilities that fail to generate viable investigative leads with DNA. The field of forensic genetic genealogy combined with genome-wide sequencing can associate relatives as distant as the seventh-degree and beyond. By leveraging volunteer-populated databases to locate near and distant relatives, genetic genealogy can effectively narrow the candidates linked to crime scene evidence or aid in determining the identity of human remains. With decreasing DNA sequencing costs and improving sensitivity of detection, forensic genetic genealogy is expanding its capabilities to generate investigative leads from a wide range of biological evidence.
Collapse
Affiliation(s)
| | | | | | - David Mittelman
- David Mittelman, Othram Inc., 2829 Technology Forest Blvd STE 100, The Woodlands, Texas 77381, USA,
| |
Collapse
|
3
|
Fan Q, Li L, Yang H, Xu D, Wang Y, Jin B, Du B. Development and validation of a new multiplex panel using SNaPshot-based DIP-TriSNP markers for forensic DNA mixtures. Electrophoresis 2024; 45:867-876. [PMID: 38651903 DOI: 10.1002/elps.202300215] [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: 09/26/2023] [Revised: 01/28/2024] [Accepted: 03/10/2024] [Indexed: 04/25/2024]
Abstract
Short tandem repeat analysis is challenging when dealing with unbalanced mixtures in forensic cases due to the presence of stutter peaks and large amplicons. In this research, we propose a novel genetic marker called DIP-TriSNP, which combines deletion/insertion polymorphism (DIP) with tri-allelic single nucleotide polymorphism in less than 230 bp length of human genome. Based on multiplex PCR and SNaPShot, a panel, including 14 autosomal DIP-TriSNPs and one Y chromosomal DIP-SNP, had been developed and applied to genotyping 102 unrelated Han Chinese individuals in Sichuan of China and simulated a mixture study. The panel sensitivity can reach as low as 0.1 ng DNA template, and the minor contributor of DNA can be detected with the highest ratio of 19:1, as indicated by the obtained results. In the Sichuan Han population, the cumulative probability of informative genotypes reached 0.997092, with a combined power of discrimination of 0.999999998801. The panel was estimated to detect more than two alleles in at least one locus in 99.69% of mixtures of the Sichuan Han population. In conclusion, DIP-TriSNPs have shown promising as an innovative DNA marker for identifying the minor contributor in unbalanced DNA mixtures, offering advantages such as short amplifications, increased polymorphism, and heightened sensitivity.
Collapse
Affiliation(s)
- Qingwei Fan
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
- Forensic Science Service Center of North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| | - Ling Li
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| | - Huiling Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
- Forensic Science Service Center of North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| | - Dongdong Xu
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
- Forensic Science Service Center of North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| | - Yun Wang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
- Forensic Science Service Center of North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| | - Bo Jin
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
- Forensic Science Service Center of North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| | - Bing Du
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
- Forensic Science Service Center of North Sichuan Medical College, Nanchong, Sichuan Province, P. R. China
| |
Collapse
|
4
|
Sharma V, Wurmbach E. Systematic evaluation of the Precision ID GlobalFiler™ NGS STR panel v2 using single-source samples of various quantity and quality and mixed DNA samples. Forensic Sci Int Genet 2024; 69:102995. [PMID: 38065030 DOI: 10.1016/j.fsigen.2023.102995] [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: 04/07/2023] [Revised: 10/19/2023] [Accepted: 11/30/2023] [Indexed: 01/29/2024]
Abstract
Massively parallel sequencing (MPS) techniques were developed approximately 15 years ago. Meanwhile, several MPS kits for forensic identification, phenotypic information, ancestry, and mitochondrial DNA analysis have been developed and their use has been established. Sequencing short tandem repeats (STRs) has certain advantages over the currently used length-based genotyping methods, which are based on PCR amplification followed by capillary electrophoresis (CE). MPS is more discriminative and includes the possibility of testing high numbers of targets (> 100), different types of markers [STRs and single nucleotide polymorphisms (SNPs)], as well as the use of smaller amplicons (< 300 bp). This study evaluated in 24 experimental runs the Precision ID GlobalFiler™ NGS STR panel v2 from ThermoFisher, which targets 31 autosomal STRs, amelogenin, and three Y-markers (one STR, SRY, and Yindel). Single-source samples were used in 18 experimental runs, for systematic evaluation. These included assessing library preparation benchmark conditions, limited DNA input, as well as testing repeatability, number of samples per run, and degraded DNA samples. Full profiles were consistently obtained from as little as 50 pg DNA input. Using the optional recovery PCR method improved outcomes for samples with low DNA input. Full profiles were also obtained from severely degraded DNA samples with degradation indices (DI) of > 60. In addition, six experimental runs were performed testing various two-person mixtures with mixture ratios ranging from 1:20 to 20:1. Major and minor contributors were distinguishable by their read counts (coverage), because less DNA input yielded lower read counts, analogous to the traditional CE technology, where less DNA produces lower peak heights. Mixture ratios of approximately 1:1 were indistinguishable, while a greater imbalance, i.e., higher mixture ratios, made the mixture more distinguishable between major and minor contributors. Based on this information, the highest success rate of correctly deconvoluted four-allelic loci was from mixtures with 1:3 ratios. At higher mixture ratios, the drop-out rate of the minor contributor increased, reducing the number of four-allelic loci.
Collapse
Affiliation(s)
- Vishakha Sharma
- New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA
| | - Elisa Wurmbach
- New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA.
| |
Collapse
|
5
|
Hughes DA, Szkuta B, van Oorschot RAH, Conlan XA. The impact of substrate characteristics on the collection and persistence of biological materials, and their implications for forensic casework. Forensic Sci Int 2024; 356:111951. [PMID: 38301431 DOI: 10.1016/j.forsciint.2024.111951] [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: 09/22/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
This study assessed the level of nucleic acid persistence on the substrate pre-, and post-swabbing, in order to assess whether biological materials (touch, saliva, semen, and blood) are collected differently depending on the substrate characteristics. A total of 48 samples per deposit and substrate variety (n = 384) were assessed by tracking the persistence of nucleic acid using Diamond™ Nucleic Acid Dye (DD) staining and Polilight photography. The number of DD nucleic acid fluorescent complexes formed post-staining were counted (fluorescent count) and in conjunction with the fluorescence signal intensity (DD nucleic acid complex accumulation) used to estimate the level of nucleic acid persistence on substrates. Touch deposits have shown to be the most persistent deposit with strong adhesion capabilities on both substrate verities. Saliva displayed a higher persistence than semen and/or blood. Semen displayed a high collection efficiency as well as a high fluorescence signal intensity. Blood displayed a low persistence on both substrates with a superior collection efficiency that may also indicate a higher probability to become dislodged from surfaces given a particular activity. Our research has shown that the persistence and recovery of biological deposits is not only measurable but more importantly, may have the potential to be estimated, as such, may build an understanding that can provide valuable guidance for collection efficiency evaluations, and the assessing of the probability of particular profiles, given alternate propositions of means of transfer occurring.
