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Avellaneda LL, Johnson DT, Gutierrez RM, Thompson L, Sturm SA, Sage KA, Houston RM, LaRue BL. Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination. Int J Legal Med 2024; 138:1233-1244. [PMID: 38369682 DOI: 10.1007/s00414-024-03196-1] [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: 05/18/2023] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
The use of genetic markers, specifically Short Tandem Repeats (STRs), has been a valuable tool for identifying persons of interest. However, the ability to analyze additional markers including Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (INDELs) polymorphisms allows laboratories to explore other investigative leads. INDELs were chosen in this study because large panels can be differentiated by size, allowing them to be genotyped by capillary electrophoresis. Moreover, these markers do not produce stutter and are smaller in size than STRs, facilitating the recovery of genetic information from degraded samples. The INDEL Ancestry Informative Markers (AIMs) in this study were selected from the 1000 Genomes Project based on a fixation index (FST) greater than 0.50, high allele frequency divergence, and genetic distance. A total of 25 INDEL-AIMs were optimized and validated according to SWGDAM guidelines in a five-dye multiplex. To validate the panel, genotyping was performed on 155 unrelated individuals from four ancestral groups (Caucasian, African, Hispanic, and East Asian). Bayesian clustering and principal component analysis (PCA) were performed revealing clear separation among three groups, with some observed overlap within the Hispanic group. Additionally, the PCA results were compared against a training set of 793 samples from the 1000 Genomes Project, demonstrating consistent results. Validation studies showed the assay to be reproducible, tolerant to common inhibitors, robust with challenging casework type samples, and sensitive down to 125 pg. In conclusion, our results demonstrated the robustness and effectiveness of a 25 loci INDEL system for ancestry inference of four ancestries commonly found in the United States.
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Affiliation(s)
- Lucio L Avellaneda
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA.
| | - Damani T Johnson
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
| | - Ryan M Gutierrez
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
| | - Lindsey Thompson
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Sarah A Sturm
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Kelly A Sage
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Rachel M Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
| | - Bobby L LaRue
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
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Pedroza Matute S, Turvey K, Iyavoo S. Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study. Forensic Sci Int Genet 2024; 71:103049. [PMID: 38653142 DOI: 10.1016/j.fsigen.2024.103049] [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: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel's performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.
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Affiliation(s)
| | - Kiera Turvey
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom
| | - Sasitaran Iyavoo
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom; School of Chemistry, College of Health and Science, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, United Kingdom.
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Stan E, Muresan CO, Dumache R, Ciocan V, Ungureanu S, Mihailescu A, Daescu E, Duda-Seiman C, Menghiu G, Hutanu D, Enache A. From Jane Doe to Sofia: DNA Extraction Protocol from Bones and Teeth without Liquid Nitrogen for Identifying Skeletal Remains. Int J Mol Sci 2024; 25:5114. [PMID: 38791155 PMCID: PMC11120754 DOI: 10.3390/ijms25105114] [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: 04/16/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
DNA analysis plays a crucial role in forensic investigations, helping in criminal cases, missing persons inquiries, and archaeological research. This study focuses on the DNA concentration in different skeletal elements to improve human identification efforts. Ten cases of unidentified skeletal remains brought to the Institute of Forensic Medicine in Timisoara, Romania, underwent DNA analysis between 2019 and 2023. The results showed that teeth are the best source for DNA extraction as they contain the highest concentration of genetic material, at 3.68 ng/µL, compared to the petrous temporal bone (0.936 ng/µL) and femur bone (0.633 ng/µL). These findings highlight the significance of teeth in forensic contexts due to their abundant genetic material. Combining anthropological examination with DNA analysis enhances the understanding and precision of identifying human skeletal remains, thus advancing forensic science. Selecting specific skeletal elements, such as the cochlea or teeth, emerges as crucial for reliable genetic analyses, emphasizing the importance of careful consideration in forensic identification procedures. Our study concludes that automated DNA extraction protocols without liquid nitrogen represent a significant advancement in DNA extraction technology, providing a faster, more efficient, and less labor-intensive method for extracting high-quality DNA from damaged bone and tooth samples.
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Affiliation(s)
- Emanuela Stan
- Department of Neuroscience, Discipline of Forensic Medicine, Bioethics, Deontology and Medical Law, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (E.S.); (R.D.); (V.C.); (S.U.); (A.E.)
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
| | - Camelia-Oana Muresan
- Department of Neuroscience, Discipline of Forensic Medicine, Bioethics, Deontology and Medical Law, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (E.S.); (R.D.); (V.C.); (S.U.); (A.E.)
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Raluca Dumache
- Department of Neuroscience, Discipline of Forensic Medicine, Bioethics, Deontology and Medical Law, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (E.S.); (R.D.); (V.C.); (S.U.); (A.E.)
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Veronica Ciocan
- Department of Neuroscience, Discipline of Forensic Medicine, Bioethics, Deontology and Medical Law, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (E.S.); (R.D.); (V.C.); (S.U.); (A.E.)
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Stefania Ungureanu
- Department of Neuroscience, Discipline of Forensic Medicine, Bioethics, Deontology and Medical Law, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (E.S.); (R.D.); (V.C.); (S.U.); (A.E.)
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
| | - Alexandra Mihailescu
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Department of Microscopic Morphology Genetics, Center of Genomic Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Ecaterina Daescu
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
- Department I of Anatomy and Embryology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Corina Duda-Seiman
- Doctoral School Medicine-Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Faculty of Chemistry-Biology-Geography, West University of Timisoara, 300115 Timișoara, Romania; (G.M.); (D.H.)
| | - Gheorghita Menghiu
- Faculty of Chemistry-Biology-Geography, West University of Timisoara, 300115 Timișoara, Romania; (G.M.); (D.H.)
| | - Delia Hutanu
- Faculty of Chemistry-Biology-Geography, West University of Timisoara, 300115 Timișoara, Romania; (G.M.); (D.H.)
| | - Alexandra Enache
- Department of Neuroscience, Discipline of Forensic Medicine, Bioethics, Deontology and Medical Law, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (E.S.); (R.D.); (V.C.); (S.U.); (A.E.)
- Institute of Legal Medicine, 300610 Timisoara, Romania; (A.M.); (E.D.)
