1
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Cooper PL, Steele NS, Hymus CM, Rye MS. Interpretation and reporting considerations of low-level DNA profiles following MinElute® purification of PowerPlex® 21 amplified products. Forensic Sci Int 2024; 360:112064. [PMID: 38805773 DOI: 10.1016/j.forsciint.2024.112064] [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: 01/29/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024]
Abstract
The generation of high-quality DNA profiles from trace amounts of DNA continues to be an issue in forensic casework. Several methods have been proposed over the years to increase recovery rates for low input DNA, including purification of PCR products, an increase in PCR cycle numbers and increasing injection time or voltage during electrophoresis. In this study, the characteristics of DNA profiles generated using QIAGEN MinElute® purification of Promega PowerPlex® 21 amplified products for low DNA input samples, ranging from 80 pg down to 4 pg, were evaluated. MinElute® purification was found to be a simple, effective and time efficient method, which can greatly improve the resolution of amplified PCR products, recovering 100% of donor concordant alleles from as little 16 pg of input template DNA and generating sufficient allelic information for interpretation from as low as 4 pg inputs. However, as is commonly observed with low template DNA samples, the results exhibited extensive disparity in the effects of stochastic variation in amplification, including increased heterozygote peak height imbalance, stutter ratios and instances of allelic drop-in and drop-out, both within and between replicates. As such, it is important that the extent and variability of these stochastic effects are appropriately incorporated in the development of robust profile interpretation guidelines for DNA profiles generated from purified PCR products.
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Affiliation(s)
- Penny L Cooper
- Forensic Biology Department, PathWest Laboratory Medicine, Perth, WA, Australia.
| | - Nicholas S Steele
- Forensic Biology Department, PathWest Laboratory Medicine, Perth, WA, Australia
| | - Colby M Hymus
- Forensic Biology Department, PathWest Laboratory Medicine, Perth, WA, Australia
| | - Marie S Rye
- Forensic Biology Department, PathWest Laboratory Medicine, Perth, WA, Australia
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2
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Qu W, Wang F, Sun D, Liu Y, Jin X, Gong Z, Liu J, Zhang N, Wen D, Wang C, Jia H, Xu R, Tang X, Chen S, Fu X, Li X, Rong H, Zhang T, Jin C, Chen L, Li J, Liu Y, Cai J, Jiang B, Zha L. Internal validation of the GA118-24B Genetic Analyzer, a stable capillary electrophoresis system for forensic DNA identification. Int J Legal Med 2024; 138:361-373. [PMID: 37843624 DOI: 10.1007/s00414-023-03106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The GA118-24B Genetic Analyzer (hereafter, "GA118-24B") is an independently developed capillary electrophoresis instrument. In the present research, we designed a series of validation experiments to test its performance at detecting DNA fragments compared to the Applied Biosystems 3500 Genetic Analyzer (hereafter, "3500"). Three commercially available autosomal short tandem repeat multiplex kits were used in this validation. The results showed that GA118-24B had acceptable spectral calibration for three kits. The results of accuracy and concordance studies were also satisfactory. GA118-24B showed excellent precision, with a standard deviation of less than 0.1 bp. Sensitivity and mixture studies indicated that GA118-24B could detect low-template DNA and complex mixtures as well as the results generated by 3500 in parallel experiments. Based on the experimental results, we set specific analytical and stochastic thresholds. Besides, GA118-24B showed superiority than 3500 within certain size ranges in the resolution study. Instead of conventional commercial multiplex kits, GA118-24B performed stably on a self-developed eight-dye multiplex system, which were not performed on 3500 Genetic Analyzer. We compared our validation results with those of previous research and found our results to be convincing. Overall, we conclude that GA118-24B is a stable and reliable genetic analyzer for forensic DNA identification.
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Affiliation(s)
- Weifeng Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Feng Wang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Dan Sun
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Yi Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xin Jin
- Public Security Department of Hainan Province, No. 9. Binya Road, Hainan, 570203, China
| | - Zheng Gong
- Criminal Technology Detachment, Public Security Bureau of Harbin, No. 35. Dongfeng Road, Harbin, 150010, China
| | - Jinjie Liu
- Criminal Investigation Detachment, Public Security Bureau of Beijing, No. 44. Banbuqiao Road, Beijing, 102611, China
| | - Ningjie Zhang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Dan Wen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Hongtao Jia
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Ruyi Xu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xuan Tang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Siqi Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xiaoyi Fu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xue Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Haibo Rong
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Tao Zhang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Chuan Jin
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Li Chen
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Ying Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Bowei Jiang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China.