Collapse
Affiliation(s)
- Deborah A Hughes
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia
| | - Bianca Szkuta
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia; School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Australia
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia.
| |
Collapse
|
6
|
McElhoe JA, Addesso A, Young B, Holland MM. A New Tool for Probabilistic Assessment of MPS Data Associated with mtDNA Mixtures. Genes (Basel) 2024; 15:194. [PMID: 38397184 PMCID: PMC10887502 DOI: 10.3390/genes15020194] [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: 12/21/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial (mt) DNA plays an important role in the fields of forensic and clinical genetics, molecular anthropology, and population genetics, with mixture interpretation being of particular interest in medical and forensic genetics. The high copy number, haploid state (only a single haplotype contributed per individual), high mutation rate, and well-known phylogeny of mtDNA, makes it an attractive marker for mixture deconvolution in damaged and low quantity samples of all types. Given the desire to deconvolute mtDNA mixtures, the goals of this study were to (1) create a new software, MixtureAceMT™, to deconvolute mtDNA mixtures by assessing and combining two existing software tools, MixtureAce™ and Mixemt, (2) create a dataset of in-silico MPS mixtures from whole mitogenome haplotypes representing a diverse set of population groups, and consisting of two and three contributors at different dilution ratios, and (3) since amplicon targeted sequencing is desirable, and is a commonly used approach in forensic laboratories, create biological mixture data associated with two amplification kits: PowerSeq™ Whole Genome Mito (Promega™, Madison, WI, USA) and Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific by AB™, Waltham, MA, USA) to further validate the software for use in forensic laboratories. MixtureAceMT™ provides a user-friendly interface while reducing confounding features such as NUMTs and noise, reducing traditionally prohibitive processing times. The new software was able to detect the correct contributing haplogroups and closely estimate contributor proportions in sequencing data generated from small amplicons for mixtures with minor contributions of ≥5%. A challenge of mixture deconvolution using small amplicon sequencing is the potential generation of spurious haplogroups resulting from private mutations that differ from Phylotree. MixtureAceMT™ was able to resolve these additional haplogroups by including known haplotype/s in the evaluation. In addition, for some samples, the inclusion of known haplotypes was also able to resolve trace contributors (minor contribution 1-2%), which remain challenging to resolve even with deep sequencing.
Collapse
Affiliation(s)
- Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; (A.A.); (M.M.H.)
| | - Alyssa Addesso
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; (A.A.); (M.M.H.)
| | - Brian Young
- NicheVision LLC, 526 South Main St., Akron, OH 44311, USA;
| | - Mitchell M Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; (A.A.); (M.M.H.)
| |
Collapse
|
7
|
Torres D, Smith C, Williams AL, Cox JO, Seashols-Williams SJ, Boone EL, Green TD. A quantifiler™ trio-based HRM screening assay for the accurate prediction of single source versus mixed biological samples. Int J Legal Med 2023; 137:1639-1651. [PMID: 37553510 DOI: 10.1007/s00414-023-03070-6] [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: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
At present, the forensic DNA workflow is not capable of providing information about the contributor status (single source vs. multiple contributors) of evidentiary samples prior to end-point analysis. This exacerbates the challenges inherent to mixtures and low-template DNA samples. If additional sample information could be provided earlier in the workflow, protocols could be implemented to mitigate these challenges. An integrated Quantiplex®- high resolution melt (HRM) assay was shown to be effective in distinguishing between single source and mixture DNA samples; however, integration of the HRM assay into a more commonly used chemistry would be beneficial to the practitioner community. Thus, the assay was redesigned as an integrated Quantifiler™ Trio-HRM assay, which included the identification of a new DNA-binding dye, an increased reaction volume, and the establishment of new data analysis and standard curve metrics for all targets. This redesigned assay produced quantification values and qualitative values that were comparable to those produced when the same samples were tested using the standard Quantifiler™ Trio chemistry and settings. Further, STR profiles generated with quantification values produced from the integrated Quantifiler™ Trio-HRM assay and standard Quantifiler™ Trio chemistry were complete and fully concordant. Most importantly, the integrated Quantifiler™ Trio-HRM assay was able to accurately predict whether a sample was single source or a mixture 79.2% of the time, demonstrating the potential of this approach. With the incorporation of an expanded training set for prediction modeling, and completion of critical developmental validation studies, this assay could prove useful to the forensic DNA practitioner community.
Collapse
Affiliation(s)
- Dayanara Torres
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Chastyn Smith
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA.
- Integrative Life Sciences, Virginia Commonwealth University, 1000 Cary Street, Richmond, VA, 23284, USA.
| | - Andrea L Williams
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Edward L Boone
- Department of Statistical Sciences & Operations Research, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| |
Collapse
|
8
|
Flores M, Ly C, Ho E, Ceberio N, Felix K, Thorner HM, Guardado M, Paunovich M, Godek C, Kalaydjian C, Rohlfs R. Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554311. [PMID: 37745566 PMCID: PMC10515773 DOI: 10.1101/2023.08.25.554311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 244 human groups. We find higher false inclusion rates for mixtures with more contributors, and for groups with lower genetic diversity. Even for two-contributor mixtures where one contributor is known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 56 out of 244 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.
Collapse
Affiliation(s)
- Maria Flores
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
- University of California, Los Angeles; Department of Molecular, Cell and Developmental Biology; Los Angeles, CA, 90095, USA
| | - Cara Ly
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Evan Ho
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Niquo Ceberio
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Kamillah Felix
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Hannah Mariko Thorner
- George Washington University; Department of Forensic Sciences - Forensic Molecular Biology; Washington, DC, 20007, USA
| | - Miguel Guardado
- University of California, San Francisco; Biological and Medical Informatics Graduate Program; San Francisco CA, 94143, USA
| | - Matt Paunovich
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Chris Godek
- San Francisco State University; Department of Mathematics; San Francisco, CA, 94132, USA
| | - Carina Kalaydjian
- San Francisco State University; Department of Mathematics; San Francisco, CA, 94132, USA
| | - Rori Rohlfs
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
- University of Oregon; Department of Data Science; Eugene, OR, 97403, USA
| |
Collapse
|
9
|
Brinkac LM, Richetelli N, Davoren JM, Bever RA, Hicklin RA. DNAmix 2021: Laboratory policies, procedures, and casework scenarios summary and dataset. Data Brief 2023; 48:109150. [PMID: 37128591 PMCID: PMC10147962 DOI: 10.1016/j.dib.2023.109150] [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: 02/27/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
DNAmix 2021 is a large-scale study conducted to evaluate the extent of consistency and variation among forensic laboratories in the interpretation of DNA mixtures, and to assess the effects of various potential sources of variability. This study utilized a multi-phasic approach designed to collect information about participating laboratories, laboratory policies, and their standard operating procedures (SOPs). It also characterizes the degree of variation in assessments of suitability and number of contributors as well as in comparisons and statistical analyses of DNA mixture profiles. This paper specifically details the study design and the data collected in the first two phases of the study: the Policies & Procedures (P&P) Questionnaire and the Casework Scenarios Questionnaire (CSQ). We report on the variation in policies and SOPs for 86 forensic laboratories-including information about their DNA workflows, systems, and type of statistics reported. We also provide details regarding various case-scenario specific decisions and the nature of mixture casework for 83 forensic laboratories. The data discussed in this article provide insight into the state of the field for forensic DNA mixture interpretation policies and SOPs at the time of the study (2021-2022).