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [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: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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Radojevic DN, Todorovic MS, Vitosevic KM, Canovic V, Pavicevic M, Slovic ZS, Andric IM, Matic S, Todorovic DV. The changes in tissue histomorphology and quality of DNA in healthy human autopsied tissues stored at -20 °C and -150 °C. Leg Med (Tokyo) 2024; 67:102396. [PMID: 38237382 DOI: 10.1016/j.legalmed.2024.102396] [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: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 03/01/2024]
Abstract
The aim of this study was to compare the changes in tissue histomorphology and DNA quality in six different healthy tissues (brain, heart, lung, liver, spleen and kidney) exempted during autopsy of healthy individuals and storage at -20 °C and -150 °C three month. Tissue samples were obtained, divided by tissue and temperature group, and for each sample, tissue histomorphology and DNA (isolated from all tissues in duplicated - 72 samples of DNA) quality were analysed. Morphology of tissue samples was studied using H&E staining. DNA was isolated using the phenol-chloroform-isoamyl alcohol method. To assess the concentration and purity of the DNA samples, we used a spectrophotometer to measure absorbance at wavelengths of 280 nm and 260 nm. The fragments of human telomerase reverse transcriptase (hTERT) gene were amplified from the DNA using PCR reaction and then visualised using the 2 % agarose gel. Samples stored at -150 °C sustained the highest degree of histomorphological damage, while samples stored at -20 °C were less degraded, compared to control. The liver samples stored at -20 °C had a mean DNA concentration (1030.4 ± 51.5 ng/μl) higher than the samples of liver tissue stored at -150 °C (497.4 ± 167.1 ng/μl) (p < 0.001). Other tissues did not have statistically significantly different DNA concentration at both temperatures. Liver samples at -20 °C had degraded DNA, showed as the absence of hTERT gene in most of samples. Other tissue samples in both temperature groups had unfragmented DNA. Storing tissue samples at -20 °C is not inferior in terms of DNA yield and integrity, and possibly superior for tissue histomorphology, comparing with samples stored at -150⁰C.
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Affiliation(s)
- Dusan N Radojevic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Genetics
| | - Milos S Todorovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia.
| | - Katarina M Vitosevic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Vanja Canovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Milena Pavicevic
- University of Kragujevac, Serbia, Faculty of Science and Mathematics
| | - Zivana S Slovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Ivana M Andric
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine
| | - Stevan Matic
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Danijela V Todorovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Genetics
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Ve K, R R, Cac P, A K, E T, Cc S, Ab O. Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579345. [PMID: 38370638 PMCID: PMC10871358 DOI: 10.1101/2024.02.07.579345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Motivation Recently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is cost and time prohibitive. Multiplexing, in which cells from unique patients are pooled into a single experiment, offers a possible solution. While multiplexing methods exist for scRNAseq, accurate demultiplexing in scDNAseq remains an unmet need. Results Here, we introduce SNACS: Single-Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting. SNACS relies on a combination of patient-level cell-surface identifiers and natural variation in genetic polymorphisms to demultiplex scDNAseq data. We demonstrated the performance of SNACS on a dataset consisting of multi-sample experiments from patients with leukemia where we knew truth from single-sample experiments from the same patients. Using SNACS, accuracy ranged from 0.948 - 0.991 vs 0.552 - 0.934 using demultiplexing methods from the single-cell literature.
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Affiliation(s)
- Kennedy Ve
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Roy R
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Peretz Cac
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
- Division of Hematology and Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Koh A
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Tran E
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Smith Cc
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Olshen Ab
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA, 94143
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Watson J, McNevin D, Grisedale K, Spiden M, Seddon S, Ward J. Operationalisation of the ForenSeq® Kintelligence Kit for Australian unidentified and missing persons casework. Forensic Sci Int Genet 2024; 68:102972. [PMID: 37918284 DOI: 10.1016/j.fsigen.2023.102972] [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: 08/14/2023] [Revised: 10/03/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
Single nucleotide polymorphism (SNP) genotyping technologies can generate investigative leads for human remains identification, including estimation of biological sex, biogeographical ancestry (BGA), externally visible characteristics (EVCs), identity, uniparental lineage and extended kinship. The ForenSeq® Kintelligence Kit provides forensic laboratories with the ability to apply this suite of genetic tools to forensic samples using one panel targeting 10,230 SNPs (including 56 ancestry-informative, 24 phenotype-informative, 94 identity-informative, 106 X chromosome, 85 Y chromosome and 9867 kinship-informative SNPs) sequenced on the MiSeq FGx® Sequencing System. The ForenSeq® Kintelligence Kit has been internally validated, optimised and operationalised by the Australian Federal Police National DNA Program for Unidentified and Missing Persons (AFP Program) for coronial casework. The internal validation was conducted according to the Scientific Working Group on DNA Analysis Methods guidelines (excluding mixture analysis), focussing on sample types typically encountered in human remains identification casework, such as bones, teeth, nail, blood and hair. The workflow was optimised for a high throughput library preparation and sequencing workflow, and additional analytical thresholds were developed to improve genotyping accuracy for low DNA input samples. Additionally, the genetic intelligence generated from the kit was compared to the self-declared biological sex, EVCs and BGA of the DNA donors to assess concordance. The kit was able to produce high quality SNP profiles from 1.0 ng down to 0.1 ng of DNA, with high repeatability and reproducibility, and minimal background noise. The prediction accuracy for biological sex (95%), hair colour (58%), eye colour (74%) and BGA inferences (consistent: 74%; partially consistent: 10%; inconclusive: 16%) was determined based on self-declared data. Additionally, SNP profiles from a volunteer family group of ten related individuals were uploaded to GEDmatch PRO™ to assess kinship accuracy. The kit was capable of detecting (97%) and accurately classifying (90%) genetic relationships spanning from first to fifth degree. The Kintelligence Kit provides the AFP Program with a robust and reliable genetic intelligence tool for unidentified and missing persons investigations, which has been designed to sequence multiple challenging samples in a single multiplexed assay using existing laboratory instrumentation.
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Affiliation(s)
- Jessica Watson
- Australian Federal Police National DNA Program for Unidentified and Missing Persons, Australia; Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Australia.
| | - Dennis McNevin
- Australian Federal Police National DNA Program for Unidentified and Missing Persons, Australia; Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Australia
| | - Kelly Grisedale
- Australian Federal Police National DNA Program for Unidentified and Missing Persons, Australia
| | - Michelle Spiden
- Australian Federal Police National DNA Program for Unidentified and Missing Persons, Australia
| | - Shelley Seddon
- Australian Federal Police National DNA Program for Unidentified and Missing Persons, Australia
| | - Jodie Ward
- Australian Federal Police National DNA Program for Unidentified and Missing Persons, Australia; Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Australia
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Panneerchelvam S, Norazmi MN. DNA Profiling in Human Identification: From Past to Present. Malays J Med Sci 2023; 30:5-21. [PMID: 38239252 PMCID: PMC10793127 DOI: 10.21315/mjms2023.30.6.2] [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: 04/27/2022] [Accepted: 12/02/2022] [Indexed: 01/22/2024] Open
Abstract
Forensic DNA typing has been widely accepted in the courts all over the world. This is because DNA profiling is a very powerful tool to identify individuals on the basis of their unique genetic makeup. DNA evidence is capable of not only identifying the presence of specific biospecimens in a crime scene, but it is also used to exonerate suspects who are innocent of a crime. Technological advancements in DNA profiling, including the development of validated kits and statistical methods have made this tool to be more precise in forensic investigations. Therefore, validated combined DNA index system (CODIS) short tandem repeats (STRs) kits which require very small amount of DNA, coupled with real-time polymerase chain reaction (PCR) and the statistical strengths are used routinely to identify human remains, establish paternity or to match suspected crime scene biospecimens. The road to modern DNA profiling has been long, and it has taken scientists decades of work and fine tuning to develop highly accurate testing and analyses that are used today. This review will discuss the various DNA polymorphisms and their utility in human identity testing.
