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Melchionda F, Silvestrini B, Robino C, Bini C, Fattorini P, Martinez-Labarga C, De Angelis F, Tagliabracci A, Turchi C. Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples. Genes (Basel) 2022; 13:genes13101688. [PMID: 36292573 PMCID: PMC9601425 DOI: 10.3390/genes13101688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/10/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers included in the HIrisPlex-S system for simultaneous prediction of eye, hair and skin colours. Forensic samples such as blood, skeletal remains, touch DNA, saliva swab, artificially degraded samples together with individuals with known phenotypes and a set of 2800 M control DNA were sequenced on the Ion Torrent platform in order to evaluate the concordance testing results and the forensic suitability of the 41-plex MPS assay. The panel was evaluated by testing a different number of PCR cycles and the volume of reagents for library preparation. The study demonstrated that full and reliable profiles were obtained with 0.1–5 ng, even with high degraded DNA. The increment of the number of PCR cycles results in an improvement of correctly genotyping and phenotyping for samples with low amounts of degraded DNA but higher frequencies of artefacts were found. The high DNA degradation level did not influence the correct genotyping and phenotyping and the critical parameter affecting the result is the quantity of input DNA. Eye and hair colour was predicted in 92.60% of individuals and skin colour in 85.15% of individuals. The results suggest that this MPS assay is robust, highly sensitive and useful for human pigmentation prediction in the forensic genetic field.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
- Correspondence: ; Tel.: +39-071-596-5044
| | - Beatrice Silvestrini
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
- Department of Surgical, Medical, Molecular Pathology, and Critical Area, University of Pisa, 56126 Pisa, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
- S.C. Medicina Legale, AOU Città della Salute e della Scienza, 10126 Turin, Italy
| | - Carla Bini
- Department of Medical and Surgical Sciences, Section of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Cristina Martinez-Labarga
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, 00173 Rome, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, 00173 Rome, Italy
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Chiara Turchi
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
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Zupanič Pajnič I, Previderè C, Zupanc T, Zanon M, Fattorini P. Isometric artifacts from polymerase chain reaction‐massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology? Electrophoresis 2022; 43:1521-1530. [PMID: 35358339 PMCID: PMC9543752 DOI: 10.1002/elps.202100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/28/2022] [Accepted: 03/26/2022] [Indexed: 11/19/2022]
Abstract
The recent introduction of polymerase chain reaction (PCR)‐massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR‐MPS could generate “isometric drop‐ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR‐MPS analyses). As expected, several well‐known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine Faculty of Medicine University of Ljubljana Ljubljana Slovenia
| | - Carlo Previderè
- Department of Public Health Experimental and Forensic Medicine Section of Legal Medicine and Forensic Sciences University of Pavia Pavia Italy
| | - Tomaž Zupanc
- Institute of Forensic Medicine Faculty of Medicine University of Ljubljana Ljubljana Slovenia
| | - Martina Zanon
- Department of Medicine, Surgery and Health University of Trieste Trieste Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health University of Trieste Trieste Italy
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3
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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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4
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Strategy for STR typing of bones from the Second World War combining CE and NGS technology: A pilot study. Forensic Sci Int Genet 2020; 50:102401. [PMID: 33171316 DOI: 10.1016/j.fsigen.2020.102401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 01/23/2023]
Abstract
The genetic identification of skeletal remains found in Second World War mass graves is complicated because of the poor quality of the samples. The aim of this study was to set up a workflow for STR typing of such samples combining PCR/CE and PCR/NGS technologies. To this end, 57 DNA samples from an equal number of 75-year-old femurs were studied. After a first round of PCR typing using GlobalFiler CE, 42 samples yielded a full profile and were therefore submitted to our standard workflow. The 15 samples that yielded no or a limited number (2-17/21) of autosomal STR markers as well four bone control samples that provided a full profile with the conventional PCR/CE test were typed in duplicate by the GlobalFiler NGS kit. Despite the degradation of the samples, which resulted in lower coverage and a lower % of on-target reads, reliable sequencing data were obtained from 16/19 samples. The use of a threshold of 30× for the locus call led to a consensus profile (cp) of 20-31/31 STR autosomal loci in 10 samples and to a cp of 8-10/31 loci in two samples, whereas the four control samples yielded a cp of 26-31/31 loci. Finally, the data of the NGS typing were combined with those of the CE typing. This last task allowed us to recover (on average) three alleles per sample and to increase the number of the heterozygous patterns in 37 cases. In total, the combined approach proposed here made possible the genetic typing of 65-100% of the autosomal STR markers in 10/15 (66.6 %) skeletal remains that yielded no or very poor results with the conventional PCR/CE approach. However, because several artefacts (such as allelic drop-out and allelic drop-in) were scored, the risk of mistyping cannot be neglected.