Collapse
|
10
|
Hicklin RA, Richetelli N, Emerick BL, Bever RA, Davoren JM. Variation in assessments of suitability and number of contributors for DNA mixtures. Forensic Sci Int Genet 2023; 65:102892. [PMID: 37267812 DOI: 10.1016/j.fsigen.2023.102892] [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: 02/14/2023] [Revised: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
The interpretation of a DNA mixture (a sample that contains DNA from two or more people) depends on a laboratory/analyst's assessment of the suitability of the sample for comparison/analysis, and an assessment of the number of contributors (NoC) present in the sample. In this study, 134 participants from 67 forensic laboratories provided a total of 2272 assessments of 29 DNA mixtures (provided as electropherograms). The laboratories' responses were evaluated in terms of the variability of suitability assessments, and the accuracy and variability of NoC assessments. Policies and procedures related to suitability and NoC varied notably among labs. We observed notable variation in whether labs would assess a given mixture as suitable or not, predominantly due to differences in lab policies: if two labs following their standard operating procedures (SOPs) were given the same mixture, they agreed on whether the mixture was suitable for comparison 66% of the time. Differences in suitability assessments have a direct effect on variability in interpretations among labs, since mixtures assessed as not suitable would not result in reported interpretations. For labs following their SOPs, 79% of assessments of NoC were correct. When two different labs provided NoC responses, 63% of the time both labs were correct, and 7% of the time both labs were incorrect. Incorrect NoC assessments have been shown to affect statistical analyses in some cases, but do not necessarily imply inaccurate interpretations or conclusions. Most incorrect NoC estimates were overestimates, which previous research has shown have less of an effect on likelihood ratios than underestimates.
Collapse
|
11
|
Lynch C, Fleming R. One-step endpoint RT-PCR assays for confirmatory body fluid identification. Forensic Sci Int Genet 2023; 64:102856. [PMID: 36921484 DOI: 10.1016/j.fsigen.2023.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Messenger RNA (mRNA) expression analysis is increasingly used in casework, in the form of multiplex two-step reverse transcriptase PCR (RT-PCR) assays such as CellTyper 2 (CT2), developed by the Institute of Environmental Science and Research (ESR). This paper presents the development of a one-step endpoint RT-PCR workflow to improve the efficiency and precision of confirmatory body fluid identification. A comparative study of commercial one-step RT-PCR kits was undertaken, with the highest performing kit (RNA to CT) retained for further development. Sensitivity, specificity across body fluids, and precision was assessed simultaneously using receiver operating characteristic (ROC) curves. An optimal RFU cut-off value which maximised sensitivity and specificity was determined for each marker. All assays performed significantly better when compared to the equivalent of a completely uninformative test (area under the curve of 0.5) for their target body fluid. Sensitivity varied between different donors, but the limit of detectionss were estimated as follows; saliva markers HTN3: 1 in 100 dilution of a whole buccal swab and FDCSP: 1 in 10 dilution of a whole buccal swab, circulatory blood marker SLC4A1: 0.1 µL blood, menstrual fluid markers STC1, MMP10: 1 in 10 dilution of a whole menstrual swab, spermatozoa markers PRM1, TNP1: 0.1 µL semen, seminal fluid markers KLK2: 0.1 µL semen and MSMB: 0.01 µL semen, and vaginal material marker CYP2B7P: 1 in 1000 dilution of a whole vaginal swab. The method successfully detected most body fluids in a range of simple mixtures with 77 out of 80 markers observed when expected. The developed one-step endpoint RT-PCR assays lack the sensitivity and precision required for forensic casework and provide little benefit when compared with standard two-step endpoint RT-PCR, other than minimal time and cost savings, similar sensitivity, and improved precision for some markers. As both methods utilise endpoint RT-PCR, they have the same narrow linear dynamic range. The novel method is therefore similarly susceptible to varied RNA input, a major disadvantage of this approach. The limited sensitivity and precision consistently encountered with endpoint RT-PCR - regardless of cDNA synthesis strategy - could be addressed by a real-time PCR approach.
Collapse
Affiliation(s)
- Courtney Lynch
- Forensic Science Programme, School of Chemical Sciences, The University of Auckland, Auckland, New Zealand; Forensic Research and Development Team, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd, Auckland, New Zealand.
| |
Collapse
|
12
|
Magnetic bead-based separation of sperm cells from semen-vaginal fluid mixed stains using an anti-ACRBP antibody. Int J Legal Med 2023; 137:511-518. [PMID: 36418581 DOI: 10.1007/s00414-022-02917-8] [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: 08/23/2021] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Forensic DNA analysis of semen-vaginal fluid mixed stains is essential and necessary in sexual assault cases. Here, we used a magnetic bead conjugated acrosin binding protein (ACRBP) antibody to separate and enrich sperm cells from mixed stains. Previously, western blotting indicated that ACRBP was specifically expressed in sperm cells, but not in female blood and epithelial cells, while immunofluorescence data showed ACRBP was localized to the acrosome in sperm cells. In our study, sperm were separated from mixed samples at three sperm cell/female buccal epithelial cell ratios (103:103; 103:104; and 103:105) using a magnetic bead conjugated ACRBP antibody. Subsequently, 23 autosomal short tandem repeat (STR) loci were amplified using the Huaxia™ Platinum PCR Amplification System and genotyped using capillary electrophoresis. The genotyping success rate for STR loci was 90% when the sperm to female buccal epithelial cell ratio was > 1:100 in mixed samples. Our results suggest that the magnetic bead conjugated ACRBP antibody is effective for isolating sperm cells in sexual assault cases.
Collapse
|
13
|
Duke K, Myers S, Cuenca D, Wallin J. Improving the Utilization of STRmix™ Variance Parameters as Semi-Quantitative Profile Modeling Metrics. Genes (Basel) 2022; 14:genes14010102. [PMID: 36672842 PMCID: PMC9859078 DOI: 10.3390/genes14010102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/17/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Distributions of the variance parameter values developed during the validation process. Comparisons of these prior distributions to the run-specific average are one measure used by analysts to assess the reliability of a STRmix deconvolution. This study examined the behavior of three different STRmix variance parameters under standard amplification and interpretation conditions, as well as under a variety of challenging conditions, with the goal of making comparisons to the prior distributions more practical and meaningful. Using information found in STRmix v2.8 Interpretation Reports, we plotted the log10 of each variance parameter against the log10 of the template amount of the highest-level contributor (Tc) for a large set of mixture data amplified under standard conditions. We observed nonlinear trends in these plots, which we regressed to fourth-order polynomials, and used the regression data to establish typical ranges for the variance parameters over the Tc range. We then compared the typical variance parameter ranges to log10(variance parameter) v log10(Tc) plots for mixtures amplified and interpreted under a variety of challenging conditions. We observed several distinct patterns to variance parameter shifts in the challenged data interpretations in comparison to the unchallenged data interpretations, as well as distinct shifts in the unchallenged variance parameters away from their prior gamma distribution modes over specific ranges of Tc. These findings suggest that employing empirically determined working ranges for variance parameters may be an improved means of detecting whether aberrations in the interpretation were meaningful enough to trigger greater scrutiny of the electropherogram and genotype interpretation.