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Affiliation(s)
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
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Zhao M, Cui W, Xu H, Zhang Y, Zhu B. Unveiling the genetic landscape of high-altitude adaptive ethnic groups with polymorphic markers: Implications of comprehensive forensic appraisals and population genetic investigations. Heliyon 2023; 9:e21229. [PMID: 38027587 PMCID: PMC10656254 DOI: 10.1016/j.heliyon.2023.e21229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background Deletion/insertion polymorphisms (DIPs), a novel class of biomarker, have been widely utilized in forensic areas for individual identification, paternity tests, and ancestral origin inference due to its applicability to degraded samples and low mutation rates. Despite the availability of a well-established commercial kit, the Investigator® DIPplex kit (Qiagen), certain loci exhibit limited levels of polymorphisms in East Asian populations, particularly in Chinese populations. Objective This dissertation seeks to undertake a comprehensive evaluation about the forensic efficiency of a self-developed multiplex amplification system in high-altitude adaptive ethnic groups of China. Healthy unrelated Tibetan individuals residing in Tibet Autonomous Region and Qinghai Province were genotyped using previously reported 43 deletion/insertion polymorphism loci. Forensic statistical analyses including allele frequencies and forensic parameters were conducted in the two Tibetan groups, and the genetic relatedness of the studied groups with reference populations from the 1000 Genomes Project Phase 3 were investigated. Results Forensic statistical results showed that the polymorphism information content values of the 43 deletion/insertion polymorphism loci in the two Tibetan groups exceeded 0.35. Moreover, the combined power of discrimination using the 43 deletion/insertion polymorphism loci was calculated to be 0.9999999999999999984 in the Qinghai Tibetan group and 0.9999999999999999921 in the Tibet Tibetan group. The cumulative power of exclusion using the 43 deletion/insertion polymorphism loci was calculated to be 0.999782512 in the Qinghai Tibetan group and 0.999886205 in the Tibet Tibetan group. Analysis of population genetics demonstrated that the two studied Tibetan groups shared close genetic relationships with East Asia populations. Conclusion The set of 43 deletion/insertion polymorphism loci exhibited remarkable forensic efficacy, rendering it a promising tool for forensic practice. Population genetic analyses indicated that the two Tibetan groups had closer genetic affinities to East Asian populations.
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Affiliation(s)
- Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Yunying Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
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Ashton M, Czado N, Harrel M, Hughes S. Genotyping strategies for tissues fixed with various embalming fluids for human identification, databasing, and traceability. J Forensic Sci 2023. [PMID: 37904606 DOI: 10.1111/1556-4029.15414] [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: 08/31/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023]
Abstract
Within anatomical willed body programs and skeletal collections, whole bodies and their disassociated limbs and organs are identified and tracked. However, if these tracking mechanisms fail, DNA recovered from the formalin-fixed tissues/organs could provide an additional layer of quality assurance. Embalming fluids preserve biological tissues; however, they also damage, fragment, and cross-link DNA and protein molecules. This project investigated the success of STR-typing from various soft tissue and bone samples that were fixed with embalming solutions with a range of formaldehyde concentrations. Formalin-fixed samples dissected from five cadavers, including skin, muscle, bone, heart, and kidney were used in Phase 1 of this study. In Phase 2, an additional 57 tissue samples from various embalmed organs and body parts were collected to demonstrate long-term fixation and direct applicability within a body donor program. DNA was extracted from the samples using the QIAamp® FFPE Tissue Kit (QIAGEN), quantified with the Investigator® QuantiPlex® Pro RGQ qPCR Kit (QIAGEN), and amplified using the Investigator® 24plex and 26plex QS Kits and the Investigator® DIPplex Kit (QIAGEN). The results show the DNA was severely damaged, degraded, and often in low amounts (after one year post-embalming). Sampling from skin and muscle tissues embalmed with ~2.5%-5% formaldehyde solutions appears to be the best strategy for identification, while also maintaining the preservation of the tissues. The results of this project can provide informative data when determining which genotyping strategy may be best suited for the identification, re-association, and establishment of a database for the provenance of formalin-fixed human remains.
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Affiliation(s)
- Madeline Ashton
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Sheree Hughes
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
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11
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Wen Y, Liu J, Su Y, Chen X, Hou Y, Liao L, Wang Z. Forensic biogeographical ancestry inference: recent insights and current trends. Genes Genomics 2023; 45:1229-1238. [PMID: 37081293 DOI: 10.1007/s13258-023-01387-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.
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Affiliation(s)
- Yufeng Wen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu, 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Linchuan Liao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Zheng Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China.
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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12
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Yang SB, Lee JE, Lee HY. Forensic genetic analysis of single-nucleotide polymorphisms and microhaplotypes in Koreans through next-generation sequencing using precision ID identity panel. Genes Genomics 2023; 45:1281-1293. [PMID: 37440105 DOI: 10.1007/s13258-023-01424-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND Forensic DNA analysis has seen remarkable advancements with the advent of Next Generation Sequencing (NGS). In particular, NGS analysis of single nucleotide polymorphisms (SNPs) offers significant advantages in the analysis of challenging samples compared to conventional STR analysis. OBJECTIVE This study aimed to investigate the SNPs of the Precision ID Identity Panel, a commercially available NGS panel for personal identification, by generating genetic profiles of 298 Koreans and comparing them with other global populations. METHODS A total of 124 SNPs, including 90 autosomal and 34 Y-SNPs, were analyzed using the Precision ID Identity Panel, and forensic parameters, microhaplotypes, and population differences were investigated. RESULTS The NGS data were successfully obtained from 298 Koreans. The analysis of forensic parameters exhibited a low combined match probability of 1.532 × 10- 34, which is comparable to that obtained from commonly used STR analysis. Additionally, the microhaplotype analysis revealed that the use of 16 microhaplotypes provided higher discriminatory power compared to single target SNPs. Furthermore, the adoption of microhaplotype data resulted in an increase of over 20% in expected heterozygosity at five loci. Inter-population analysis showed a close genetic relationship between Koreans and individuals from China and Myanmar in East and Southeast Asia, which are geographically adjacent to Korea. CONCLUSIONS The results of this study show that the Precision ID Identity panel can be a useful alternative where traditional STR typing is not feasible. Also, the data from our study will be useful as a reference for Koreans in forensic investigations and the prosecution of criminal justice.
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Affiliation(s)
- Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Eun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea.