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Holland CA, McElhoe JA, Gaston-Sanchez S, Holland MM. Damage patterns observed in mtDNA control region MPS data for a range of template concentrations and when using different amplification approaches. Int J Legal Med 2020; 135:91-106. [PMID: 32940843 DOI: 10.1007/s00414-020-02410-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows practitioners the ability to fully resolve heteroplasmic sites. In forensic DNA analysis, identifying heteroplasmy (a naturally occurring mixture of two mtDNA profiles) can provide additional mtDNA profile information which can lead to an increase in the discrimination potential of an mtDNA match between an evidentiary sample and reference source. Forensic samples such as hair and skeletal remains, especially older, more compromised samples, can often exhibit DNA damage. Because both damage and heteroplasmy can manifest as a mixture of two nucleotides, it is important to differentiate between the two conditions when interpreting mtDNA MPS data. In this study, DNA damage was applied under controlled conditions to samples containing a range of template concentrations, including some with identified heteroplasmy. Damage was applied via storage in water at room temperature on samples diluted before or after storage to mimic low template scenarios. Damage was assessed with respect to the following areas: mtDNA quantification and degradation ratios, MPS read depth, MPS profile results, overall damage rates, and the interpretation of heteroplasmy. Datasets were generated to assess and compare two different amplification and library preparation strategies: the Promega PowerSeq™ CRM Nested System kit and a 1.16 kb target amplicon of the entire mtDNA control region followed by a Nextera® XT library preparation. The results of this study provide an evaluation of the Promega 10-plex MPS procedure as an improved process to mitigate the impact of mtDNA damage on low template samples. Some of the negative effects of damage observed in this study were a decrease in mtDNA yield by 20-30% and lower quality MPS sequencing results. These effects were observed more frequently when samples were diluted prior to inducing damage, illustrating that low template samples are more susceptible to damage. The findings of this study will assist forensic laboratories in differentiating between damage and heteroplasmy, which is essential when developing robust mtDNA MPS interpretation guidelines such as setting appropriate reporting thresholds.
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Affiliation(s)
- Charity A Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Sidney Gaston-Sanchez
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.,Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, USA
| | - Mitchell M Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.
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Louhelainen J, Miller D. Forensic Investigation of a Shawl Linked to the "Jack the Ripper" Murders. J Forensic Sci 2020; 65:295-303. [PMID: 30859587 DOI: 10.1111/1556-4029.14038] [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: 11/14/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 11/28/2022]
Abstract
A set of historic murders, known as the "Jack the Ripper murders," started in London in August 1888. The killer's identity has remained a mystery to date. Here, we describe the investigation of, to our knowledge, the only remaining physical evidence linked to these murders, recovered from one of the victims at the scene of the crime. We applied novel, minimally destructive techniques for sample recovery from forensically relevant stains on the evidence and separated single cells linked to the suspect, followed by phenotypic analysis. The mtDNA profiles of both the victim and the suspect matched the corresponding reference samples, fortifying the link of the evidence to the crime scene. Genomic DNA from single cells recovered from the evidence was amplified, and the phenotypic information acquired matched the only witness statement regarded as reliable. To our knowledge, this is the most advanced study to date regarding this case.
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Affiliation(s)
- Jari Louhelainen
- Pharmacy and Biomolecular Sciences, James Parsons Building Byrom Street, Room 10.06, Liverpool, L3 3AF, UK
| | - David Miller
- Reproduction and Early Development Group, Institute of Genetics, Health and Therapeutics, University of Leeds, Clarendon Way, Leeds, LS2 9JT, UK
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Fattorini P, Marrubini G, Bonin S, Bertoglio B, Grignani P, Recchia E, Pitacco P, Procopio F, Cantoni C, Pajnič IZ, Sorçaburu-Cigliero S, Previdere C. Prolonged DNA hydrolysis in water: A study on DNA stability. Data Brief 2018; 20:1237-1243. [PMID: 30238033 PMCID: PMC6143716 DOI: 10.1016/j.dib.2018.08.120] [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: 03/14/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022] Open
Abstract
This work provides a protocol for the in vitro production of damaged DNA samples. In particular, heat-mediated hydrolysis of the samples at 70 °C in ultrapure water was performed in 1.7 mL Eppendorf tubes sealed by Parafilm for 0-36 h. The chemical/physical features of the resulting samples are described. After normalization of the qPCR data, these were compared with those obtained from samples treated for 0-10 h in a previous study.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | | | - Serena Bonin
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy
| | - Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy
| | - Elisa Recchia
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | - Paola Pitacco