Collapse
|
14
|
A new implementation of a semi-continuous method for DNA mixture interpretation. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
15
|
Miller JM, Lee C, Ingram S, Yadavalli VK, Greenspoon SA, Ehrhardt CJ. Use of hormone-specific antibody probes for differential labeling of contributor cell populations in trace DNA mixtures. Int J Legal Med 2022; 136:1551-1564. [PMID: 36076079 DOI: 10.1007/s00414-022-02887-x] [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: 03/11/2022] [Accepted: 08/29/2022] [Indexed: 11/27/2022]
Abstract
A significant proportion of casework analyzed by forensic science laboratories is often "touch" or trace forensic DNA evidence, which is deposited through physical contact and is comprised of sloughed epidermal cells. These samples can be challenging to analyze due to low DNA concentrations, frequent degradation, and the presence of cells from multiple individuals in the same sample. To address these challenges, we investigated a new approach for characterizing trace evidence prior to DNA profiling that labels epidermal cells with antibody probes targeting hormone molecules testosterone and dihydrotestosterone (DHT). The goal was to test whether cell populations derived from separate individuals showed different binding efficiencies to hormone probes and, thus, could be used to detect the presence of multiple cell populations. Additionally, we investigated whether antibody probes could be used to isolate contributor cell populations from an epidermal cell mixture and facilitate deconvolution of mixed DNA profiles recovered from touch/trace evidence. Results showed that cell populations from some individuals could differentiated in trace samples based on fluorescence histograms following probe labeling. However, certain pairs of contributors showed largely or completely overlapping histogram profiles and could not be resolved. Preliminary efforts to separate cell populations that could be differentiated with hormone probes with fluorescence-activated cell sorting (FACS) coupled to DNA profiling and probabilistic modeling indicated that it is possible to enrich contributor cell populations from touch/trace samples and produce more probative DNA profiles compared to the original mixture sample. The variability in labeling, differentiation, and physical separation of cell populations may be impacted by similarities in biochemical profiles across some contributors as well as imbalance of contributor DNA quantities in certain mixtures as is typical in casework involving touch/trace evidence. Ultimately, screening and separation of trace DNA samples with this approach may be presumptive and constrained by sample-specific parameters of the original mixture.
Collapse
Affiliation(s)
- Jennifer M Miller
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Christin Lee
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah Ingram
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Vamsi K Yadavalli
- Chemical and Life Sciences Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | | | | |
Collapse
|
16
|
Griffin A, Kirkbride KP, Henry J, Painter B, Linacre A. Recovery of integrated and surface trace DNA from illicit drug tablets. Forensic Sci Int Genet 2022; 61:102772. [PMID: 36099863 DOI: 10.1016/j.fsigen.2022.102772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 09/06/2022] [Indexed: 11/04/2022]
Abstract
In many parts of the world, tablets are a commonly encountered form of illicit drug preparation. Whilst previous research has investigated the feasibility of detecting trace DNA on illicit drug capsules, this has not been performed for tablets. Tablets have a unique substrate surface and therefore the amount of DNA transferring to them and persisting on them may be different to capsules; there may also be differences in the collection efficiency and the outcome of downstream DNA processing and analysis steps. The ability to profile the DNA from individuals who handled tablets during their preparation and distribution would add another level of discrimination between various drug seizures or corroborate chemical profiling outcomes which may link various seizures to a common origin. DNA from two different individuals (male and female) was added to the tablets in two stages. Firstly, tablet powder was spiked with DNA from one individual to mimic the situation where DNA traces are incorporated during the drug synthesis or final drying stages. The powder was then pressed into tablets in a clean environment without intentional addition of DNA. Subsequently, a second individual counted out the tablets into bags of ten to mimic the preparation for distribution at a user level. The exterior of the tablet was swabbed and then the entire tablet and the swab were put through separate DNA extractions, yielding two DNA extracts for each tablet. Swabs of the exterior tablet surface yielded single source DNA profiles that identified the tablet handler in 100 % of samples. The tablet extract yielded the donor of the DNA intentionally added within the drug powder in 80% of samples with varying levels of support, however contributions of the exterior handler were detected in 60 % of samples. The identification of individuals potentially involved in the synthesis of the drugs compared to the distribution of the tablets will provide invaluable strategic intelligence related to illicit drug investigations and to law enforcement agencies.
Collapse
Affiliation(s)
- Amy Griffin
- College of Science & Engineering, Flinders University, Adelaide 5042, Australia.
| | - K Paul Kirkbride
- College of Science & Engineering, Flinders University, Adelaide 5042, Australia
| | - Julianne Henry
- College of Science & Engineering, Flinders University, Adelaide 5042, Australia; Forensic Science SA, GPO Box 2790, Adelaide 5000, Australia
| | - Ben Painter
- College of Science & Engineering, Flinders University, Adelaide 5042, Australia; Forensic Science SA, GPO Box 2790, Adelaide 5000, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide 5042, Australia
| |
Collapse
|
17
|
Adamowicz MS, Rambo TN, Clarke JL. Internal Validation of MaSTR™ Probabilistic Genotyping Software for the Interpretation of 2–5 Person Mixed DNA Profiles. Genes (Basel) 2022; 13:genes13081429. [PMID: 36011340 PMCID: PMC9408203 DOI: 10.3390/genes13081429] [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: 06/17/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Mixed human deoxyribonucleic acid (DNA) samples present one of the most challenging pieces of evidence that a forensic analyst can encounter. When multiple contributors, stochastic amplification, and allele drop-out further complicate the mixture profile, interpretation by hand becomes unreliable and statistical analysis problematic. Probabilistic genotyping software has provided a tool to address complex mixture interpretation and provide likelihood ratios for defined sets of propositions. The MaSTR™ software is a fully continuous probabilistic system that considers a wide range of STR profile data to provide likelihood ratios on DNA mixtures. Mixtures with two to five contributors and a range of component ratios and allele peak heights were created to test the validity of MaSTR™ with data similar to real casework. Over 280 different mixed DNA profiles were used to perform more than 2600 analyses using different sets of propositions and numbers of contributors. The results of the analyses demonstrated that MaSTR™ provided accurate and precise statistical data on DNA mixtures with up to five contributors, including minor contributors with stochastic amplification effects. Tests for both Type I and Type II errors were performed. The findings in this study support that MaSTR™ is a robust tool that meets the current standards for probabilistic genotyping.
Collapse
|
18
|
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.
Collapse
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:
| |
Collapse
|
19
|
Noël J, Noël S, Mailly F, Granger D, Lefebvre JF, Milot E, Séguin D. Total allele count distribution (TAC curves) improves number of contributor estimation for complex DNA mixtures. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2022. [DOI: 10.1080/00085030.2022.2028359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Josée Noël
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Montréal, Québec, Canada
| | - Sarah Noël
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Montréal, Québec, Canada
| | - France Mailly
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Montréal, Québec, Canada
| | - Dominic Granger
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Montréal, Québec, Canada
| | | | - Emmanuel Milot
- Laboratoire de Recherche en Criminalistique, Department of Chemistry, Biochemistry and Physics and Centre International de Criminologie Comparée, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Diane Séguin
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Montréal, Québec, Canada
| |
Collapse
|
20
|
Sheth N, Duffy KR, Grgicak CM. High-quality data from a forensically relevant single-cell pipeline enabled by low PBS and proteinase K concentrations. J Forensic Sci 2021; 67:697-706. [PMID: 34936089 DOI: 10.1111/1556-4029.14956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/01/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Interpreting forensic DNA signal is arduous since the total intensity is a cacophony of signal from noise, artifact, and allele from an unknown number of contributors (NOC). An alternate to traditional bulk-processing pipelines is a single-cell one, where the sample is collected, and each cell is sequestered resulting in n single-source, single-cell EPGs (scEPG) that must be interpreted using applicable strategies. As with all forensic DNA interpretation strategies, high quality electropherograms are required; thus, to enhance the credibility of single-cell forensics, it is necessary to produce an efficient direct-to-PCR treatment that is compatible with prevailing downstream laboratory processes. We incorporated the semi-automated micro-fluidic DEPArray™ technology into the single-cell laboratory and optimized its implementation by testing the effects of four laboratory treatments on single-cell profiles. We focused on testing effects of phosphate buffer saline (PBS) since it is an important reagent that mitigates cell rupture but is also a PCR inhibitor. Specifically, we explored the effect of decreasing PBS concentrations on five electropherogram-quality metrics from 241 leukocytes: profile drop-out, allele drop-out, allele peak heights, peak height ratios, and scEPG sloping. In an effort to improve reagent use, we also assessed two concentrations of proteinase K. The results indicate that decreasing PBS concentrations to 0.5X or 0.25X improves scEPG quality, while modest modifications to proteinase K concentrations did not significantly impact it. We, therefore, conclude that a lower than recommended proteinase K concentration coupled with a lower than recommended PBS concentration results in enhanced scEPGs within the semi-automated single-cell pipeline.