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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13
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Budowle B. Unraveling crime scenes strand by strand: the forensic odyssey of Bruce Budowle. Biotechniques 2023; 75:85-89. [PMID: 37622321 DOI: 10.2144/btn-2023-0069] [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] [Indexed: 08/26/2023] Open
Abstract
Bruce Budowle speaks to Ashling Cannon, Journal Development Editor for BioTechniques, about advancements & challenges in forensic science. Budowle completed his doctorate in genetics at Virginia Tech (VA, USA) formally known as Virginia Polytechnic Institute and State University. He then went on to complete a postdoctoral fellowship at the University of Alabama at Birmingham (AL, USA) to study genetic risk factors for acute lymphocytic leukemia, diabetes and melanoma. Budowle was early in his career and hadn't spent much time in forensics at this stage, but in 1982 an advert caught his eye for a job with the FBI to develop genetic marker systems to identify people who have left biological evidence at crime scenes. Budowle spent 26 years with the FBI and helped develop a plethora of genetic analysis methods. In 1985, it became a reality that DNA could be a signature for identifying people, and there were huge developments in DNA forensic analysis. In 2009, Budowle moved into academia and went to the University of North Texas Health Science Center (TX, USA), eventually becoming the Director of the Center for Human Identification, where he oversaw missing person and traditional crime cases, taught students and carried out fundamental and applied research. Budowle feels incredibly lucky to have had the resources, opportunities and academic infrastructure to learn and develop his knowledge. Budowle recently retired from academia and now spends his time building capacity for DNA forensics applications in Africa through the Department of Justice, with a well-established program known as the International Criminal Investigative Training Assistance Program (ICITAP) as well as with the non-government organization (NGO) DNAforAfrica.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Radford University Forensic Science Institute, Radford University, Radford, VA, USA
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14
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Rahmat RA, Humphries MA, Saedon NA, Self PG, Linacre AMT. Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth. Int J Legal Med 2023; 137:1353-1360. [PMID: 37306739 DOI: 10.1007/s00414-023-03017-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: 08/19/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Melissa A Humphries
- School and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, 5006, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, the University of Adelaide, Adelaide, South Australia, Australia
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor, 46661, Malaysia
| | - Peter G Self
- CSIRO, Land and Water, Locked Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, 5042, Australia
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15
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Fattorini P, Previderè C, Livieri T, Zupanc T, Pajnič IZ. SNP analysis of challenging bone DNA samples using the HID-Ion AmpliSeq™ Identity Panel: facts and artefacts. Int J Legal Med 2023:10.1007/s00414-023-03019-9. [PMID: 37212920 PMCID: PMC10247551 DOI: 10.1007/s00414-023-03019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
PCR-MPS is an emerging tool for the analysis of low-quality DNA samples. In this study, we used PCR-MPS to analyse 32 challenging bone DNA samples from three Second World War victims, which previously yielded no results in conventional STR PCR-CE typing. The Identity Panel was used with 27 cycles of PCR. Despite that we only had an average of 6.8 pg of degraded DNA as template, 30 out of 32 libraries (93.8%) produced sequencing data for about 63/90 autosomal markers per sample. Out of the 30 libraries, 14 (46.7%) yielded single source genetic profiles in agreement with the biological identity of the donor, whereas 12 cases (40.0%) resulted in SNP profiles that did not match or were mixed. The misleading outcomes for those 12 cases were likely due to hidden exogenous human contamination, as shown by the higher frequencies of allelic imbalance, unusual high frequencies of allelic drop-ins, high heterozygosity levels in the consensus profiles generated from challenging samples, and traces of amplified molecular products in four out of eight extraction negative controls. Even if the source and the time of the contamination were not identified, it is likely that it occurred along the multi-step bone processing workflow. Our results suggest that only positive identification by statistical tools (e.g. likelihood ratio) should be accepted as reliable; oppositely, the results leading to exclusion should be treated as inconclusive because of potential contamination issues. Finally, strategies are discussed for monitoring the workflow of extremely challenging bone samples in PCR-MPS experiments with an increased number of PCR cycles.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Tommaso Livieri
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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16
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Zupanič Pajnič I, Leskovar T, Črešnar M. Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. Int J Legal Med 2023:10.1007/s00414-023-03003-3. [PMID: 37127762 DOI: 10.1007/s00414-023-03003-3] [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: 02/02/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 107 (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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17
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Joo SM, Kwon YL, Moon MH, Shin KJ. Genetic investigation of 124 SNPs in a Myanmar population using the Precision ID Identity Panel and the Illumina MiSeq. Leg Med (Tokyo) 2023; 63:102256. [PMID: 37058993 DOI: 10.1016/j.legalmed.2023.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/16/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs). The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs, enabled human identification studies on global populations through next-generation sequencing (NGS). However, most previous studies on the panel have used the Ion Torrent platform, and there are few reports on the Southeast Asian population. Here, a total of 96 unrelated males from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter and a custom variant caller, Visual SNP. The sequencing performance evaluated by locus balance and heterozygote balance was comparable to that of the Ion Torrent platform. For 90 autosomal SNPs, the combined match probability (CMP) was 6.994 × 10-34, lower than that of 22 PowerPlex Fusion autosomal STRs (3.130 × 10-26). For 34 Y-SNPs, 14 Y-haplogroups (mostly O2 and O1b) were observed. We found 51 cryptic variations (42 haplotypes) around target SNPs, of which haplotypes corresponding to 33 autosomal SNPs decreased CMP. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations. In conclusion, the Precision ID Identity Panel can be successfully analyzed on the Illumina MiSeq and provides high discrimination power for human identification in the Myanmar population. This study broadened the accessibility of the NGS-based SNP panel by expanding the available NGS platforms and adopting a robust NGS data analysis tool.
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Affiliation(s)
- Su Min Joo
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ye-Lim Kwon
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Mi Hyeon Moon
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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18
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Advancement in Human Face Prediction Using DNA. Genes (Basel) 2023; 14:genes14010136. [PMID: 36672878 PMCID: PMC9858985 DOI: 10.3390/genes14010136] [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: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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19
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Keerti A, Ninave S. DNA Fingerprinting: Use of Autosomal Short Tandem Repeats in Forensic DNA Typing. Cureus 2022; 14:e30210. [DOI: 10.7759/cureus.30210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
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20
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Yin Y, Zhang P, Xing Y. A New Computational Deconvolution Algorithm for the Analysis of Forensic DNA Mixtures with SNP Markers. Genes (Basel) 2022; 13:genes13050884. [PMID: 35627269 PMCID: PMC9141285 DOI: 10.3390/genes13050884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) support robust analysis on degraded DNA samples. However, the development of a systematic method to interpret the profiles derived from the mixtures is less studied, and it remains a challenge due to the bi-allelic nature of SNP markers. To improve the discriminating power of SNPs, this study explored bioinformatic strategies to analyze mixtures. Then, computer-generated mixtures were produced using real-world massively parallel sequencing (MPS) data from the single samples processed with the Precision ID Identity Panel. Moreover, the values of the frequency of major allele reads (FMAR) were calculated and applied as key parameters to deconvolve the two-person mixtures and estimate mixture ratios. Four custom R language scripts (three for autosomes and one for Y chromosome) were designed with the K-means clustering method as a core algorithm. Finally, the method was validated with real-world mixtures. The results indicated that the deconvolution accuracy for evenly balanced mixtures was 100% or close to 100%, which was the same as the deconvolution accuracy of inferring the genotypes of the major contributor of unevenly balanced mixtures. Meanwhile, the accuracy of inferring the genotypes of the minor contributor decreased as its proportion in the mixture decreased. Moreover, the estimated mixture ratio was almost equal to the actual ratio between 1:1 and 1:6. The method proposed in this study provides a new paradigm for mixture interpretation, especially for inferring contributor profiles of evenly balanced mixtures and the major contributor profile of unevenly balanced mixtures.