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | - Francesca Procopio
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | | | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Slovenia
| | | | - Carlo Previdere
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy
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8
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Fattorini P, Marrubini G, Bonin S, Bertoglio B, Grignani P, Recchia E, Pitacco P, Procopio F, Cantoni C, Pajnič IZ, Sorçaburu-Cigliero S, Previderè C. Producing standard damaged DNA samples by heating: pitfalls and suggestions. Anal Biochem 2018; 549:107-112. [PMID: 29551671 DOI: 10.1016/j.ab.2018.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 11/29/2022]
Abstract
Heat-mediated hydrolysis of DNA is a simple and inexpensive method for producing damaged samples in vitro. Despite heat-mediated DNA hydrolysis is being widely used in forensic and clinical validation procedures, the lack of standardized procedures makes it impossible to compare the intra and inter-laboratory outcomes of the damaging treatments. In this work, a systematic approach to heat induced DNA hydrolysis was performed at 70 °C for 0-18 h to test the role both of the hydrolysis buffer and of the experimental conditions. Specifically, a trial DNA sample, resuspended in three different media (ultrapure water, 0.1% DEPC-water and, respectively, TE) was treated both in Eppendorf tubes ("Protocol P") and in Eppendorf tubes provided with screwcaps ("Protocol S"). The results of these comparative tests were assessed by normalization of the qPCR results. DEPC-water increased the degradation of the samples up to about 100 times when compared to the ultrapure water. Conversely, the TE protected the DNA from degradation whose level was about 1700 times lower than in samples treated in ultrapure water. Even the employment of the "Protocol S" affected the level of degradation, by consistently increasing it (up to about 180 times in DEPC-water). Thus, this comparative approach showed that even seemingly apparently trivial and often underestimated parameters modify the degradation level up to 2-3 orders of magnitude. The chemical-physical reasons of these findings are discussed together with the role of potential factors such as enhanced reactivity of CO2, ROS, NOx and pressure, which are likely to be involved. Since the intra and inter-laboratory comparison of the outcomes of the hydrolytic procedure is the first step toward its standardization, the normalization of the qPCR data by the UV/qPCR ratio seems to be the simplest and most reliable way to allow this. Finally, the supplying (provided with the commercial qPCR kits) of a DNA sample whose degree of degradation is well documented could be helpful in ISO/IEC 17025 validation procedures and in proficiency testing.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Italy.
| | | | - Serena Bonin
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy
| | - Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy
| | - Elisa Recchia
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | - Paola Pitacco
- Department of Medicine, Surgery and Health, University of Trieste, Italy
| | - Francesca Procopio
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | | | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Slovenia
| | | | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy
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Fattorini P, Previderé C, Carboni I, Marrubini G, Sorçaburu-Cigliero S, Grignani P, Bertoglio B, Vatta P, Ricci U. Performance of the ForenSeqTMDNA Signature Prep kit on highly degraded samples. Electrophoresis 2017; 38:1163-1174. [DOI: 10.1002/elps.201600290] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/16/2016] [Accepted: 01/02/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Paolo Fattorini
- Department of Medicine; Surgery and Health; University of Trieste; Trieste Italy
| | - Carlo Previderé
- Department of Public Health; Experimental and Forensic Medicine; Section of Legal Medicine and Forensic Sciences; University of Pavia; Pavia Italy
| | | | | | | | - Pierangela Grignani
- Department of Public Health; Experimental and Forensic Medicine; Section of Legal Medicine and Forensic Sciences; University of Pavia; Pavia Italy
| | - Barbara Bertoglio
- Department of Public Health; Experimental and Forensic Medicine; Section of Legal Medicine and Forensic Sciences; University of Pavia; Pavia Italy
| | - Paolo Vatta
- Scuola Internazionale Superiore di Studi Avanzati (SISSA); Functional and Structural Genomics sector; Trieste Italy
| | - Ugo Ricci
- SOD Diagnostica Genetica, A.O-U Careggi; Firenze Italy
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Goecker ZC, Swiontek SE, Lakhtakia A, Roy R. Comparison of Quantifiler ® Trio and InnoQuant™ human DNA quantification kits for detection of DNA degradation in developed and aged fingerprints. Forensic Sci Int 2016; 263:132-138. [DOI: 10.1016/j.forsciint.2016.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/18/2016] [Accepted: 04/07/2016] [Indexed: 10/21/2022]
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Marrubini G, Previderè C, Sorçaburu-Ciglieri S, Grignani P, Pitacco P, Consoloni L, di Cusano CM, Fattorini P. Systematic study on the analytical parameters relevant to achieve reliable STR profiles, as assessed in a multicentre data set. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Carboni I, Fattorini P, Previderè C, Ciglieri SS, Iozzi S, Nutini A, Contini E, Pescucci C, Torricelli F, Ricci U. Evaluation of the reliability of the data generated by Next Generation Sequencing from artificially degraded DNA samples. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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