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Kampmann ML, Tfelt-Hansen J, Børsting C. Cleaning protocols in forensic genetic laboratories. Int J Legal Med 2024:10.1007/s00414-024-03232-0. [PMID: 38649547 DOI: 10.1007/s00414-024-03232-0] [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: 01/15/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
It is pivotal to avoid cross-sample contamination in forensic genetic laboratories and optimal cleaning protocols for the removal of DNA are essential. A survey was performed, and ten forensic genetic laboratories shared their cleaning protocols in pre-PCR and post-PCR laboratories. The cleaning frequencies on different surface areas were somewhat similar, whereas none of the laboratories used the same cleaning reagents. Therefore, the efficiencies of the cleaning protocol utilised were tested and compared. The results showed that freshly made household bleach and Virkon® removed all amplifiable DNA from the surfaces, whereas DNA AWAY™ and the disinfection reagents ethanol, isopropanol, and ChemGene HLD4L did not.
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Affiliation(s)
- Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Sullivan HC, Gandhi MJ, Gaitonde S, Narasimhan R, Gendzekhadze K, Pandey S, Roby RK, Maha GC, Kaur H, Schiller JJ, McDowell J, Smith M, Liu C, Morris GP. Seventy-five years of service: an overview of the College of American Pathologists' proficiency testing program in histocompatibility and identity testing. Front Genet 2023; 14:1331169. [PMID: 38169613 PMCID: PMC10758433 DOI: 10.3389/fgene.2023.1331169] [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: 10/31/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
The Histocompatibility and Identity Testing Committee offers an overview of the College of American Pathologists' (CAP) Proficiency Testing (PT) program, commemorating its significant 75th anniversary in 2024. The CAP PT program has undergone significant growth and evolution over the years, ultimately achieving Centers for Medicare and Medicaid Services approval. In 1979, CAP's partnership with the American Association for Clinical Histocompatibility Testing marked a pivotal moment, leading to the creation of the first proficiency testing survey in 1980. This laid the foundation for various PT programs managed by the CAP Histocompatibility and Identity Testing Committee, including HLA antibody testing, HLA molecular typing, engraftment monitoring, parentage/relationship testing, HLA disease associations and drug risk, and HLA-B27 typing. Each program's distinctive considerations, grading methodologies, and future prospects are detailed here, highlighting the continual evolution of histocompatibility and identity testing PT to support emerging technologies and evolving laboratory practices in the field.
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Affiliation(s)
- H. Cliff Sullivan
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Manish J. Gandhi
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Sujata Gaitonde
- Department of Pathology, University of Illinois Chicago, Chicago, IL, United States
| | - Ramya Narasimhan
- Boston University Medical Center, Department of Pathology and Laboratory Medicine, Boston, MA, United States
| | | | - Soumya Pandey
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Rhonda K. Roby
- Alameda County Sheriff’s Office Crime Laboratory, Oakland, CA, United States
| | | | - Harmeet Kaur
- Cuyahoga County Regional Forensic Science Lab, Cleveland, OH, United States
| | | | - Julie McDowell
- College of American Pathologist (CAP), Chicago, IL, United States
| | - Maria Smith
- College of American Pathologist (CAP), Chicago, IL, United States
| | - Chang Liu
- Washington University in St. Louis, Department of Pathology and Immunology, Saint Louis, MO, United States
| | - Gerald P. Morris
- Department of Pathology, Univeristy of California San Diego, San Diego, CA, United States
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Cardinali I, Tancredi D, Lancioni H. The Revolution of Animal Genomics in Forensic Sciences. Int J Mol Sci 2023; 24:ijms24108821. [PMID: 37240167 DOI: 10.3390/ijms24108821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Nowadays, the coexistence between humans and domestic animals (especially dogs and cats) has become a common scenario of daily life. Consequently, during a forensic investigation in civil or criminal cases, the biological material from a domestic animal could be considered "evidence" by law enforcement agencies. Animal genomics offers an important contribution in attacks and episodes of property destruction or in a crime scene where the non-human biological material is linked to the victim or perpetrator. However, only a few animal genetics laboratories in the world are able to carry out a valid forensic analysis, adhering to standards and guidelines that ensure the admissibility of data before a court of law. Today, forensic sciences focus on animal genetics considering all domestic species through the analysis of STRs (short tandem repeats) and autosomal and mitochondrial DNA SNPs (single nucleotide polymorphisms). However, the application of these molecular markers to wildlife seems to have gradually gained a strong relevance, aiming to tackle illegal traffic, avoid the loss of biodiversity, and protect endangered species. The development of third-generation sequencing technologies has glimmered new possibilities by bringing "the laboratory into the field", with a reduction of both the enormous cost management of samples and the degradation of the biological material.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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Weight of evidence of Y-STR matches computed with the discrete Laplace method: Impact of adding a suspect's profile to a reference database. Forensic Sci Int Genet 2023; 64:102839. [PMID: 36731195 DOI: 10.1016/j.fsigen.2023.102839] [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: 08/26/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023]
Abstract
The discrete Laplace method is recommended by multiple parties (including the International Society for Forensic Genetics, ISFG) to estimate the weight of evidence in criminal cases when a suspect's Y-STR profile matches the crime scene Y-STR profile. Unfortunately, modelling the distribution of Y-STR profiles in the population reference database is time-consuming and requires expert knowledge. When the suspect's Y-STR profile is added to the database, as would be the protocol in many cases, the parameters of the discrete Laplace model must be re-estimated. We found that the likelihood ratios with and without adding the suspect's Y-STR profile were almost identical with 1,000 or more Y-STR profiles in the database for Y-STR profiles with 8, 12, and 17 loci. Thus, likelihood ratio calculations can be performed in seconds if an established discrete Laplace model based on at least 1,000 Y-STR profiles is used. A match in a population reference database with 17 Y-STR loci from at least 1,000 male individuals results in a likelihood ratio above 10,000 in approximately 94% of the cases, and above 100,000 in approximately 82% of the cases. We offer free software accessible without restrictions to estimate a discrete Laplace model using a Y-STR reference database and subsequently to calculate likelihood ratios.