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China.
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3
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Tozzo P, Mazzobel E, Marcante B, Delicati A, Caenazzo L. Touch DNA Sampling Methods: Efficacy Evaluation and Systematic Review. Int J Mol Sci 2022; 23:15541. [PMID: 36555182 PMCID: PMC9779423 DOI: 10.3390/ijms232415541] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although the main aspects of this type of evidence have been extensively studied, some controversial issues remain. For instance, there is no conclusive evidence indicating which sampling method results in the highest rate of biological material recovery. Thus, this study aimed to describe the actual considerations on touch DNA and to compare three different sampling procedures, which were "single-swab", "double-swab", and "other methods" (i.e., cutting out, adhesive tape, FTA® paper scraping), based on the experimental results published in the recent literature. The data analysis performed shows the higher efficiency of the single-swab method in DNA recovery in a wide variety of experimental settings. On the contrary, the double-swab technique and other methods do not seem to improve recovery rates. Despite the apparent discrepancy with previous research, these results underline certain limitations inherent to the sampling procedures investigated. The application of this information to forensic investigations and laboratories could improve operative standard procedures and enhance this almost fundamental investigative tool's probative value.
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Affiliation(s)
- Pamela Tozzo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Legal Medicine Section, University of Padova, 35121 Padova, Italy
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Doniec A, Januła M, Grzmil P, Kupiec T. Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes. Forensic Sci Int Genet 2022; 60:102751. [PMID: 35914369 DOI: 10.1016/j.fsigen.2022.102751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022]
Abstract
In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.
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Affiliation(s)
- Andrzej Doniec
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland; Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
| | - Miłosz Januła
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland
| | - Paweł Grzmil
- Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Tomasz Kupiec
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland.
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5
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Jäger R. New Perspectives for Whole Genome Amplification in Forensic STR Analysis. Int J Mol Sci 2022; 23:ijms23137090. [PMID: 35806097 PMCID: PMC9267064 DOI: 10.3390/ijms23137090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Modern PCR-based analytical techniques have reached sensitivity levels that allow for obtaining complete forensic DNA profiles from even tiny traces containing genomic DNA amounts as small as 125 pg. Yet these techniques have reached their limits when it comes to the analysis of traces such as fingerprints or single cells. One suggestion to overcome these limits has been the usage of whole genome amplification (WGA) methods. These methods aim at increasing the copy number of genomic DNA and by this means generate more template DNA for subsequent analyses. Their application in forensic contexts has so far remained mostly an academic exercise, and results have not shown significant improvements and even have raised additional analytical problems. Until very recently, based on these disappointments, the forensic application of WGA seems to have largely been abandoned. In the meantime, however, novel improved methods are pointing towards a perspective for WGA in specific forensic applications. This review article tries to summarize current knowledge about WGA in forensics and suggests the forensic analysis of single-donor bioparticles and of single cells as promising applications.
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Affiliation(s)
- Richard Jäger
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany;
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Institute of Safety and Security Research, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
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6
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Martin B, Kaesler T, Linacre A. Analysis of rapid HIT application to touch DNA samples. J Forensic Sci 2022; 67:1233-1240. [PMID: 34978082 DOI: 10.1111/1556-4029.14964] [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: 08/26/2021] [Revised: 12/02/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022]
Abstract
Rapid DNA technology is being utilized for reference profiles worldwide. There is also strong data in the literature to support its use for high-template DNA sources, the same is not true for low-template sources, such as touch DNA; this is a requirement before wider implementation to forensic casework is considered. We report on the Rapid HIT Intel cartridge's ability to facilitate successful amplification of touch DNA to obtain profiles from template deposited on items commonly encountered in forensic casework. Eight items were touched in ten replicates- two were tapelifted, three swabbed, and three directly inserted. Significance was observed in the alleles amplified and RFU with respect to sample type. Three samples performed well: cable tie, fabric, and matchstick. As two of these were directly inserted, this should be considered for any sample small enough. Placement of highly absorbent substrates into the cartridge is not advised as it can cause a lysate-pull error. Heterozygote loci often presented as homozygous (32%-78% loci per profile); this was influenced by substrate type and profile RFU. Loci with larger masses exhibited higher false homozygosity also. Comparison of the donor's profile analyzed was performed against previous datasets analyzing touch DNA through standard workflow, including manual DNA extraction, PCR, and CE separation. These data show that for all substrates, except for a fabric swatch, standard processing is preferential to Rapid HIT analysis. In its current form, rapid DNA technology is not fit for the routine analysis of touch DNA samples in forensic casework.