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Affiliation(s)
- Yu Yin
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; (Y.Y.); (P.Z.)
| | - Peng Zhang
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; (Y.Y.); (P.Z.)
- Public Security Bureau of Chongqing Nanchan District, #11 Jinshan Avenue, Nanchang District, Chongqing 408499, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; (Y.Y.); (P.Z.)
- Correspondence:
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21
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Chahin N, Escobar-Nassar S, Osma J, Bashammakh AS, AlYoubi AO, Ortiz M, O’Sullivan CK. Low-Cost Platform for Multiplexed Electrochemical Melting Curve Analysis. ACS MEASUREMENT SCIENCE AU 2022; 2:147-156. [PMID: 35479100 PMCID: PMC9031717 DOI: 10.1021/acsmeasuresciau.1c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Detection and identification of single nucleotide polymorphisms (SNPs) have garnered increasing interest in the past decade, finding potential application in detection of antibiotic resistance, advanced forensic science, as well as clinical diagnostics and prognostics, moving toward the realization of personalized medicine. Many different techniques have been developed for genotyping SNPs, and ideally these techniques should be rapid, easy-to-use, cost-effective, flexible, scalable, easily automated, and requiring minimal end-user intervention. While high-resolution melting curve analysis has been widely used for the detection of SNPs, fluorescence detection does not meet many of the desired requirements, and electrochemical detection is an attractive alternative due to its high sensitivity, simplicity, cost-effectiveness, and compatibility with microfabrication. Herein, we describe the multiplexed electrochemical melting curve analysis of duplex surfaces tethered to electrodes of an array. In this approach, thiolated probes designed to hybridize to a DNA sequence containing the SNP to be interrogated are immobilized on gold electrodes. Asymmetric PCR using a ferrocene-labeled forward primer is used to generate this single-stranded redox-labeled PCR amplicon. Following hybridization with the probe immobilized on the electrode surface, the electrode array is exposed to a controlled ramping of temperature, with concomitant constant washing of the electrode array surface while simultaneously carrying out voltammetric measurements. The optimum position of the site complementary to the SNP site in the immobilized probe to achieve maximum differentiation in melting temperature between wild-type and single base mismatch, thus facilitating allelic discrimination, was determined and applied to the detection of a cardiomyopathy associated SNP.
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Affiliation(s)
- Nassif Chahin
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Santiago Escobar-Nassar
- Department
of Electrical and Electronics Engineering, Universidad de los Andes, Cra. 1E No. 19a-40, Bogotá, DC 111711, Colombia
| | - Johann Osma
- Department
of Electrical and Electronics Engineering, Universidad de los Andes, Cra. 1E No. 19a-40, Bogotá, DC 111711, Colombia
| | - Abdulaziz S. Bashammakh
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, 21589 Jeddah, Kingdom of Saudi
Arabia
| | - Abdulrahman O. AlYoubi
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, 21589 Jeddah, Kingdom of Saudi
Arabia
| | - Mayreli Ortiz
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ciara K. O’Sullivan
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
- ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain
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22
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Dabas P, Jain S, Khajuria H, Nayak BP. Forensic DNA phenotyping: Inferring phenotypic traits from crime scene DNA. J Forensic Leg Med 2022; 88:102351. [DOI: 10.1016/j.jflm.2022.102351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/01/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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23
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Zho Z, Zhou Y, Li Z, Yao Y, Yang Q, Qian J, Shao C, Qian X, Sun K, Tang Q, Xie J. Identification and assessment of a subset of Y-SNPs with recurrent mutation for forensic purpose. Forensic Sci Int 2022; 334:111270. [DOI: 10.1016/j.forsciint.2022.111270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/18/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022]
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24
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Dash HR, Avila E, Jena SR, Kaitholia K, Agarwal R, Alho CS, Srivastava A, Singh AK. Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing. Int J Legal Med 2021; 136:465-473. [PMID: 34748086 DOI: 10.1007/s00414-021-02742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis-based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10-37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.
| | - Eduardo Avila
- Pontifical Catholic University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Soumya Ranjan Jena
- Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | | | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
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Ge J, King J, Mandape S, Budowle B. Enhanced mixture interpretation with macrohaplotypes based on long-read DNA sequencing. Int J Legal Med 2021; 135:2189-2198. [PMID: 34378071 DOI: 10.1007/s00414-021-02679-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022]
Abstract
Deconvoluting mixture samples is one of the most challenging problems confronting DNA forensic laboratories. Efforts have been made to provide solutions regarding mixture interpretation. The probabilistic interpretation of Short Tandem Repeat (STR) profiles has increased the number of complex mixtures that can be analyzed. A portion of complex mixture profiles, particularly for mixtures with a high number of contributors, are still being deemed uninterpretable. Novel forensic markers, such as Single Nucleotide Variants (SNV) and microhaplotypes, also have been proposed to allow for better mixture interpretation. However, these markers have both a lower discrimination power compared with STRs and are not compatible with CODIS or other national DNA databanks worldwide. The short-read sequencing (SRS) technologies can facilitate mixture interpretation by identifying intra-allelic variations within STRs. Unfortunately, the short size of the amplicons containing STR markers and sequence reads limit the alleles that can be attained per STR. The latest long-read sequencing (LRS) technologies can overcome this limitation in some samples in which larger DNA fragments (including both STRs and SNVs) with definitive phasing are available. Based on the LRS technologies, this study developed a novel CODIS compatible forensic marker, called a macrohaplotype, which combines a CODIS STR and flanking variants to offer extremely high number of haplotypes and hence very high discrimination power per marker. The macrohaplotype will substantially improve mixture interpretation capabilities. Based on publicly accessible data, a panel of 20 macrohaplotypes with sizes of ~ 8 k bp and the maximum high discrimination powers were designed. The statistical evaluation demonstrates that these macrohaplotypes substantially outperform CODIS STRs for mixture interpretation, particularly for mixtures with a high number of contributors, as well as other forensic applications. Based on these results, efforts should be undertaken to build a complete workflow, both wet-lab and bioinformatics, to precisely call the variants and generate the macrohaplotypes based on the LRS technologies.