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Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing. Int J Legal Med 2023; 137:57-61. [PMID: 36318298 DOI: 10.1007/s00414-022-02901-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.
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Sacco M, Lancellotti S, Branchini A, Tardugno M, Testa MF, Lunghi B, Bernardi F, Pinotti M, Giusti B, Castaman G, De Cristofaro R. The p.P1127S pathogenic variant lowers von Willebrand factor levels through higher affinity for the macrophagic scavenger receptor LRP1: Clinical phenotype and pathogenic mechanisms. J Thromb Haemost 2022; 20:1818-1829. [PMID: 35596664 PMCID: PMC9545986 DOI: 10.1111/jth.15765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/28/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND The index case is a 21-year-old Italian woman with a mild hemorrhagic syndrome and von Willebrand factor antigen (VWF:Ag) = 34.3 U/dl, VWF recombinant glycoprotein Ib (VWF:GpIbR) = 32.8 U/dl, and factor VIII (FVIII) = 55.3 IU/dl. AIMS The aim of this study is to characterize from a genetic and biochemical standpoint this low VWF phenotype. METHODS Coagulation and biochemical methods were used to study the structural and functional pattern of VWF multimers in the index case's plasma. Recombinant wild-type and p.P1127S VWF variants were produced using human embryonic kidney (HEK)-293 cells. In addition, genetic screening was carried out to detect single nucleotide variants of some scavenger VWF/FVIII receptor genes such as CLEC4M, STAB2, and ASGR2. RESULTS Genetic investigation revealed that the index case inherited from her mother the heterozygous missense mutation c.3379C > T (VWF exon 25), causing the p.P1127S substitution in the VWF D'D3 domain. The index case was also homozygous for the scavenger receptor ASGR2 c.-95 CC-genotype. Desmopressin normalized the VWF level of the patient, although its clearance was faster (t1/2 = 6.7 h) than in normal subjects (t1/2 = 12 ± 0.7 h). FVIII-VWF interaction, A Disintegrin And Metalloprotease with ThromboSpondin type 1 motif-13 levels, ristocetin-induced-platelet-aggregation, and VWF multimeric pattern were normal. The p.P1127S variant was normally synthesized and secreted by HEK-293 cells, and molecular modeling predicts a conformational change showing higher affinity for the macrophagic scavenger receptor lipoprotein receptor-related protein 1 (LRP1), as also experimentally verified. CONCLUSIONS The p.P1127S variant may cause a low VWF phenotype, stemming from an increased VWF affinity for the scavenger receptor LRP1 and, consequently, an accelerated clearance of VWF.
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Affiliation(s)
- Monica Sacco
- Dipartimento di Medicina e Chirurgia TraslazionaleFacoltà di Medicina e Chirurgia “Agostino Gemelli,” Università Cattolica S. CuoreRomaItaly
| | - Stefano Lancellotti
- Servizio Malattie Emorragiche e TromboticheFondazione Policlinico Universitario “A. Gemell” IRCCSRomaItaly
| | - Alessio Branchini
- Dipartimento di Scienze della Vita e BiotecnologieUniversità di FerraraFerraraItaly
| | - Maira Tardugno
- Dipartimento di Medicina e Chirurgia TraslazionaleFacoltà di Medicina e Chirurgia “Agostino Gemelli,” Università Cattolica S. CuoreRomaItaly
| | | | - Barbara Lunghi
- Dipartimento di Scienze della Vita e BiotecnologieUniversità di FerraraFerraraItaly
| | - Francesco Bernardi
- Dipartimento di Scienze della Vita e BiotecnologieUniversità di FerraraFerraraItaly
| | - Mirko Pinotti
- Dipartimento di Scienze della Vita e BiotecnologieUniversità di FerraraFerraraItaly
| | - Betti Giusti
- Dipartimento di Medicina Sperimentale e ClinicaUniversità di FirenzeFirenzeItaly
- Laboratorio Genetico Molecolare Avanzato, SOD Malattie AterotromboticheAzienda Ospedaliero‐ Universitaria “Careggi"FirenzeItaly
| | - Giancarlo Castaman
- Dipartimento di Oncologia, Centro Malattie Emorragiche e della CoagulazioneOspedale Universitario “Careggi”FirenzeItaly
| | - Raimondo De Cristofaro
- Dipartimento di Medicina e Chirurgia TraslazionaleFacoltà di Medicina e Chirurgia “Agostino Gemelli,” Università Cattolica S. CuoreRomaItaly
- Servizio Malattie Emorragiche e TromboticheFondazione Policlinico Universitario “A. Gemell” IRCCSRomaItaly
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Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing. PLoS One 2022; 17:e0266332. [PMID: 35363835 PMCID: PMC8974964 DOI: 10.1371/journal.pone.0266332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/19/2022] [Indexed: 11/23/2022] Open
Abstract
Objectives To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) haplotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. Subsequentlly, the paternity testing parameters were attributed to each case quantitatively. Results The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699–99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.