Collapse
Affiliation(s)
- Nidhi Sheth
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Catherine M Grgicak
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA.,Department of Chemistry, Rutgers University, Camden, New Jersey, USA
| |
Collapse
|
21
|
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.
Collapse
|
22
|
Lucassen A, Ehlers K, Grobler PJ, Brenner CH. Evaluating Mixture Solution™- rapid and non-MCMC probabilistic mixture analysis. Int J Legal Med 2021; 135:2275-2284. [PMID: 34599363 DOI: 10.1007/s00414-021-02680-2] [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: 04/19/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
We compare DNA mixture analysis via DNAˑVIEW® Mixture Solution™ and the current combined probability of inclusion (CPI) method of the South African Police Service (SAPS). South Africa has a high incidence of property-related crimes and sexual offences and consequently a great deal of low-template (LT-DNA) forensic DNA mixture casework and a perpetual backlog. A range of casework and laboratory-prepared sexual assault mixtures with initial male DNA amounts varying from about 2 to 200 cells were analysed to evaluate the benefits of a continuous model program. Unfortunately CPI methods are nearly useless for LT-DNA cases because of dropout-common from a mixture contribution of fewer than 20 or 30 cells. We further argue that proposed CPI elaborations to circumvent dropout lack supporting research or even explanation. Mixture Solution models mixture data as continuous rather than binary, with a mathematically coherent ("probabilistic") model which incorporates dropout and other phenomena realistically. Much more information is thereby utilised resulting in applicability to more cases (7 or fewer contributor cells suffice), stronger evidence against a suspect who is a mixture contributor and stronger evidence to absolve a non-contributor. Mixture Solution incidentally provides information which, along with rfu data, allows estimating contributions in terms of number of cells, which is a useful perspective. The method of calculation is explained.
Collapse
Affiliation(s)
- Anton Lucassen
- Quality Management Section (Biology), Division Forensic Services, South African Police Service, Private Bag 18, Arcadia, Pretoria, 0007, South Africa. .,Faculty of Natural and Agricultural Sciences, Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
| | - Karen Ehlers
- Faculty of Natural and Agricultural Sciences, Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Paul J Grobler
- Faculty of Natural and Agricultural Sciences, Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | | |
Collapse
|
23
|
Developments in forensic DNA analysis. Emerg Top Life Sci 2021; 5:381-393. [PMID: 33792660 PMCID: PMC8457771 DOI: 10.1042/etls20200304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022]
Abstract
The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.
Collapse
|
24
|
Chong KWY, Syn CKC. Uncertainty in estimating the number of contributors from simulated DNA mixture profiles, with and without allele dropout, from Chinese, Malay, Indian, and Caucasian ethnic populations. Sci Rep 2021; 11:5249. [PMID: 33664303 PMCID: PMC7933404 DOI: 10.1038/s41598-021-84580-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/09/2021] [Indexed: 11/09/2022] Open
Abstract
Determining the number of contributors (NOC) accurately in a forensic DNA mixture profile can be challenging. To address this issue, there have been various studies that examined the uncertainty in estimating the NOC in a DNA mixture profile. However, the focus of these studies lies primarily on dominant populations residing within Europe and North America. Thus, there is limited representation of Asian populations in these studies. Further, the effects of allele dropout on the NOC estimation has not been explored. As such, this study assesses the uncertainty of NOC in simulated DNA mixture profiles of Chinese, Malay, and Indian populations, which are the predominant ethnic populations in Asia. The Caucasian ethnic population was also included to provide a basis of comparison with other similar studies. Our results showed that without considering allele dropout, the NOC from DNA mixture profiles derived from up to four contributors of the same ethnic population could be estimated with confidence in the Chinese, Malay, Indian and Caucasian populations. The same results can be observed on DNA mixture profiles originating from a combination of differing ethnic populations. The inclusion of an overall 30% allele dropout rate increased the probability (risk) of underestimating the NOC in a DNA mixture profile; even a 3-person DNA mixture profile has a > 99% risk of underestimating the NOC as two or fewer contributors. However, such risks could be mitigated when the highly polymorphic SE33 locus was included in the dataset. Lastly there was a negligible level of risk in misinterpreting the NOC in a mixture profile as deriving from a single source profile. In summary, our studies showcased novel results representative of the Chinese, Malay, and Indian ethnic populations when examining the uncertainty in NOC estimation in a DNA mixture profile. Our results would be useful in the estimation of NOC in a DNA mixture profile in the Asian context.
Collapse
Affiliation(s)
- Kevin Wai Yin Chong
- DNA Profiling Laboratory, Biology Division, Applied Sciences Group, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore
| | - Christopher Kiu-Choong Syn
- DNA Profiling Laboratory, Biology Division, Applied Sciences Group, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore.
| |
Collapse
|
25
|
Jian H, Wang L, Lv M, Tan Y, Zhang R, Qu S, Wang J, Zha L, Zhang L, Liang W. A Novel SNP-STR System Based on a Capillary Electrophoresis Platform. Front Genet 2021; 12:636821. [PMID: 33613649 PMCID: PMC7893108 DOI: 10.3389/fgene.2021.636821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Various compound markers encompassing two or more variants within a small region can be regarded as generalized microhaplotypes. Many of these markers have been investigated for various forensic purposes, such as individual identification, deconvolution of DNA mixtures, or forensic ancestry inference. SNP-STR is a compound biomarker composed of a single nucleotide polymorphism (SNP) and a closely linked short tandem repeat polymorphism (STR), and possess the advantages of both SNPs and STRs. In addition, in conjunction with a polymerase chain reaction (PCR) technique based on the amplification refractory mutation system (ARMS), SNP-STRs can be used for forensic unbalanced DNA mixture analysis based on capillary electrophoresis (CE), which is the most commonly used platform in worldwide forensic laboratories. Our previous research reported 11 SNP-STRs, but few of them are derived from the commonly used STR loci, for which existing STR databases can be used as a reference. For maximum compatibility with existing DNA databases, in this study, we screened 18 SNP-STR loci, of which 14 were derived from the expanded CODIS core loci set. Stable and sensitive SNP-STR multiplex PCR panels based on the CE platform were established. Assays on simulated two-person DNA mixtures showed that all allele-specific primers could detect minor DNA components in 1:500 mixtures. Population data based on 113 unrelated Chengdu Han individuals were investigated. A Bayesian framework was developed for the likelihood ratio (LR) evaluation of SNP-STR profiling results obtained from two-person mixtures. Furthermore, we report on the first use of SNP-STRs in casework to show the advantages and limitations for use in practice. Compared to 2.86 × 103 for autosomal STR kits, the combined LR reached 7.14 × 107 using the SNP-STR method in this casework example.