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Affiliation(s)
- Belinda Martin
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - Todd Kaesler
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, Australia
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7
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Chong MD, Wallin J. A single direct amplification method for forensic casework references on a variety of substrates. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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8
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Huang Y, Chen X, Li X, Shu P, Wang H, Hou T, Wang Y, Song F, Zhang J. A proof-of-principle study on implementing polymerase chain displacement reaction (PCDR) to improve forensic low-template DNA analysis. Forensic Sci Int Genet 2021; 56:102609. [PMID: 34717077 DOI: 10.1016/j.fsigen.2021.102609] [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: 05/18/2021] [Revised: 10/06/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022]
Abstract
Polymerase chain reaction (PCR) plays an important role in forensic DNA analysis. However, the amplification of low-template DNA (LTDNA) samples usually encounters unsatisfactory results for the limited efficiency of PCR, which would interfere with the subsequent profile interpretation. Polymerase chain displacement reaction (PCDR) is a highly-efficient technique characterized by combining PCR and strand displacement reaction into a single PCDR cycle. This study explored the feasibility of PCDR for improving forensic LTDNA analysis. STR markers commonly used in forensic genetics were subjected to PCDR amplification and capillary electrophoresis detection. The results of singleplex reactions indicated that PCDR surpassed original PCR in efficiency for STR amplification. The average peak height of alleles in PCDR profiles was linearly correlated to the number of outer primers adopted for initiating the strand displacement process. Further, we assessed the multiplexing potential of PCDR by incorporating 17 STRs included in the expanded CODIS core loci and Amelogenin gene into a multiplex PCDR system. For pristine DNA templates ranged from 200 pg to 12.5 pg, the multiplex PCDR system consistently exhibited higher allele peak height as well as less allele dropout compared to the multiplex PCR references. Meanwhile, a significant reduction of stutter ratio was extensively observed in PCDR profiles. We also tested mock casework samples to verify the practical ability of multiplex PCDR for LTDNA detection. With DNA input varying from 48.1 pg to 6.6 pg, the multiplex PCDR system consistently obtained more allelic information than multiplex PCR methods. Our data collectively suggested that it is feasible to apply PCDR in forensic LTDNA analysis.
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Affiliation(s)
- Yuguo Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaogang Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xi Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Panyin Shu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Haoyu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Tingyun Hou
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuting Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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9
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Lozano-Peral D, Rubio L, Santos I, Gaitán MJ, Viguera E, Martín-de-Las-Heras S. DNA degradation in human teeth exposed to thermal stress. Sci Rep 2021; 11:12118. [PMID: 34108558 PMCID: PMC8190102 DOI: 10.1038/s41598-021-91505-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
Human identification from burned remains poses a challenge to forensic laboratories, and DNA profiling is widely used for this purpose. Our aim was to evaluate the effect of temperature on DNA degradation in human teeth. Thirty teeth were exposed to temperatures of 100, 200, or 400 °C for 60 min. DNA was quantified by Real-Time qPCR (Quantifiler Human DNA Quantification Kit) and fluorescence spectroscopy (Qubit 3.0 Fluorometer). DNA degradation was evaluated by using STR markers (AmpFLSTR Identifiler Plus PCR Amplification Kit) to determine the allele and locus dropout, inter-locus balance, and degradation slope (observed (Oa) to expected (Ea) locus peak height ratio against the molecular weight). Most of the genomic DNA was degraded between 100 °C and 200 °C. At 100 °C, locus dropout ratios showed significant differences between the largest loci (FGA, D7S820, D18S51, D16S539, D2S1338 and CSF1PO) and amelogenin. Inter-locus balance values significantly differed between all dye channels except between NED and PET. The dropout ratio between D18S51 (NED) and amelogenin (PET) can be recommended for the evaluation of DNA degradation. The Oa/Ea regression model can predict locus peak heights in DNA degradation (R2 = 0.7881). These findings may be useful to assess the reliability of DNA typing for human identification in teeth subjected to prolonged incineration.