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Dash HR, Vajpayee K, Agarwal R, Gang A, Shukla R, Srivastava A. Evaluation of diallelic STR markers with inter-population allelic database for their usefulness in paternity trios in the Central Indian population. Ann Hum Biol 2021; 48:605-613. [PMID: 34866517 DOI: 10.1080/03014460.2021.2014567] [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] [Indexed: 10/19/2022]
Abstract
BACKGROUND Most of the forensic DNA laboratories have migrated to new generation STR kits of 6 dye chemistry with more than 20 autosomal STRs. The population-specific databases of such STR markers are lacking in many regions. AIM To evaluate the effect of the inter-population database in 100 paternity trios with no inconsistencies at 23 STRs. SUBJECTS AND METHODS 100 paternity trios were evaluated considering inter-population allelic frequency values for calculation of Combined Paternity Index (CPI) and Probability of Paternity (POP). RESULTS No significant variation (p < 0.05) among the allele frequencies at the interpopulation level was observed. The number of obligate alleles and the likelihood of transferring obligate alleles from the putative father showed a positive correlation (p < 0.005) with Power of Discrimination (PD), Polymorphic Information Content (PIC), Power of Exclusion (PE), Paternity Index (PI), Observed and Expected Heterozygosity (Ho and He), and a statistically significant negative correlation (p < 0.005) with Matching Probability (Pm). The average Combined Paternity Index (CPI) and Probability of Paternity (POP) did not show any statistically significant difference (p < 0.05) at the interpopulation level. CONCLUSION The allelic database showed no effect on the CPI and POP in 100 paternity trios. This suggests no urgent need for using population-specific databases for statistical evaluation of paternity trios without inconsistencies.
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Affiliation(s)
| | - Kamayani Vajpayee
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India.,Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India
| | - Anubha Gang
- Regional Forensic Science Laboratory, Indore, India
| | - Ritesh Shukla
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, India
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Noncanonical type 2B von Willebrand disease associated with mutations in the VWF D'D3 and D4 domains. Blood Adv 2020; 4:3405-3415. [PMID: 32722784 DOI: 10.1182/bloodadvances.2020002334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/22/2020] [Indexed: 11/20/2022] Open
Abstract
We observed a 55-year-old Italian man who presented with mucosal and cutaneous bleeding. Results of his blood analysis showed low levels of von Willebrand factor (VWF) antigen and VWF activity (both VWF ristocetin cofactor and VWF collagen binding), mild thrombocytopenia, increased ristocetin-induced platelet aggregation, and a deficiency of high-molecular-weight multimers, all typical phenotypic hallmarks of type 2B von Willebrand disease (VWD). The analysis of the VWF gene sequence revealed heterozygous in cis mutations: (1) c.2771G>A and (2) c.6532G>T substitutions in the exons 21 and 37, respectively. The first mutation causes the substitution of an Arg residue with a Gln at position 924, in the D'D3 domain. The second mutation causes an Ala to Ser substitution at position 2178 in the D4 domain. The patient's daughter did not present the same fatherly mutations but showed only the heterozygous polymorphic c.3379C>T mutation in exon 25 of the VWF gene causing the p.P1127S substitution, inherited from her mother. The in vitro expression of the heterozygous in cis VWF mutant rVWFWT/rVWF924Q-2178S confirmed and recapitulated the ex vivo VWF findings. Molecular modeling showed that these in cis mutations stabilize a partially stretched and open conformation of the VWF monomer. Transmission electron microscopy and atomic force microscopy showed in the heterozygous recombinant form rVWFWT/rVWF924Q-2178S a stretched conformation, forming strings even under static conditions. Thus, the heterozygous in cis mutations 924Q/2178S promote conformational transitions in the VWF molecule, causing a type 2B-like VWD phenotype, despite the absence of typical mutations in the A1 domain of VWF.
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Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives. Forensic Sci Int Genet 2020; 46:102255. [DOI: 10.1016/j.fsigen.2020.102255] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/12/2019] [Accepted: 01/20/2020] [Indexed: 11/22/2022]
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Yuan L, Xu X, Ren H, Zhao Z, Wang T, Hao S, Zhang J, Liu Y, Xu Y. Study of autosomal short tandem repeat loci using ITO method in full-sibling identification. JOURNAL OF FORENSIC SCIENCE AND MEDICINE 2020. [DOI: 10.4103/jfsm.jfsm_4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Mogensen HS, Tvedebrink T, Børsting C, Pereira V, Morling N. Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel. Forensic Sci Int Genet 2020; 44:102154. [DOI: 10.1016/j.fsigen.2019.102154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/25/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
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Non-invasive prenatal paternity testing using a standard forensic genetic massively parallel sequencing assay for amplification of human identification SNPs. Int J Legal Med 2019; 133:1361-1368. [PMID: 31243529 DOI: 10.1007/s00414-019-02106-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023]
Abstract
Prenatal paternity testing often relies on invasive procedures that cause risk to both the mother and the foetus. Non-invasive, prenatal paternity testing by investigating paternally inherited single nucleotide polymorphisms (SNPs) in cell-free foetal DNA (cffDNA) in maternal plasma was performed at consecutive time points during early gestation. Plasma from 15 pregnant women was investigated at consecutive time points from gestational weeks (GWs) 4-20. The Precision ID Identity Panel and an Ion S5 Sequencer was used to analyse the cffDNA. Paternally inherited foetal SNP alleles were detected from GW7. The median foetal fractions were 0%, 3.9%, 5.1%, 5.2%, and 4.7% at GWs 4, 7, 12, 16, and 20, respectively. The corresponding median numbers of detected paternally inherited foetal autosomal SNP alleles were 0, 3, 9, 10, and 12, respectively. The typical (i.e. geometric mean) paternity indices at GW12 and GW20 were 24 (range 0.0035-8389) and 199 (range 5.1-30,137), respectively. The method is very promising. However, the method can be improved by shortening the lengths of the PCR amplicons and increasing the number of SNPs. To our knowledge, this is the first study to successfully identify paternally inherited foetal SNP alleles at consecutive time points in early gestation independently of the foetal gender.