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Affiliation(s)
- Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA.
| | - Jonathan King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Sammed Mandape
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
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26
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Cusick MF, Clark L, Tu T, Goforth J, Zhang X, LaRue B, Gutierrez R, Jindra PT. Performance characteristics of chimerism testing by next generation sequencing. Hum Immunol 2021; 83:61-69. [PMID: 34728094 DOI: 10.1016/j.humimm.2021.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Chimerism testing provides informative clinical data regarding the status of a biological sample mixture. For years, this testing was achieved by measuring the peaks of informative short tandem repeat (STR) loci using capillary electrophoresis (CE). With the advent of next generation sequencing (NGS) technology, the quantification of the percentage of donor/recipient mixtures is more easily done using sequence reads in large batches of samples run on a single flow cell. In this study, we present data on using a FORENSIC NGS chimerism platform to accurately measure the percentage of donor/recipient mixtures. We were able to detect chimerism to a limit threshold of 1% using both STR and single nucleotide polymorphism (SNP) informative loci. Importantly, a significant correlation was observed between NGS and CE chimerism methods when compared at donor detection ranges from 1% to 10%. Furthermore, 100% accuracy was achieved through proficiency testing over six surveys. Its usefulness was expanded beyond this to help identify suitable donors for solid organ transplant patients using ancestry SNP profiles. In summary, the NGS method provides a sensitive and reliable alternative to traditional CE for chimerism testing of clinical samples.
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Affiliation(s)
- Matthew F Cusick
- Department of Pathology, University of Michigan Medicine, 2800 Plymouth Rd., Building 36, Ann Arbor, MI 48109, USA.
| | - Lauren Clark
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Thuydung Tu
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - John Goforth
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Xiaohai Zhang
- HLA and Immunogenetics, Laboratory, Cedars-Sinai Medical Center, Lab-SSB 197, 8723 Alden D, Los Angeles, CA 90048, USA
| | - Bobby LaRue
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Ryan Gutierrez
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Peter T Jindra
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA.
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27
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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28
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Fast, highly sensitive and label free detection of small genetic sequence difference of DNA using novel Surface-Enhanced Raman Spectroscopy nanostructured sensor. SENSING AND BIO-SENSING RESEARCH 2021. [DOI: 10.1016/j.sbsr.2021.100406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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30
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Ishak S, Dormontt E, Young JM. Microbiomes in forensic botany: a review. Forensic Sci Med Pathol 2021; 17:297-307. [PMID: 33830453 DOI: 10.1007/s12024-021-00362-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 11/24/2022]
Abstract
Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.
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Affiliation(s)
- Sarah Ishak
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
| | - Eleanor Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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31
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Jordan D, Mills D. Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.646130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.
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32
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Caputo M, Amador MA, Sala A, Riveiro Dos Santos A, Santos S, Corach D. Ancestral genetic legacy of the extant population of Argentina as predicted by autosomal and X-chromosomal DIPs. Mol Genet Genomics 2021; 296:581-590. [PMID: 33580820 DOI: 10.1007/s00438-020-01755-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/14/2020] [Indexed: 12/01/2022]
Abstract
Aiming to determine their ancestry diagnostic potential, we selected two sets of nuclear deletion/insertion polymorphisms (DIPs), including 30 located on autosomal chromosomes and 33 on the X chromosome. We analysed over 200 unrelated Argentinean individuals living in urban areas of Argentina. As in most American countries, the extant Argentinean population is the result of tricontinental genetic admixture. The peopling process within the continent was characterised by mating bias involving Native American and enslaved African females and European males. Differential results were detected between autosomal DIPs and X-DIPs. The former showed that the European component was the largest (77.8%), followed by the Native American (17.9%) and African (4.2%) components, in good agreement with the previously published results. In contrast, X-DIPs showed that the European genetic contribution was also predominant but much smaller (52.9%) and considerably larger Native American and African contributions (39.6% and 7.5%, respectively). Genetic analysis revealed continental genetic contributions whose associated phenotypic traits have been mostly lost. The observed differences between the estimated continental genetic contribution proportions based on autosomal DIPs and X-DIPs reflect the effects of autosome and X-chromosome transmission behaviour and their different recombination patterns. This work shows the ability of the tested DIP panels to infer ancestry and confirm mating bias. To the best of our knowledge, this is the first study focusing on ancestry-informative autosomal DIP and X-DIP comparisons performed in a sample representing the entire Argentinean population.
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Affiliation(s)
- M Caputo
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina. .,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina. .,Department of Forensic Genetics and DNA Fingerprinting Service, School of Pharmacy and Biochemistry, Junin 956, 7th floor, C1113AAD, CABA, Argentina.
| | - M A Amador
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - A Sala
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
| | - A Riveiro Dos Santos
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - S Santos
- Laboratorio de Genética Humana E Médica, Departamento de Patologia, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - D Corach
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense Y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
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33
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Sukumar S, Krishnan A, Banerjee S. An Overview of Bioinformatics Resources for SNP Analysis. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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34
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Parfenchyk MS, Kotava SA. The Theoretical Framework for the Panels of DNA Markers Formation in the Forensic Determination of an Individual Ancestral Origin. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Turchi C, Previderè C, Bini C, Carnevali E, Grignani P, Manfredi A, Melchionda F, Onofri V, Pelotti S, Robino C, Sorçaburu-Ciglieri S, Tagliabracci A, Fattorini P. Assessment of the Precision ID Identity Panel kit on challenging forensic samples. Forensic Sci Int Genet 2020; 49:102400. [DOI: 10.1016/j.fsigen.2020.102400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/28/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022]
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36
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Gomes I, Pinto N, Antão-Sousa S, Gomes V, Gusmão L, Amorim A. Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics. Front Genet 2020; 11:926. [PMID: 33093840 PMCID: PMC7527635 DOI: 10.3389/fgene.2020.00926] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmission characteristics, besides the obvious clinical impact (sex chromosome aneuploidies are extremely frequent), make the X chromosome an irreplaceable genetic tool for population genetic-based studies as well as for kinship and forensic investigations. In the early 2000s, the number of publications using X-chromosomal polymorphisms in forensic and population genetic applications increased steadily. However, nearly 20 years later, we observe a conspicuous decrease in the rate of these publications. In light of this observation, the main aim of this article is to provide a comprehensive review of the advances and applications of X-chromosomal markers in population and forensic genetics over the last two decades. The foremost relevant topics are addressed as: (i) developments concerning the number and types of markers available, with special emphasis on short tandem repeat (STR) polymorphisms (STR nomenclatures and practical concerns); (ii) overview of worldwide population (frequency) data; (iii) the use of X-chromosomal markers in (complex) kinship testing and the forensic statistical evaluation of evidence; (iv) segregation and mutation studies; and (v) current weaknesses and future prospects.