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Affiliation(s)
- Diego Lozano-Peral
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
- Supercomputing and Bioinnovation Center, Servicios Centrales de Apoyo a la Investigación, University of Malaga, 29590, Malaga, Spain
| | - Leticia Rubio
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain.
| | - Ignacio Santos
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
| | - María Jesús Gaitán
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
| | - Enrique Viguera
- Department of Cellular Biology, Genetics and Physiology, University of Malaga, 29071, Malaga, Spain
| | - Stella Martín-de-Las-Heras
- Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain
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10
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Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. Genes (Basel) 2020; 11:genes11111345. [PMID: 33202822 PMCID: PMC7709034 DOI: 10.3390/genes11111345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology—Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge—has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.
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11
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A comprehensive study of allele drop-in over an extended period of time. Forensic Sci Int Genet 2020; 48:102332. [DOI: 10.1016/j.fsigen.2020.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/22/2020] [Accepted: 06/04/2020] [Indexed: 11/19/2022]
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12
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Hayden DD, Wallin JM. A comparative study for the isolation of exogenous trace DNA from fingernails. Forensic Sci Int Genet 2019; 39:119-128. [PMID: 30640083 DOI: 10.1016/j.fsigen.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/19/2018] [Accepted: 12/19/2018] [Indexed: 11/15/2022]
Abstract
Often fingernails from a victim or suspect involved in a physical assault, such as murder or sexual assault, are submitted to crime laboratories for DNA testing of foreign/exogenous biological material; however, very few studies have been conducted comparing the effectiveness of different sampling methods on the removal of foreign/exogenous DNA while minimizing the fingernail endogenous DNA. In this study three different sampling methods (swabbing, PBS soak, and PrepFiler® lysis buffer soak) were compared in order to identify one that minimizes the amount of endogenous DNA removed and maximizes the amount of foreign/exogenous male DNA removed. The samples were processed using the Tecan HIDEVO150 robot in order to reduce analyst time and the DNA mixtures were interpreted using the probabilistic genotyping software STRmix™. For each sampling method the quantity of male DNA, the mixture proportions, the number of foreign/exogenous male alleles detected, the amount of DNA degradation, and the discrimination power via the likelihood ratio obtained for the foreign/exogenous male DNA donor were determined and compared. The PrepFiler® lysis buffer soak and swabbing sampling methods appear to be equally effective at removing foreign/exogenous DNA from fingernails; however, the lysis buffer soak sampling method extracts more female endogenous DNA from the fingernail and the female DNA is degraded. Marginally higher likelihood ratios were obtained for the swab samples versus the PrepFiler® lysis buffer soak samples; therefore, it was determined that the swabbing sampling method was the best sampling method for the recovery of foreign exogenous DNA from fingernails while minimizing the amount of endogenous DNA removed.
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Affiliation(s)
- Deanna D Hayden
- State of California, Department of Justice, Bureau of Forensic Services, 1001 West Cutting Boulevard, Richmond, CA 94804, United States.
| | - Jeanette M Wallin
- State of California, Department of Justice, Bureau of Forensic Services, 1001 West Cutting Boulevard, Richmond, CA 94804, United States
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13
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Deconvolution of blood-blood mixtures using DEPArrayTM separated single cell STR profiling. Rechtsmedizin (Berl) 2018. [DOI: 10.1007/s00194-018-0291-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Norsworthy S, Lun DS, Grgicak CM. Determining the number of contributors to DNA mixtures in the low-template regime: Exploring the impacts of sampling and detection effects. Leg Med (Tokyo) 2018; 32:1-8. [PMID: 29453054 DOI: 10.1016/j.legalmed.2018.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/15/2017] [Accepted: 02/06/2018] [Indexed: 11/30/2022]
Abstract
The interpretation of DNA evidence may rely upon the assumption that the forensic short tandem repeat (STR) profile is composed of multiple genotypes, or partial genotypes, originating from n contributors. In cases where the number of contributors (NOC) is in dispute, it may be justifiable to compute likelihood ratios that utilize different NOC parameters in the numerator and denominator, or present different likelihoods separately. Therefore, in this work, we evaluate the impact of allele dropout on estimating the NOC for simulated mixtures with up to six contributors in the presence or absence of a major contributor. These simulations demonstrate that in the presence of dropout, or with the application of an analytical threshold (AT), estimating the NOC using counting methods was unreliable for mixtures containing one or more minor contributors present at low levels. The number of misidentifications was only slightly reduced when we expand the number of STR loci from 16 to 21. In many of the simulations tested herein, the minimum and actual NOC differed by more than two, suggesting that low-template, high-order mixtures with allele counts fewer than six may be originating from as many as four-, five-, or six-persons. Thus, there is justification for the use of differing or multiple assumptions on the NOC when computing the weight of DNA evidence for low-template mixtures, particularly when the peak heights are in the vicinity of the signal threshold or allele counting methods are the mechanism by which the NOC is assessed.