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S B S Silva D, Sawitzki FR, Scheible MKR, Bailey SF, S Alho C, Faith SA. Paternity testing using massively parallel sequencing and the PowerSeq™ AUTO/Y system for short tandem repeat sequencing. Electrophoresis 2018; 39:2669-2673. [PMID: 30132945 DOI: 10.1002/elps.201800072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 06/28/2018] [Accepted: 08/15/2018] [Indexed: 11/09/2022]
Abstract
Massively parallel sequencing (MPS) is gaining attention as a new technology for routine forensic casework, including paternity testing. Recently released MPS multiplex panels provide many more loci compared to CE methods, plus provide sequence-based alleles that together improve the statistical power of the genetic testing. Here, an MPS system (PowerSeq™ AUTO/Y) was applied for STR sequencing in the study of first-degree STR sequence allele inheritance from families in Southern Brazil. In 29 trios (mother-child-father) analyzed, the paternity index values generally increased when data from sequence-based analysis were used in comparison to length-based data. Further, allele inconsistencies (e.g., single repeat mutation events) between child and parents could be resolved with MPS by assessing the core repeat and flanking region sequences. Lastly, the sequence information allowed for identification of isoalleles (alleles of the same size, but different sequence) to determine specific paternal and maternal inheritances. The results from this study showed advantages of implementing sequence-based analysis, MPS, in paternity testing with improved statistical calculations and a greater resolution for the trios/families tested.
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Affiliation(s)
- Deborah S B S Silva
- Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Fernanda R Sawitzki
- Laboratory of Human and Molecular Genetics, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre-RS, Brazil
| | - Melissa K R Scheible
- Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sarah F Bailey
- Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Clarice S Alho
- Laboratory of Human and Molecular Genetics, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre-RS, Brazil
| | - Seth A Faith
- Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
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Gittelson S, Berger CEH, Jackson G, Evett IW, Champod C, Robertson B, Curran JM, Taylor D, Weir BS, Coble MD, Buckleton JS. A response to "Likelihood ratio as weight of evidence: A closer look" by Lund and Iyer. Forensic Sci Int 2018; 288:e15-e19. [PMID: 29857959 PMCID: PMC7306225 DOI: 10.1016/j.forsciint.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/15/2018] [Indexed: 11/24/2022]
Abstract
Recently, Lund and Iyer (L&I) raised an argument regarding the use of likelihood ratios in court. In our view, their argument is based on a lack of understanding of the paradigm. L&I argue that the decision maker should not accept the expert's likelihood ratio without further consideration. This is agreed by all parties. In normal practice, there is often considerable and proper exploration in court of the basis for any probabilistic statement. We conclude that L&I argue against a practice that does not exist and which no one advocates. Further we conclude that the most informative summary of evidential weight is the likelihood ratio. We state that this is the summary that should be presented to a court in every scientific assessment of evidential weight with supporting information about how it was constructed and on what it was based.
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Affiliation(s)
- Simone Gittelson
- Centre for Forensic Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia.
| | - Charles E H Berger
- Leiden University, Institute for Criminal Law and Criminology, P.O. Box 9520, 2300 RA Leiden, The Netherlands
| | - Graham Jackson
- Advance Forensic Science, St. Andrews, Scotland, UK; School of Science, Engineering and Technology, Abertay University, Dundee, Scotland, UK
| | - Ian W Evett
- Principal Forensic Services Ltd., 34 Southborough Road, Bickley, Bromley, Kent BR1 2EB, UK
| | - Christophe Champod
- Ecole des Sciences Criminelles, Faculty of Law, Criminal Justice and Public Administration, Université de Lausanne, Batochime - Quartier Sorge, CH-1015 Lausanne-Dorigny, Switzerland
| | | | - James M Curran
- Department of Statistics, University of Auckland, PB 92019, Auckland, New Zealand
| | - Duncan Taylor
- Forensic Science South Australia, 21 Divett Place, Adelaide, SA 5000, Australia; School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Bruce S Weir
- University of Washington, Department of Biostatistics, Seattle, WA 98195, United States
| | - Michael D Coble
- National Institute of Standards and Technology, Applied Genetics Group, 100 Bureau Drive, Gaithersburg, MD 20899, United States; Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, United States
| | - John S Buckleton
- University of Washington, Department of Biostatistics, Seattle, WA 98195, United States; Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
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Hussing C, Huber C, Bytyci R, Mogensen HS, Morling N, Børsting C. Sequencing of 231 forensic genetic markers using the MiSeq FGx™ forensic genomics system - an evaluation of the assay and software. Forensic Sci Res 2018; 3:111-123. [PMID: 30483659 PMCID: PMC6197110 DOI: 10.1080/20961790.2018.1446672] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
The MiSeq FGx™ Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay. The markers include core forensic short tandem repeats (STRs) as well as identity, ancestry and phenotype informative short nucleotide polymorphisms (SNPs). In this work, the MiSeq FGx™ Forensic Genomics System was evaluated by analysing reproducibility, sensitivity, mixture identification and forensic phenotyping capabilities of the assay. Furthermore, the genotype calling of the ForenSeq™ Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx™ platform using the softwares STRinNGS and GATK. Overall, the performance of the MiSeq FGx™ Forensic Genomics System was high. However, locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances, and the stutter ratios were larger than those observed with conventional STR genotyping methods. The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg. Two-person 50:1 mixtures were identified as mixtures, whereas 100:1 and 1 000:1 mixtures were not. Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100:1 and 1 000:1 female/male mixtures. The ForenSeq™ Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers. Many of the alerts were due to user-defined, locus-specific criteria. The results shown here indicated that the default settings should be altered for some loci. Also, recommended changes to the assay and software are discussed.