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Affiliation(s)
- Iva Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Nádia Pinto
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Center of Mathematics, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sofia Antão-Sousa
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Verónica Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - António Amorim
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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37
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Liu Y, Jin X, Mei S, Lan Q, Fang Y, Liu C, Zhu B. A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies. Electrophoresis 2020; 41:2036-2046. [DOI: 10.1002/elps.202000128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/10/2020] [Accepted: 08/23/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yanfang Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- College of Forensic Medicine Xi'an Jiaotong University Health Science Center Shaanxi P. R. China
| | - Shuyan Mei
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Qiong Lan
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Yating Fang
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Chao Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Bofeng Zhu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
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38
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Cooley AM, Meiklejohn KA, Damaso N, Robertson JM, Dawson Cruz T. Performance Comparison of Massively Parallel Sequencing (MPS) Instruments Using Single-Nucleotide Polymorphism (SNP) Panels for Ancestry. SLAS Technol 2020; 26:103-112. [PMID: 32914686 DOI: 10.1177/2472630320954180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Thermo Fisher Scientific released the Precision ID Ancestry Panel, a 165-single-nucleotide polymorphism (SNP) panel for ancestry prediction that was initially compatible with the manufacturer's massively parallel sequencer, the Ion Torrent Personal Genome Machine (PGM). The semiautomated workflow using the panel with the PGM involved several time-consuming manual steps across three instruments, including making templating solutions and loading sequencing chips. In 2014, the manufacturer released the Ion Chef robot, followed by the Ion S5 massively parallel sequencer in late 2015. The robot performs the templating with reagent cartridges and loads the chips, thus creating a fully automated workflow across two instruments. The objective of the work reported here is to compare the performance of two massively parallel sequencing systems and ascertain if the change in the workflow produces different ancestry predictions. For performance comparison of the two systems, forensic-type samples (n = 16) were used to make libraries. Libraries were templated either with the Ion OneTouch 2 system (for the PGM) or on the Ion Chef robot (for the S5). Sequencing results indicated that the ion sphere particle performance metrics were similar for the two systems. The total coverages per SNP and SNP quality were both higher for the S5 system. Ancestry predictions were concordant for the mock forensic-type samples sequenced on both massively parallel sequencing systems. The results indicated that automating the workflow with the Ion Chef system reduced the labor involved and increased the sequencing quality.
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Affiliation(s)
- Ashley M Cooley
- Research Support Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA.,Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Kelly A Meiklejohn
- Research Support Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA.,Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Natalie Damaso
- Research Support Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA
| | - James M Robertson
- Research Support Unit, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA
| | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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Nwawuba Stanley U, Mohammed Khadija A, Bukola AT, Omusi Precious I, Ayevbuomwan Davidson E. Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation. Malays J Med Sci 2020; 27:22-35. [PMID: 32863743 PMCID: PMC7444828 DOI: 10.21315/mjms2020.27.4.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/12/2020] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeat (STR) typing continues to be the primary workhorse in forensic DNA profiling. Therefore, the present review discusses the prominent role of STR marker in criminal justice system. All over the world, deoxyribonucleic acid (DNA) profiling provides evidence that may be used to convict criminals, as an irrefutable proof of wrongful convictions, invaluable links to the actual perpetrators of crimes, and could also deter some offenders from committing more serious offences. Clearly, DNA profiling tools have also aided forensic scientists to re-evaluate old cases that were considered closed as a result of inadequate evidence. In carrying out this review, a comprehensive electronic literature search using PubMed, ScienceDirect, Google Scholar and Google Search were used, and all works meeting the subject matter were considered, including reviews, retrospective studies, observational studies and original articles. Case reports presented here, further demonstrates the crucial role of forensic DNA profiling in mitigating and providing compelling evidence for the resolution of crimes. For case report 1, there was a 100% match between the DNA recovered from the items found in the crime scene, and the suspect’s DNA sample collected via buccal swab following 15 STR loci examination. Case report 2 further highlights the indispensable contribution of DNA database in solving crime. Therefore, it has become very necessary for developing countries like Nigeria to develop a national DNA database and make policies and legislatures that will further expand and enable the practice of forensic genetics, particularly DNA profiling.
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Affiliation(s)
| | - Abdullahi Mohammed Khadija
- Molecular Drug Metabolism and Toxicology, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Imose Omusi Precious
- Department of Medical Laboratory Science, College of Medicine, University of Benin, Benin City, Nigeria
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Miao X, Shen Y, Gong X, Yu H, Li B, Chang L, Wang Y, Fan J, Liang Z, Tan B, Li S, Zhang B. A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. Int J Legal Med 2020; 135:709-718. [PMID: 32851473 DOI: 10.1007/s00414-020-02403-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/21/2020] [Indexed: 01/23/2023]
Abstract
The MiSeq® FGX Forensic system and the HID-Ion AmpliSeq Panel were previously developed for massively parallel sequencing (MPS) for forensic casework. Among the three major sequencing platforms, BGISEQ-500TM, which is based on multiple PCRs, is still lacking in forensics. Here, a novel forensic panel was constructed to detect 186 single-nucleotide polymorphisms (SNPs) and 123 short tandem repeats (STRs) with MPS technology on the BGISEQ-500™ platform. First, the library preparation, sequencing process, and data analysis were performed, focusing on the average depth of coverage and heterozygote balance. We calculated the allelic frequencies and forensic parameters of STR and SNP loci in 73 unrelated Chinese Han individuals. In addition, performance was evaluated with accuracy, uniformity, sensitivity, PCR inhibitor, repeatability and reproducibility, mixtures, degraded samples, case-type samples, and pedigree analyses. The results showed that 100% accurate and concordant genotypes can be obtained, and the loci with an abundance in the interquartile range accounted for 92.90% of the total, suggesting reliable uniformity in this panel. We obtained a locus detection rate that was higher than 98.78% from 78 pg of input DNA, and the optimal amount was 1.25-10 ng. The maximum concentrations of hematin and humic acid were 200 and 100 μM, respectively (the ratios of detected loci were 96.52% and 92.41%), in this panel. As a mixture, compared with those of SNPs, minor-contributor alleles of STRs could be detected at higher levels. For the degraded sample, the ratio of detected loci was 98.41%, and most profiles from case-type samples were not significantly different in abundance in our studies. As a whole, this panel showed high-performance, reliable, robust, repeatable, and reproducible results, which are sufficient for paternity testing, individual identification, and use for potentially degraded samples in forensic science.