Collapse
Affiliation(s)
- Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yu Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jijun Wang
- HI-TECH Industrial Sub-Branch of Chengdu Municipal Public Security Bureau, Chengdu, China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| |
Collapse
|
26
|
Li R, Shen X, Chen H, Peng D, Wu R, Sun H. Developmental validation of the MGIEasy Signature Identification Library Prep Kit, an all-in-one multiplex system for forensic applications. Int J Legal Med 2021; 135:739-753. [PMID: 33523251 DOI: 10.1007/s00414-021-02507-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/08/2021] [Indexed: 01/23/2023]
Abstract
Analyzing genetic markers in nuclear and mitochondrial genomes is helpful in various forensic applications, such as individual identifications and kinship analyses. However, most commercial kits detect these markers separately, which is time-consuming, laborious, and more error-prone (mislabelling, contamination, ...). The MGIEasy Signature Identification Library Prep Kit (hereinafter "MGIEasy identification system"; MGI Tech, Shenzhen, China) has been designed to provide a simple, fast, and robust way to detect appropriate markers in one multiplex PCR reaction: 52 autosomal STRs, 27 X-chromosomal STRs, 48 Y-chromosomal STRs, 145 identity-informative SNPs, 53 ancestry-informative SNPs, 29 phenotype-informative SNPs, and the hypervariable regions of mitochondrial DNA (mtDNA). Here, we validated the performance of MGIEasy identification system following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), assessing species specificity, sensitivity, mixture identification, stability under non-optimal conditions (degraded samples, inhibitor contamination, and various substrates), repeatability, and concordance. Libraries prepared using MGIEasy identification system were sequenced on a MGISEQ-2000 instrument (MGI Tech). MGIEasy-derived STR, SNP, and mtDNA genotypes were highly concordant with CE-based STR genotypes (99.79%), MiSeq FGx-based SNP genotypes (99.78%), and Sanger-based mtDNA genotypes (100%), respectively. This system was strongly human-specific, resistant to four common PCR inhibitors, and reliably amplified both low quantities of DNA (as low as 0.125 ng) and degraded DNA (~ 150 nt). Most of the unique alleles from the minor contributor were detected in 1:10 male-female and male-male mixtures; some minor Y-STR alleles were even detected in 1:1000 male-female mixtures. MGIEasy also successfully directly amplified markers from blood stains on FTA cards, filter papers, and swabs. Thus, our results demonstrated that MGIEasy identification system was suitable for use in forensic analyses due to its robust and reliable performance on samples of varying quality and quantity.
Collapse
Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
| |
Collapse
|
27
|
Wu R, Li H, Li R, Peng D, Wang N, Shen X, Sun H. Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures. Int J Legal Med 2021; 135:1137-1149. [PMID: 33502549 DOI: 10.1007/s00414-020-02483-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Mixture detection remains one of the major challenges within a forensic science context. In recent years, microhaplotypes were proposed to have great potential in mixture detection, although many of them are not as polymorphic as widely used short tandem repeat (STR) markers. In this study, 59 new highly polymorphic microhaplotypes were identified and sequenced with the NextSeq 500 Sequencer. Based on the whole 1000 Genomes Project dataset, the average effective number of alleles (Ae) of the 59 microhaplotypes was 5.44, and the Ae values of 36 of these microhaplotypes were > 5.00. Their genetic variations in 187 Han Chinese individuals were evaluated. The average allele coverage ratio (ACR) of heterozygotes across all loci was 0.96 ± 0.05. The number of observed alleles varied from 4 to 23, with an average of 8.8 alleles per microhaplotype locus. The average observed heterozygosity (Ho) of 59 loci was 0.77 ± 0.05, and the Ho values of 15 of these loci were > 0.80. All loci showed high polymorphisms with a discrimination power (DP) ranging from 0.80 to 0.97, and the average DP was 0.92 ± 0.03. The analysis of simulated mixtures demonstrated that the microhaplotypes reported here were highly polymorphic and performed well in forensic DNA mixture analysis. This study not only demonstrated the applicability of microhaplotypes in mixture analysis but also provided new choices for highly polymorphic microhaplotypes because after adding the markers identified here, the number of microhaplotypes with Ae values of > 4.00 will increase from ~ 50 to ~ 110.
Collapse
Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.
| |
Collapse
|
28
|
Buckleton JS, Pugh SN, Bright JA, Taylor DA, Curran JM, Kruijver M, Gill P, Budowle B, Cheng K. Are low LRs reliable? Forensic Sci Int Genet 2020; 49:102350. [DOI: 10.1016/j.fsigen.2020.102350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 12/20/2022]
|
29
|
Rasool N, Rasool M. DNA evidence in sexual assault cases in Pakistan. MEDICINE, SCIENCE, AND THE LAW 2020; 60:270-277. [PMID: 32576088 DOI: 10.1177/0025802420934240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sexual assault is becoming a global epidemic, affecting close to a billion women throughout the world. This paper explores the challenges in the admissibility of DNA evidence in rape cases in Pakistan. Delays in the medical examination of victims, and improper collection and packaging of evidentiary material, compromise the probative biological evidence. In the last few years, existing laws have been amended to increase the utility of DNA evidence during criminal trials. However, various issues - for example lack of proper knowledge of DNA evidence by lawyers and judicial officers, inadequacies in existing laws and conflicting decisions of apex courts - can affect the admissibility of DNA evidence during criminal trials.