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Affiliation(s)
- Christian Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina Huber
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajmonda Bytyci
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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17
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Weight of the evidence of genetic investigations of ancestry informative markers. Theor Popul Biol 2018; 120:1-10. [DOI: 10.1016/j.tpb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 01/03/2023]
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18
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García-Aceves ME, Romero Rentería O, Díaz-Navarro XX, Rangel-Villalobos H. Paternity tests in Mexico: Results obtained in 3005 cases. J Forensic Leg Med 2018; 55:1-7. [PMID: 29433009 DOI: 10.1016/j.jflm.2018.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/25/2018] [Accepted: 02/04/2018] [Indexed: 11/28/2022]
Abstract
National and international reports regarding the paternity testing activity scarcely include information from Mexico and other Latin American countries. Therefore, we report different results from the analysis of 3005 paternity cases analyzed during a period of five years in a Mexican paternity testing laboratory. Motherless tests were the most frequent (77.27%), followed by trio cases (20.70%); the remaining 2.04% included different cases of kinship reconstruction. The paternity exclusion rate was 29.58%, higher but into the range reported by the American Association of Blood Banks (average 24.12%). We detected 65 mutations, most of them involving one-step (93.8% and the remaining were two-step mutations (6.2%) thus, we were able to estimate the paternal mutation rate for 17 different STR loci: 0.0018 (95% CI 0.0005-0.0047). Five triallelic patterns and 12 suspected null alleles were detected during this period; however, re-amplification of these samples with a different Human Identification (HID) kit confirmed the homozygous genotypes, which suggests that most of these exclusions actually are one-step mutations. HID kits with ≥20 STRs detected more exclusions, diminishing the rate of inconclusive results with isolated exclusions (<3 loci), and leading to higher paternity indexes (PI). However, the Powerplex 21 kit (20 STRs) and Powerplex Fusion kit (22 STRs) offered similar PI (p = 0.379) and average number of exclusions (PE) (p = 0.339) when a daughter was involved in motherless tests. In brief, besides to report forensic parameters from paternity tests in Mexico, results describe improvements to solve motherless paternity tests using HID kits with ≥20 STRs instead of one including 15 STRs.
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Affiliation(s)
- M E García-Aceves
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCiénega-UdeG), Av Universidad 1115, Paso Blanco, 47810 Ocotlán, Jalisco, Mexico; Doctorado en Genética Humana, Universidad de Guadalajara (CU Ciencias de la Salud), Sierra Mojada 950, Independencia, 44348, Guadalajara, Jalisco, Mexico
| | - O Romero Rentería
- DNA Profile SC, Laboratorio de Genética, Jamaica 90, Col. El Rosario, Ocotlán, Jalisco, Mexico
| | - X X Díaz-Navarro
- DNA Profile SC, Laboratorio de Genética, Jamaica 90, Col. El Rosario, Ocotlán, Jalisco, Mexico
| | - H Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCiénega-UdeG), Av Universidad 1115, Paso Blanco, 47810 Ocotlán, Jalisco, Mexico.
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19
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Santoro C, Giugliano T, Bifano D, D'Anna C, D'Onofrio V, Perrotta S. From Gardner fibroma diagnosis to constitutional APC mutation detection: a one-way street. Clin Case Rep 2017; 5:1557-1560. [PMID: 29026543 PMCID: PMC5628198 DOI: 10.1002/ccr3.1065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 05/29/2017] [Accepted: 06/07/2017] [Indexed: 12/29/2022] Open
Abstract
We report a young child without a family history of FAP, who promptly underwent APC testing after the histological confirmation of a paraspinal GAF that was not isolated. Our case report reinforces the suggestion advanced by previous authors for an APC analysis in all patients with GAF.
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Affiliation(s)
- Claudia Santoro
- Dipartimento della Donnadel Bambino e della Chirurgia generale e specialistica Università degli Studi della Campania Luigi Vanvitelli Naples Italy
| | - Teresa Giugliano
- Dipartimento di Biochimica Biofisica e Patologia Generale Università degli Studi della Campania Luigi Vanvitelli Naples Italy.,Telethon Institute of Genetics and Medicine Pozzuoli Italy
| | - Delfina Bifano
- Department of Anatomopathology Santobono-Pausilipon Children's Hospital Naples Italy
| | - Carolina D'Anna
- Department of Pediatric Emergency Santobono-Pausilipon Children's Hospital Naples Italy
| | - Vittoria D'Onofrio
- Department of Anatomopathology Santobono-Pausilipon Children's Hospital Naples Italy
| | - Silverio Perrotta
- Dipartimento della Donnadel Bambino e della Chirurgia generale e specialistica Università degli Studi della Campania Luigi Vanvitelli Naples Italy
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Li H, Zhao X, Ma K, Cao Y, Zhou H, Ping Y, Shao C, Xie J, Liu W. Applying massively parallel sequencing to paternity testing on the Ion Torrent Personal Genome Machine. Forensic Sci Int Genet 2017; 31:155-159. [PMID: 28946114 DOI: 10.1016/j.fsigen.2017.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 11/30/2022]
Abstract
Massively parallel sequencing (MPS) is a promising supplementary method for forensic genetics and has gradually been applied to forensic casework. In this study, we applied MPS to forensic casework on an Ion Torrent Personal Genome Machine to evaluate its performance in paternity testing with mismatched STR loci. A total of 15 samples from seven cases containing one mismatched locus by capillary electrophoresis typing were analyzed. Combined paternity index (CPI) and relative chance of paternity were calculated according to the International Society for Forensic Genetics guidelines and the Chinese national standards recommended for paternity testing. With simultaneous analysis of enough STR loci, the results support the certainty of paternity, and the mismatched alleles were considered to be mutations (CPI>10,000). With the detection of allele sequence structures, the origins of the mutations were inferred in some cases. Meanwhile, nine STRs (CSF1PO, D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D12S391, D21S11 and D4S2408) were found in an increased number of unique alleles and three new alleles in three STRs (D2S441, D21S11, and FGA) that have not been reported before were detected. Therefore, MPS can provide valuable information for forensic genetics research and play a promising role in paternity testing.