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Affiliation(s)
- Xinyao Miao
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yuesheng Shen
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Xiaojuan Gong
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
- School of Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Huiyun Yu
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Bowen Li
- School of Life Science, Sichuan University, Chengdu, People's Republic of China
| | - Liao Chang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yinan Wang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jingna Fan
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zuhuan Liang
- Forensic Genomics International, The Beijing Genomics Institute (BGI), Shenzhen, People's Republic of China
| | - Bowen Tan
- School of Computer Science, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Shengbin Li
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Bao Zhang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
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Jiang HH, Li B, Ma Y, Bai SY, Dahmer TD, Linacre A, Xu YC. Forensic validation of a panel of 12 SNPs for identification of Mongolian wolf and dog. Sci Rep 2020; 10:13249. [PMID: 32764603 PMCID: PMC7413520 DOI: 10.1038/s41598-020-70225-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 11/26/2022] Open
Abstract
Wolf (Canis lupus) is a species included in appendices of CITES and is often encountered in cases of alleged poaching and trafficking of their products. When such crimes are suspected, those involved may attempt to evade legal action by claiming that the animals involved are domestic dogs (C. l. familiaris). To respond effectively to such claims, law enforcement agencies require reliable and robust methods to distinguish wolves from dogs. Reported molecular genetic methods are either unreliable (mitogenome sequence based), or operationally cumbersome and require much DNA (un-multiplexed microsatellites), or financially expensive (genome wide SNP genotyping). We report on the validation of a panel of 12 ancestral informative single nucleotide polymorphism (SNP) markers for discriminating wolves from dogs. A SNaPshot multiplex genotyping system was developed for the panel, and 97 Mongolian wolves (C. l. chanco) and 108 domestic dogs were used for validation. Results showed this panel had high genotyping success (0.991), reproducibility (1.00) and origin assignment accuracy (0.97 ± 0.05 for dogs and 1.00 ± 0.03 for wolves). Species-specificity testing suggested strong tolerance to DNA contamination across species, except for Canidae. The minimum DNA required for reliable genotyping was 6.25 pg/μl. The method and established gene frequency database are available to support identification of wolves and dogs by law enforcement agencies.
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Affiliation(s)
- Hong Hui Jiang
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Bo Li
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Detecting Center of Wildlife, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
| | - Yue Ma
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Su Ying Bai
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | | | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042, Australia
| | - Yan Chun Xu
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Detecting Center of Wildlife, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
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Rauf S, Zahra N, Malik SS, Zahra SAE, Sughra K, Khan MR. Extraction of Mitochondrial Genome from Whole Genome Next Generation Sequencing Data and Unveiling of Forensically Relevant Markers. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420080128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sathirapatya T, Worrapitirungsi W, Sukawutthiya P, Rasmeepaisarn K, Vongpaisarnsin K. A SNP panel for early detection of artificial chimerism in HSCT patients using TaqMan technology. Int J Legal Med 2020; 134:1553-1561. [PMID: 32248307 DOI: 10.1007/s00414-020-02276-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/12/2020] [Indexed: 11/26/2022]
Abstract
The monitoring of chimerism status in a hematopoietic stem cell transplantation patient is a crucial process and is performed periodically in a short time interval. A short tandem repeat marker is widely used for chimerism analysis due to its high discrimination power. However, the sensitivity of this approach was limited to 5% of a minor contributor and the interpretation is usually interrupted with PCR stochastic phenomena. Here, we developed an SNP panel for chimerism analysis using TaqMan technology. A set of SNPs was selected from Thai ancestry informative markers and open-access databases with proper criteria. We examined the 30 recipient-donor pairs that underwent HSCT and showed that the panel can provide an informative marker from 90% of all pairs. An early detection of artificial chimerism in post-HSCT samples was observed when compared with STR analysis. In addition, the detail of cases was discussed.
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Affiliation(s)
- Tikumphorn Sathirapatya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Kawin Rasmeepaisarn
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, 10300, Thailand.
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Xie T, Shen C, Liu C, Fang Y, Guo Y, Lan Q, Wang L, Ge J, Zhou Y, Wen S, Yang Q, Zhu B. Ancestry inference and admixture component estimations of Chinese Kazak group based on 165 AIM-SNPs via NGS platform. J Hum Genet 2020; 65:461-468. [DOI: 10.1038/s10038-020-0725-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
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45
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Hwa HL, Wu MY, Lee JCI, Yin HI, Hsu PM, Li SF, Hwu WL, Su CW. Analysis of nondegraded and degraded DNA mixtures of close relatives using massively parallel sequencing. Leg Med (Tokyo) 2020; 42:101631. [DOI: 10.1016/j.legalmed.2019.101631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 09/21/2019] [Indexed: 10/25/2022]
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Analysis of 124 SNP loci included in HID Ampliseq identity panel in a small population of Rio de Janeiro, Brazil. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Michalak E, Abreu-Głowacka M, Konarzewska M, Pepiński W, Skawrońska M, Wójcik M, Sołtyszewski I, Żaba C. Population genetics of 30 insertion-deletion polymorphism in polish Populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Kardam P, Mehendiratta M, Rehani S, Sharma R, Sahay K. A crude method of DNA extraction and identification from exfoliated human buccal mucosa cells. Indian J Dent Res 2019; 30:595-599. [PMID: 31745059 DOI: 10.4103/ijdr.ijdr_67_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background DNA analysis has a key role in forensic dentistry. However, techniques of DNA extraction and analysis are far from the reach of majority of medical professionals owing to its expensive set up. Aim The present study was aimed at formulating a crude method of extracting DNA from human buccal mucosa cells using materials commonly available in the laboratory so that the medical professionals could get more exposure to molecular biology techniques. The objectives were to identify the DNA and to assess its purity. Methods Buccal mucosa cells from 10 healthy volunteers were taken for DNA extraction following the protocol of cell lysis, purification, and precipitation. DNA was identified using standardized techniques like Diphenylamine test and its purity was assessed using a spectrophotometer. A gel electrophoresis apparatus was also constructed using readily available materials. Results DNA was extracted from human buccal mucosa cells using a crude method. The standardized tests confirmed the presence of DNA contaminated with proteins. The locally made Gel electrophoresis model exhibited a faint halo around the wells instead of DNA bands. Conclusion DNA extraction from human buccal mucosa cells was made possible using locally available materials and a crude method, but it was not of high purity.
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Affiliation(s)
- Priyanka Kardam
- Department of Oral Pathology and Microbiology, Sudha Rustagi College of Dental Sciences and Research, Faridabad, Haryana, India
| | - Monica Mehendiratta
- Department of Oral Pathology and Microbiology, ITS Dental College, Greater Noida, Uttar Pradesh, India
| | - Shweta Rehani
- Department of Oral Pathology and Microbiology, Sudha Rustagi College of Dental Sciences and Research, Faridabad, Haryana, India
| | - Rashi Sharma
- Department of Oral Pathology and Microbiology, Sudha Rustagi College of Dental Sciences and Research, Faridabad, Haryana, India
| | - Khushboo Sahay
- Department of Oral Pathology and Microbiology, Sudha Rustagi College of Dental Sciences and Research, Faridabad, Haryana, India
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Ohta J, Sakurada K. Oral gram-positive bacterial DNA-based identification of saliva from highly degraded samples. Forensic Sci Int Genet 2019; 42:103-112. [DOI: 10.1016/j.fsigen.2019.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/22/2019] [Indexed: 12/29/2022]
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50
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Sun L, Fu L, Liu Q, Zhou J, Ma C, Cong B, Li S. Population data using Precision ID Identity Panel in a Chinese Han population from Hebei Province. Forensic Sci Int Genet 2019; 42:e27-e29. [DOI: 10.1016/j.fsigen.2019.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/14/2019] [Accepted: 07/14/2019] [Indexed: 11/30/2022]
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