Collapse
Affiliation(s)
- Nouman Rasool
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
- Center for Professional Studies, Pakistan
| | - Muzamal Rasool
- Advocate, Lahore High Court, Pakistan
- Post Graduate Institute of Law, University of Lahore, Pakistan
| |
Collapse
|
30
|
McGovern C, Cheng K, Kelly H, Ciecko A, Taylor D, Buckleton JS, Bright JA. Performance of a method for weighting a range in the number of contributors in probabilistic genotyping. Forensic Sci Int Genet 2020; 48:102352. [DOI: 10.1016/j.fsigen.2020.102352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/10/2020] [Accepted: 07/02/2020] [Indexed: 11/27/2022]
|
31
|
Liu Z, Gao Z, Wang J, Shi J, Liu J, Chen D, Li W, Guo J, Cheng X, Hao T, Li Z, Li Y, Yan J, Zhang G. A method of identifying the blood contributor in mixture stains through detecting blood‐specific mRNA polymorphism. Electrophoresis 2020; 41:1364-1373. [DOI: 10.1002/elps.202000053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/31/2020] [Accepted: 05/04/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Zidong Liu
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Zhe Gao
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiaqi Wang
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jie Shi
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jinding Liu
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Deqing Chen
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Wenyan Li
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiangling Guo
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Xiaojuan Cheng
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Ting Hao
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Zeqin Li
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Yanhua Li
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiangwei Yan
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Gengqian Zhang
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| |
Collapse
|
32
|
Schuerman C, Kalafut T, Buchanan C, Sutton J, Bright JA. Using the Nondonor Distribution to Improve Communication and Inform Decision Making for Low LRs from Minor Contributors in Mixed DNA Profiles. J Forensic Sci 2020; 65:1072-1084. [PMID: 32134501 DOI: 10.1111/1556-4029.14306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022]
Abstract
The reporting of a likelihood ratio (LR) calculated from probabilistic genotyping software has become more popular since 2015 and has allowed for the use of more complex mixtures at court. The meaning of "inconclusive" LRs and how to communicate the significance of low LRs at court is now important. We present a method here using the distribution of LRs obtained from nondonors. The nondonor distribution is useful for examining calibration and discrimination for profiles that have produced LRs less than about 104 . In this paper, a range of mixed DNA profiles of varying quantity were constructed and the LR distribution considering the minor contributor for a number of nondonors was compared to the expectation given a calibrated system. It is demonstrated that conditioning genotypes should be used where reasonable given the background information to decrease the rate of nondonor LRs above 1. In all 17 cases examined, the LR for the minor donor was higher than the nondonor LRs, and in 12 of the 17 cases, the 99.9 percentile of the nondonor distribution was lower when appropriate conditioning information was used. The output of the tool is a graph that can show the position of the LR for the person of interest set against the nondonor LR distribution. This may assist communication between scientists and the court.
Collapse
Affiliation(s)
- Curt Schuerman
- US Army Criminal Investigation Laboratory (USACIL), 4930 N 31st Street, Forest Park, GA, 30297
| | - Tim Kalafut
- US Army Criminal Investigation Laboratory (USACIL), 4930 N 31st Street, Forest Park, GA, 30297
| | - Clint Buchanan
- US Army Criminal Investigation Laboratory (USACIL), 4930 N 31st Street, Forest Park, GA, 30297
| | - Joel Sutton
- US Army Criminal Investigation Laboratory (USACIL), 4930 N 31st Street, Forest Park, GA, 30297
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142, New Zealand
| |
Collapse
|
33
|
Emery MV, Bolhofner K, Winingear S, Oldt R, Montes M, Kanthaswamy S, Buikstra JE, Fulginiti LC, Stone AC. Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques. Forensic Sci Int Genet 2020; 46:102272. [PMID: 32172220 DOI: 10.1016/j.fsigen.2020.102272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/19/2022]
Abstract
Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.
Collapse
Affiliation(s)
- M V Emery
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States.
| | - K Bolhofner
- Center for Bioarchaeological Research, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Winingear
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States
| | - R Oldt
- School of Life Sciences, Arizona State University, United States
| | - M Montes
- School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Kanthaswamy
- School of Life Sciences, Arizona State University, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - J E Buikstra
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeological Research, Arizona State University, United States
| | - L C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States
| | - A C Stone
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeological Research, Arizona State University, United States.
| |
Collapse
|
34
|
Butler JM, Willis S. Interpol review of forensic biology and forensic DNA typing 2016-2019. Forensic Sci Int Synerg 2020; 2:352-367. [PMID: 33385135 PMCID: PMC7770417 DOI: 10.1016/j.fsisyn.2019.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/23/2022]
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.
Collapse
|
35
|
Petrovick MS, Boettcher T, Fremont-Smith P, Peragallo C, Ricke DO, Watkins J, Schwoebel E. Analysis of complex DNA mixtures using massively parallel sequencing of SNPs with low minor allele frequencies. Forensic Sci Int Genet 2020; 46:102234. [PMID: 32018060 DOI: 10.1016/j.fsigen.2020.102234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/05/2019] [Accepted: 01/02/2020] [Indexed: 11/18/2022]
Abstract
DNA mixtures from 3 or more contributors have proven difficult to analyze using the current state-of-the-art method of short-tandem repeat (STR) amplification followed by capillary electrophoresis (CE). Here we analyze samples from both laboratory-defined mixtures and complex multi-contributor touch samples using a single nucleotide polymorphism (SNP) panel comprised of 2311 low-minor-allele-frequency loci, combined with massively parallel sequencing (MPS). This approach demonstrates that as many as 10 people can be identified in touch samples using a threshold of -Log P(RMNE) of 6, and a detection rate of 18-94 % across 10 different materials using a threshold of -Log P(RMNE) of 2. Thirty-two false positives were observed in 100 touch samples.
Collapse
Affiliation(s)
- Martha S Petrovick
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States.
| | - Tara Boettcher
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Philip Fremont-Smith
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Chelsea Peragallo
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Darrell O Ricke
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - James Watkins
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Eric Schwoebel
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| |
Collapse
|
36
|
Karkar S, Alfonse LE, Grgicak CM, Lun DS. Statistical modeling of STR capillary electrophoresis signal. BMC Bioinformatics 2019; 20:584. [PMID: 31787097 PMCID: PMC6886162 DOI: 10.1186/s12859-019-3074-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND In order to isolate an individual's genotype from a sample of biological material, most laboratories use PCR and Capillary Electrophoresis (CE) to construct a genetic profile based on polymorphic loci known as Short Tandem Repeats (STRs). The resulting profile consists of CE signal which contains information about the length and number of STR units amplified. For samples collected from the environment, interpretation of the signal can be challenging given that information regarding the quality and quantity of the DNA is often limited. The signal can be further compounded by the presence of noise and PCR artifacts such as stutter which can mask or mimic biological alleles. Because manual interpretation methods cannot comprehensively account for such nuances, it would be valuable to develop a signal model that can effectively characterize the various components of STR signal independent of a priori knowledge of the quantity or quality of DNA. RESULTS First, we seek to mathematically characterize the quality of the profile by measuring changes in the signal with respect to amplicon size. Next, we examine the noise, allele, and stutter components of the signal and develop distinct models for each. Using cross-validation and model selection, we identify a model that can be effectively utilized for downstream interpretation. Finally, we show an implementation of the model in NOCIt, a software system that calculates the a posteriori probability distribution on the number of contributors. CONCLUSION The model was selected using a large, diverse set of DNA samples obtained from 144 different laboratory conditions; with DNA amounts ranging from a single copy of DNA to hundreds of copies, and the quality of the profiles ranging from pristine to highly degraded. Implemented in NOCIt, the model enables a probabilisitc approach to estimating the number of contributors to complex, environmental samples.