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Affiliation(s)
- Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
| | - Xueying Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Huaigu Zhou
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Yuan Ping
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Chengchen Shao
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
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21
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Yuan L, Xu X, Zhao D, Ren H, Hu C, Chen W, Hao S, Lu D, Zhang L. Study of autosomal STR loci with IBS method in full sibling identification. Leg Med (Tokyo) 2017; 26:14-17. [PMID: 28549542 DOI: 10.1016/j.legalmed.2017.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 01/25/2017] [Accepted: 01/31/2017] [Indexed: 10/20/2022]
Abstract
OBJECTIVE We investigated the application of 51 autosomal short tandem repeat (STR) loci with the identity by state (IBS) method and a discriminant function algorithm in full-sib identification. METHODS A total of 342 pairs of full sibs (FSs) and 3900 pairs of unrelated individuals (UIs) were genotyped for 51 STR loci. Groups were formed in accordance with discrimination power (DP) values and the number of loci, and IBS scores of FSs and UIs were analyzed and compared. The discriminant functions of FS-UI were determined by using the Fisher discriminant with SPSS software. RESULTS All IBS in FSs and UIs groups showed normal distributions and there were significant differences between FS-UI. Receiver operating characteristic curves revealed that the detection efficiency of full-sib identification was affected by both the locus polymorphism and the number of loci detected. Comparing the rate of false positive and false negative of discriminant function between groups, a higher average DP value and larger number of loci detected were associated with a lower rate of miscarriage of justice and were more helpful for full-sib identification. CONCLUSION STRs with higher DP values should be selected when additional autosomal markers are required for FS identification. Discriminant analysis with the IBS method is highly applicable for the FS-UI test.
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Affiliation(s)
- Li Yuan
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, PR China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, PR China.
| | - Xu Xu
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, PR China
| | - Dong Zhao
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, PR China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, PR China
| | - He Ren
- Beijing Police College, Beijing 102022, PR China
| | - Chaohui Hu
- College of Mathematics and Computer Science, Hunan Normal University, Changsha 410081, PR China
| | - Wen Chen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, PR China
| | - Shicheng Hao
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, PR China
| | - Di Lu
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, PR China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, PR China
| | - Lin Zhang
- West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
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22
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Pereira V, Mogensen HS, Børsting C, Morling N. Evaluation of the Precision ID Ancestry Panel for crime case work: A SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet 2017; 28:138-145. [DOI: 10.1016/j.fsigen.2017.02.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
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23
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He GL, Chen PY, Gao B, Han YY, Zou X, Song F, Yan J, Hou YP. Phylogenetic analysis among 27 Chinese populations and genetic polymorphisms of 20 autosomal STR loci in a Chinese Uyghur ethnic minority group. AUST J FORENSIC SCI 2017. [DOI: 10.1080/00450618.2016.1275793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Guang-Lin He
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
| | - Peng-Yu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University , Zunyi, China
- Department of Forensic Medicine, Zunyi Medical University , Zunyi, China
| | - Bo Gao
- Institute of Forensic Science, Yili Public Security Bureau of Xinjiang , Kuitun, China
| | - Yan-Yan Han
- Department of Nutrition and Food Hygiene, School of Public Health, Zunyi Medical University , Zunyi, China
| | - Xing Zou
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University , Chongqing, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
| | - Jing Yan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
| | - Yi-Ping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
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24
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Chen J, Xie B, Yang Y, Yang M, Liu C, Lv Y, Chen C, Liu X, Fang X, Wu H, Yan J. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea. Ann Hum Biol 2016; 44:467-474. [PMID: 27670224 DOI: 10.1080/03014460.2016.1241300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. AIM The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. SUBJECTS AND METHODS Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. RESULTS A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10-38. CONCLUSION The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.
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Affiliation(s)
- Jing Chen
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Bingbing Xie
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Yaran Yang
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Meng Yang
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Chao Liu
- b Guangzhou Forensic Science Institute , Guangdong , PR China
| | - Yuexin Lv
- c Beijing Microread Genetics Co., Ltd , Beijing , PR China
| | - Chuguang Chen
- c Beijing Microread Genetics Co., Ltd , Beijing , PR China
| | - Xu Liu
- d Beijing Center for Physical and Chemical Analysis , Beijing , PR China.,e Beijing Engineering Technology Research Center of Gene Sequencing and Gene Function Analysis , Beijing , PR China
| | - Xiangdong Fang
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Huijuan Wu
- d Beijing Center for Physical and Chemical Analysis , Beijing , PR China.,e Beijing Engineering Technology Research Center of Gene Sequencing and Gene Function Analysis , Beijing , PR China
| | - Jiangwei Yan
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
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25
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Coble M, Buckleton J, Butler J, Egeland T, Fimmers R, Gill P, Gusmão L, Guttman B, Krawczak M, Morling N, Parson W, Pinto N, Schneider P, Sherry S, Willuweit S, Prinz M. DNA Commission of the International Society for Forensic Genetics: Recommendations on the validation of software programs performing biostatistical calculations for forensic genetics applications. Forensic Sci Int Genet 2016; 25:191-197. [DOI: 10.1016/j.fsigen.2016.09.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
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26
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Jin B, Su Q, Luo H, Li Y, Wu J, Yan J, Hou Y, Liang W, Zhang L. Mutational analysis of 33 autosomal short tandem repeat (STR) loci in southwest Chinese Han population based on trio parentage testing. Forensic Sci Int Genet 2016; 23:86-90. [DOI: 10.1016/j.fsigen.2016.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/17/2016] [Accepted: 03/28/2016] [Indexed: 11/27/2022]
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27
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Gou H, Zhou J, Zhang Y, Wang C, Ma X, Ma H, Li S, Hu X, Shang M, Zhang J, Wang M, Zhou Y, Ye Y, Song X, Wang J, Lu X, Ying B. Allele frequency distribution of 21 forensic autosomal STR loci of Goldeneye™ DNA ID 22NC Kit in Chinese Tibetan group. Forensic Sci Int Genet 2016; 22:e21-e24. [PMID: 26961075 DOI: 10.1016/j.fsigen.2016.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Haimei Gou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Yuwei Zhang
- Department of Endocrinology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Chunwei Wang
- Department of Clinical Laboratory Medicine, Qinghai Red Cross Hospital, Xining 810000, Qinghai Province, PR China
| | - Xiaoyan Ma
- Department of Clinical Laboratory Medicine, Qinghai Red Cross Hospital, Xining 810000, Qinghai Province, PR China
| | - Huiying Ma
- Department of Clinical Laboratory Medicine, Qinghai Red Cross Hospital, Xining 810000, Qinghai Province, PR China
| | - Shengmei Li
- Department of Clinical Laboratory Medicine, Qinghai Red Cross Hospital, Xining 810000, Qinghai Province, PR China
| | - Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Mengqiao Shang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Jingya Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Yi Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Yuanxin Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Jun Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Xiaojun Lu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, PR China.