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Affiliation(s)
- Sarah Norsworthy
- Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, MA 02118, USA
| | - Desmond S Lun
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA; Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Catherine M Grgicak
- Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, MA 02118, USA; Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Chemistry, Rutgers University, Camden, NJ 08102, USA.
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15
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Cavanaugh SE, Bathrick AS. Direct PCR amplification of forensic touch and other challenging DNA samples: A review. Forensic Sci Int Genet 2018; 32:40-49. [DOI: 10.1016/j.fsigen.2017.10.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
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16
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Duffy KR, Gurram N, Peters KC, Wellner G, Grgicak CM. Exploring STR signal in the single- and multicopy number regimes: Deductions from an in silico model of the entire DNA laboratory process. Electrophoresis 2017; 38:855-868. [DOI: 10.1002/elps.201600385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/10/2016] [Accepted: 11/29/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Ken R. Duffy
- Hamilton Institute; Maynooth University; Maynooth Ireland
| | - Neil Gurram
- Research Laboratory of Electronics; Massachusetts Institute of Technology; Cambridge MA USA
| | - Kelsey C. Peters
- Biomedical Forensic Sciences; Boston University School of Medicine; Boston MA USA
| | - Genevieve Wellner
- Biomedical Forensic Sciences; Boston University School of Medicine; Boston MA USA
| | - Catherine M. Grgicak
- Biomedical Forensic Sciences; Boston University School of Medicine; Boston MA USA
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17
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Hansson O, Egeland T, Gill P. Characterization of degradation and heterozygote balance by simulation of the forensic DNA analysis process. Int J Legal Med 2016; 131:303-317. [PMID: 27807625 PMCID: PMC5306348 DOI: 10.1007/s00414-016-1453-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/14/2016] [Indexed: 12/04/2022]
Abstract
Simulation experiments were used to show the impact of varying extraction efficiency, aliquot proportion, and PCR efficiency on the heterozygote balance of a range of diploid and haploid cells. Reducing either parameters introduces variance. It is well-known that the variance in heterozygote balance increases as the amount of DNA is reduced. Surprisingly the distribution is in fact diamond shaped — the variance start to decrease at very low amounts of DNA. Simulations suggest that pristine diluted DNA is an acceptable approximation in validations to infer heterozygote balance. However, the difference in distribution of the variance between diploid and haploid cell types may, under some circumstances, need to be considered in statistical models. Finally, we exemplify how simulations can be used to predict the outcome of PCR for degraded samples. Visualizing the predicted DNA profile as an electropherogram can help to identify the best approach for sample processing.
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Affiliation(s)
- Oskar Hansson
- Norwegian Institute of Public Health, Department of Forensic Biology, Oslo, Norway.
- Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Thore Egeland
- Norwegian Institute of Public Health, Department of Forensic Biology, Oslo, Norway
- Norwegian University of Life Sciences, Ås, Norway
| | - Peter Gill
- Norwegian Institute of Public Health, Department of Forensic Biology, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
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18
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Bieber FR, Buckleton JS, Budowle B, Butler JM, Coble MD. Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion. BMC Genet 2016; 17:125. [PMID: 27580588 PMCID: PMC5007818 DOI: 10.1186/s12863-016-0429-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/18/2016] [Indexed: 12/02/2022] Open
Abstract
Background The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quantity or degraded evidence leading to allele and locus dropout; allele sharing of contributors leading to allele stacking; and differentiation of PCR stutter artifacts from true alleles. There is variation in statistical approaches used to evaluate the strength of the evidence when inclusion of a specific known individual(s) is determined, and the approaches used must be supportable. There are concerns that methods utilized for interpretation of complex forensic DNA mixtures may not be implemented properly in some casework. Similar questions are being raised in a number of U.S. jurisdictions, leading to some confusion about mixture interpretation for current and previous casework. Results Key elements necessary for the interpretation and statistical evaluation of forensic DNA mixtures are described. Given the most common method for statistical evaluation of DNA mixtures in many parts of the world, including the USA, is the Combined Probability of Inclusion/Exclusion (CPI/CPE). Exposition and elucidation of this method and a protocol for use is the focus of this article. Formulae and other supporting materials are provided. Conclusions Guidance and details of a DNA mixture interpretation protocol is provided for application of the CPI/CPE method in the analysis of more complex forensic DNA mixtures. This description, in turn, should help reduce the variability of interpretation with application of this methodology and thereby improve the quality of DNA mixture interpretation throughout the forensic community. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0429-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederick R Bieber
- Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| | - John S Buckleton
- ESR (The Institute of Environmental Science and Research), Private Bag 92021, Auckland, 1142, New Zealand.,Statistical Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8980, Gaithersburg, MD, 20899, USA
| | - Bruce Budowle
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, 100 Bureau Drive, Mail Stop 4701, Gaithersburg, MD, 20899, USA
| | - Michael D Coble
- National Institute of Standards and Technology, Applied Genetics Group, 100 Bureau Drive, Mail Stop 8314, Gaithersburg, MD, 20899, USA
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Revealing the challenges of low template DNA analysis with the prototype Ion AmpliSeq™ Identity panel v2.3 on the PGM™ Sequencer. Forensic Sci Int Genet 2016; 22:25-36. [DOI: 10.1016/j.fsigen.2015.07.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 06/08/2015] [Accepted: 07/13/2015] [Indexed: 01/18/2023]
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20
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Factors affecting peak height variability for short tandem repeat data. Forensic Sci Int Genet 2016; 21:126-33. [DOI: 10.1016/j.fsigen.2015.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 11/19/2022]
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21
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Gill P, Haned H, Bleka O, Hansson O, Dørum G, Egeland T. Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development. Forensic Sci Int Genet 2015; 18:100-17. [PMID: 25866376 DOI: 10.1016/j.fsigen.2015.03.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022]
Abstract
The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with the ability to multiplex several loci together. Use of the polymerase chain reaction (PCR) increased the sensitivity of the method to enable the analysis of a handful of cells. The first multiplexes were simple: 'the quad', introduced by the defunct UK Forensic Science Service (FSS) in 1994, rapidly followed by a more discriminating 'six-plex' (Second Generation Multiplex) in 1995 that was used to create the world's first national DNA database. The success of the database rapidly outgrew the functionality of the original system - by the year 2000 a new multiplex of ten-loci was introduced to reduce the chance of adventitious matches. The technology was adopted world-wide, albeit with different loci. The political requirement to introduce pan-European databases encouraged standardisation - the development of European Standard Set (ESS) of markers comprising twelve-loci is the latest iteration. Although development has been impressive, the methods used to interpret evidence have lagged behind. For example, the theory to interpret complex DNA profiles (low-level mixtures), had been developed fifteen years ago, but only in the past year or so, are the concepts starting to be widely adopted. A plethora of different models (some commercial and others non-commercial) have appeared. This has led to a confusing 'debate' about the 'best' to use. The different models available are described along with their advantages and disadvantages. A section discusses the development of national DNA databases, along with details of an associated controversy to estimate the strength of evidence of matches. Current methodology is limited to searches of complete profiles - another example where the interpretation of matches has not kept pace with development of theory. STRs have also transformed the area of Disaster Victim Identification (DVI) which frequently requires kinship analysis. However, genotyping efficiency is complicated by complex, degraded DNA profiles. Finally, there is now a detailed understanding of the causes of stochastic effects that cause DNA profiles to exhibit the phenomena of drop-out and drop-in, along with artefacts such as stutters. The phenomena discussed include: heterozygote balance; stutter; degradation; the effect of decreasing quantities of DNA; the dilution effect.
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Affiliation(s)
- Peter Gill
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Forensic Medicine, Sognsvannsveien 20, Rikshospitalet, 0372 Oslo, Norway.
| | - Hinda Haned
- Netherlands Forensic Institute, Department of Human Biological Traces, The Hague, The Netherlands
| | - Oyvind Bleka
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Oskar Hansson
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Guro Dørum
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
| | - Thore Egeland
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
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