Collapse
Affiliation(s)
- Slim Karkar
- Center for Computational and Integrative Biology, Rutgers University, Camden, 08102, NJ, USA
| | - Lauren E Alfonse
- Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, 02118, MA, USA
| | - Catherine M Grgicak
- Center for Computational and Integrative Biology, Rutgers University, Camden, 08102, NJ, USA.,Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, 02118, MA, USA.,Department of Chemistry, Rutgers University, Camden, 08102, NJ, USA
| | - Desmond S Lun
- Center for Computational and Integrative Biology, Rutgers University, Camden, 08102, NJ, USA. .,Department of Computer Science, Rutgers University, Camden, 08102, NJ, USA. .,Department of Plant Biology, Rutgers University, New Brunswick, 08901, NJ, USA.
| |
Collapse
|
37
|
Curley LJ, Munro J, Lages M, MacLean R, Murray J. Assessing Cognitive Bias in Forensic Decisions: A Review and Outlook. J Forensic Sci 2019; 65:354-360. [DOI: 10.1111/1556-4029.14220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Lee J. Curley
- Faculty of Arts and Social Sciences School of Psychology and Counselling The Open University Milton Keynes England
| | - James Munro
- School of Applied Sciences Edinburgh Napier University Edinburgh U.K
| | - Martin Lages
- College of Science and Engineering The School of Psychology The University of Glasgow Glasgow Scotland
| | - Rory MacLean
- School of Applied Sciences Edinburgh Napier University Edinburgh U.K
| | - Jennifer Murray
- School of Health and Social Care Edinburgh Napier University Edinburgh U.K
| |
Collapse
|
38
|
Transcriptome variation in human populations and its potential application in forensics. J Appl Genet 2019; 60:319-328. [PMID: 31401728 PMCID: PMC6803616 DOI: 10.1007/s13353-019-00510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/04/2022]
Abstract
This review presents the state-of-the-art in the forensic application of genetic methods driven by the research in population transcriptomics. In the first part of the review, the constraints of using classical genomic markers are shortly reviewed. In the second part, the developments in the field of inter-population diversity at the transcriptomic level are presented. Subsequently, a potential of population-specific transcriptomic markers in forensic science applications, including ascertaining population affiliation of human samples and cell mixtures separation, are presented.
Collapse
|
39
|
STRmix™ put to the test: 300 000 non-contributor profiles compared to four-contributor DNA mixtures and the impact of replicates. Forensic Sci Int Genet 2019; 41:24-31. [DOI: 10.1016/j.fsigen.2019.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/24/2022]
|
40
|
McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| |
Collapse
|
41
|
Coble MD, Bright JA. Probabilistic genotyping software: An overview. Forensic Sci Int Genet 2019; 38:219-224. [PMID: 30458407 DOI: 10.1016/j.fsigen.2018.11.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
The interpretation of mixed profiles from DNA evidentiary material is one of the more challenging duties of the forensic scientist. Traditionally, analysts have used a "binary" approach to interpretation where inferred genotypes are either included or excluded from the mixture using a stochastic threshold and other biological parameters such as heterozygote balance, mixture ratio, and stutter ratios. As the sensitivity of STR multiplexes and capillary electrophoresis instrumentation improved over the past 25 years, coupled with the change in the type of evidence being submitted for analysis (from high quality and quantity (often single-source) stains to low quality and quantity (often mixed) "touch" samples), the complexity of DNA profile interpretation has equally increased. This review provides a historical perspective on the movement from binary methods of interpretation to probabilistic methods of interpretation. We describe the two approaches to probabilistic genotyping (semi-continuous and fully continuous) and address issues such as validation and court acceptance. Areas of future needs for probabilistic software are discussed.
Collapse
Affiliation(s)
- Michael D Coble
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142 New Zealand
| |
Collapse
|
42
|
Young BA, Gettings KB, McCord B, Vallone PM. Estimating number of contributors in massively parallel sequencing data of STR loci. Forensic Sci Int Genet 2019; 38:15-22. [DOI: 10.1016/j.fsigen.2018.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
|
43
|
Buckleton JS, Bright JA, Cheng K, Budowle B, Coble MD. NIST interlaboratory studies involving DNA mixtures (MIX13): A modern analysis. Forensic Sci Int Genet 2018; 37:172-179. [DOI: 10.1016/j.fsigen.2018.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 11/30/2022]
|
44
|
NIST interlaboratory studies involving DNA mixtures (MIX05 and MIX13): Variation observed and lessons learned. Forensic Sci Int Genet 2018; 37:81-94. [DOI: 10.1016/j.fsigen.2018.07.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 11/19/2022]
|
45
|
Hwa HL, Wu MY, Chung WC, Ko TM, Lin CP, Yin HI, Lee TT, Lee JCI. Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq™ system in combination with EuroForMix software. Int J Legal Med 2018; 133:25-37. [DOI: 10.1007/s00414-018-1961-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
|
46
|
Buckleton JS, Bright JA, Gittelson S, Moretti TR, Onorato AJ, Bieber FR, Budowle B, Taylor DA. The Probabilistic Genotyping Software STRmix: Utility and Evidence for its Validity. J Forensic Sci 2018; 64:393-405. [PMID: 30132900 DOI: 10.1111/1556-4029.13898] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 01/08/2023]
Abstract
Forensic DNA interpretation is transitioning from manual interpretation based usually on binary decision-making toward computer-based systems that model the probability of the profile given different explanations for it, termed probabilistic genotyping (PG). Decision-making by laboratories to implement probability-based interpretation should be based on scientific principles for validity and information that supports its utility, such as criteria to support admissibility. The principles behind STRmix™ are outlined in this study and include standard mathematics and modeling of peak heights and variability in those heights. All PG methods generate a likelihood ratio (LR) and require the formulation of propositions. Principles underpinning formulations of propositions include the identification of reasonably assumed contributors. Substantial data have been produced that support precision, error rate, and reliability of PG, and in particular, STRmix™. A current issue is access to the code and quality processes used while coding. There are substantial data that describe the performance, strengths, and limitations of STRmix™, one of the available PG software.
Collapse
Affiliation(s)
- John S 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, New Zealand
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142, New Zealand
| | - Simone Gittelson
- Centre for Forensic Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Tamyra R Moretti
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Anthony J Onorato
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Frederick R Bieber
- Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115
| | - Bruce Budowle
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107
| | - Duncan A Taylor
- Forensic Science South Australia, 21 Divett Place, Adelaide, SA, Australia.,Flinders University - School of Biology, Stuart Road, Bedford Park, Adelaide, SA, Australia
| |
Collapse
|
47
|
Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
Collapse
Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| |
Collapse
|
48
|
Just RS, Irwin JA. Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results. Forensic Sci Int Genet 2018. [DOI: 10.1016/j.fsigen.2018.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
49
|
A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures. Biochem Biophys Res Commun 2018; 497:591-596. [PMID: 29448110 DOI: 10.1016/j.bbrc.2018.02.109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 02/11/2018] [Indexed: 11/22/2022]
Abstract
Unbalanced DNA mixture is still a difficult problem for forensic practice. DIP-STRs are useful markers for detection of minor DNA but they are not widespread in the human genome and having long amplicons. In this study, we proposed a novel type of genetic marker, termed DIP-SNP. DIP-SNP refers to the combination of INDEL and SNP in less than 300bp length of human genome. The multiplex PCR and SNaPshot assay were established for 14 DIP-SNP markers in a Chinese Han population from Shanxi, China. This novel compound marker allows detection of the minor DNA contributor with sensitivity from 1:50 to 1:1000 in a DNA mixture of any gender with 1 ng-10 ng DNA template. Most of the DIP-SNP markers had a relatively high probability of informative alleles with an average I value of 0.33. In all, we proposed DIP-SNP as a novel kind of genetic marker for detection of minor contributor from unbalanced DNA mixture and established the detection method by associating the multiplex PCR and SNaPshot assay. DIP-SNP polymorphisms are promising markers for forensic or clinical mixture examination because they are shorter, widespread and higher sensitive.
Collapse
|
50
|
Alfonse LE, Garrett AD, Lun DS, Duffy KR, Grgicak CM. A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt. Forensic Sci Int Genet 2018; 32:62-70. [DOI: 10.1016/j.fsigen.2017.10.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023]
|