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28
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Yuan L, Liu H, Liao Q, Xu X, Chen W, Hao S. Genetics analysis of 38 STR loci in Uygur population from Southern Xinjiang of China. Int J Legal Med 2015; 130:687-8. [PMID: 26438047 DOI: 10.1007/s00414-015-1270-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/25/2015] [Indexed: 11/30/2022]
Abstract
The allele frequencies and statistical parameters of 38 autosomal short tandem repeat (STR) loci were analyzed in the Uygur population from Southern Xinjiang of China with 290 unrelated individuals. The results show these 38 STR loci have high or medium power of discrimination and probabilities of exclusion. All loci are in Hardy-Weinberg equilibrium. The genetic distances between the Uygur population and other Chinese populations were also estimated.
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Affiliation(s)
- Li Yuan
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, People's Republic of China. .,Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, People's Republic of China.
| | - Haibo Liu
- Institute of Forensic Science, Bingtuan Public Security Bureau, Urumqi, 830000, People's Republic of China
| | - Qinxiang Liao
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, People's Republic of China
| | - Xu Xu
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, People's Republic of China
| | - Wen Chen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, People's Republic of China
| | - Shicheng Hao
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, People's Republic of China
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29
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Tamura T, Osawa M, Ochiai E, Suzuki T, Nakamura T. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis. Leg Med (Tokyo) 2015; 17:320-5. [DOI: 10.1016/j.legalmed.2015.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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30
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U.S. initiatives to strengthen forensic science & international standards in forensic DNA. Forensic Sci Int Genet 2015; 18:4-20. [PMID: 26164236 PMCID: PMC4573542 DOI: 10.1016/j.fsigen.2015.06.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/15/2015] [Accepted: 06/24/2015] [Indexed: 11/23/2022]
Abstract
A number of initiatives are underway in the United States in response to the 2009 critique of forensic science by a National Academy of Sciences committee. This article provides a broad review of activities including efforts of the White House National Science and Technology Council Subcommittee on Forensic Science and a partnership between the Department of Justice (DOJ) and the National Institute of Standards and Technology (NIST) to create the National Commission on Forensic Science and the Organization of Scientific Area Committees. These initiatives are seeking to improve policies and practices of forensic science. Efforts to fund research activities and aid technology transition and training in forensic science are also covered. The second portion of the article reviews standards in place or in development around the world for forensic DNA. Documentary standards are used to help define written procedures to perform testing. Physical standards serve as reference materials for calibration and traceability purposes when testing is performed. Both documentary and physical standards enable reliable data comparison, and standard data formats and common markers or testing regions are crucial for effective data sharing. Core DNA markers provide a common framework and currency for constructing DNA databases with compatible data. Recent developments in expanding core DNA markers in Europe and the United States are discussed.
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Perrotta S, Di Iorgi N, Ragione FD, Scianguetta S, Borriello A, Allegri AEM, Ferraro M, Santoro C, Napoli F, Calcagno A, Giaccardi M, Cappa M, Salerno MC, Cozzolino D, Maghnie M. Early-onset central diabetes insipidus is associated with de novo arginine vasopressin-neurophysin II or Wolfram syndrome 1 gene mutations. Eur J Endocrinol 2015; 172:461-72. [PMID: 25740874 DOI: 10.1530/eje-14-0942] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Idiopathic early-onset central diabetes insipidus (CDI) might be due to mutations of arginine vasopressin-neurophysin II (AVP-NPII (AVP)) or wolframin (WFS1) genes. DESIGN AND METHODS Sequencing of AVP and WFS1 genes was performed in nine children with CDI, aged between 9 and 68 months, and negative family history for polyuria and polydipsia. RESULTS Two patients carried a mutation in the AVP gene: a heterozygous G-to-T transition at nucleotide position 322 of exon 2 (c.322G>T) resulting in a stop codon at position 108 (p.Glu108X), and a novel deletion from nucleotide 52 to 54 (c.52_54delTCC) producing a deletion of a serine at position 18 (p.Ser18del) of the AVP pre-prohormone signal peptide. A third patient carried two heterozygous mutations in the WFS1 gene localized on different alleles. The first change was A-to-G transition at nucleotide 997 in exon 8 (c.997A>G), resulting in a valine residue at position 333 in place of isoleucine (p.Ile333Val). The second novel mutation was a 3 bp insertion in exon 8, c.2392_2393insACG causing the addition of an aspartate residue at position 797 and the maintenance of the correct open reading frame (p. Asp797_Val798insAsp). While similar WFS1 protein levels were detected in fibroblasts from healthy subjects and from the patient and his parents, a major sensitivity to staurosporine-induced apoptosis was observed in the patient fibroblasts as well as in patients with Wolfram syndrome. CONCLUSIONS Early-onset CDI is associated with de novo mutations of the AVP gene and with hereditary WFS1 gene changes. These findings have valuable implications for management and genetic counseling.
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Affiliation(s)
- Silverio Perrotta
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Natascia Di Iorgi
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Fulvio Della Ragione
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Saverio Scianguetta
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Adriana Borriello
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Anna Elsa Maria Allegri
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Marcella Ferraro
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Claudia Santoro
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Flavia Napoli
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Annalisa Calcagno
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Marta Giaccardi
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Marco Cappa
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Maria Carolina Salerno
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Domenico Cozzolino
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
| | - Mohamad Maghnie
- Dipartimento della Donnadel Bambino e di Chirurgia Generale e Specialistica, Second University of Naples, via De Crecchio 4, Naples, ItalyIstituto Giannina GasliniUniversity of Genova, 16147 Genova, ItalyDepartment of BiochemistryBiophysics, and General Pathology, Second University of Naples, via De Crecchio 7, Naples, ItalyIstituto Giannina GasliniLargo Gerolamo Gaslini 5, 16147 Genova, ItalyUnit of Endocrinology and DiabetologyBambino Gesù Children's Hospital, IRCCS, Rome, ItalyPediatric Endocrinology UnitDepartment of Translational Medical Sciences, University 'Federico II' of Naples, Naples, ItalyDivision of Internal MedicineSecond University of Naples, 80100 Naples, Italy
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Aufgaben und Struktur des Faches. Rechtsmedizin (Berl) 2015. [DOI: 10.1007/978-3-662-43500-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yuan L, Ou Y, Liao Q, Gui J, Bai X, Ge J, Ye J, Zhang L. Population genetics analysis of 38 STR loci in the She population from Fujian Province of China. Leg Med (Tokyo) 2014; 16:314-8. [DOI: 10.1016/j.legalmed.2014.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 04/15/2014] [Accepted: 05/23/2014] [Indexed: 11/30/2022]
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Lindner I, von Wurmb-Schwark N, Meier P, Fimmers R, Büttner A. Usefulness of SNPs as Supplementary Markers in a Paternity Case with 3 Genetic Incompatibilities at Autosomal and Y Chromosomal Loci. Transfus Med Hemother 2014; 41:117-21. [PMID: 24847187 PMCID: PMC4025154 DOI: 10.1159/000357989] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In kinship testing, investigation of 15 short tandem repeats (STRs) usually provides decisive genetic information for resolving relationship cases. However, in complex deficiency cases, in cases with more than 2 mutations at different STR loci or when close (untested) relatives of the alleged father are suggested to be the biological father of the child, STR typing alone may not be sufficient. In these cases, the application of supplementary markers such as single nucleotide polymorphisms (SNPs) is recommended. METHODS We describe a paternity case with 3 genetic incompatibilities (Penta D, VWA, and DYS385) between the alleged father and the child after analyzing 23 autosomal and 16 Y chromosomal STR loci. The question arose as to whether the alleged father could be excluded and a related person could be the biological father of the child, or whether the observed genetic incompatibilities were mutations. Interestingly, the 2 excluded full brothers of the alleged father possessed identical genetic incompatibilities at locus VWA and DYS385 as the alleged father. RESULTS AND CONCLUSIONS Additional performance of a 50-plex SNP assay demonstrated that the observed mismatches were indeed mutations and the alleged father was the biological father of the child. The results show the usefulness of SNPs as supplementary markers in relationship testing when STR analyses show ambiguous results.
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Affiliation(s)
- Iris Lindner
- Institute of Legal Medicine, University of Rostock, Kiel, Germany
| | | | - Patrick Meier
- Institute of Legal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rolf Fimmers
- Institute for Medical Biometry, Informatics and Epidemiology, Rheinische Friedrich Wilhelms University Bonn, Germany
| | - Andreas Büttner
- Institute of Legal Medicine, University of Rostock, Kiel, Germany
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A report of the 2009–2011 paternity and relationship testing workshops of the English Speaking Working Group of the International Society For Forensic Genetics. Forensic Sci Int Genet 2014; 9:e1-2. [DOI: 10.1016/j.fsigen.2013.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/09/2013] [Indexed: 11/18/2022]
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36
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Geserick G, Wirth I. Ein Jahrhundert hämogenetische Abstammungsbegutachtung. Rechtsmedizin (Berl) 2013. [DOI: 10.1007/s00194-013-0883-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Estimating Y-STR allelic drop-out rates and adjusting for interlocus balances. Forensic Sci Int Genet 2013; 7:327-36. [DOI: 10.1016/j.fsigen.2013.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 01/17/2013] [Accepted: 01/28/2013] [Indexed: 11/18/2022]
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38
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Polymorphic analysis of 21 new STR loci in Chinese Uigur group. Forensic Sci Int Genet 2013; 7:e97-8. [DOI: 10.1016/j.fsigen.2013.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 01/21/2013] [Accepted: 02/23/2013] [Indexed: 11/22/2022]
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Huang YM, Wang J, Jiao Z, Yang L, Zhang X, Tang H, Liu Y. Assessment of application value of 19 autosomal short tandem repeat loci of GoldenEyeTM 20A kit in forensic paternity testing. Int J Legal Med 2013; 127:587-90. [DOI: 10.1007/s00414-013-0842-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 02/25/2013] [Indexed: 11/24/2022]
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Builes J, Castro J, Velilla C, Manrique A, Aguirre D, Mendoza L, Bravo M, Gusmão L. Results of Colombian exercise interlaboratory quality control 2012. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gill P, Gusmão L, Haned H, Mayr WR, Morling N, Parson W, Prieto L, Prinz M, Schneider H, Schneider PM, Weir BS. DNA commission of the International Society of Forensic Genetics: Recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods. Forensic Sci Int Genet 2012; 6:679-88. [PMID: 22864188 DOI: 10.1016/j.fsigen.2012.06.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/03/2012] [Indexed: 11/19/2022]
Abstract
DNA profiling of biological material from scenes of crimes is often complicated because the amount of DNA is limited and the quality of the DNA may be compromised. Furthermore, the sensitivity of STR typing kits has been continuously improved to detect low level DNA traces. This may lead to (1) partial DNA profiles and (2) detection of additional alleles. There are two key phenomena to consider: allelic or locus 'drop-out', i.e. 'missing' alleles at one or more genetic loci, while 'drop-in' may explain alleles in the DNA profile that are additional to the assumed main contributor(s). The drop-in phenomenon is restricted to 1 or 2 alleles per profile. If multiple alleles are observed at more than two loci then these are considered as alleles from an extra contributor and analysis can proceed as a mixture of two or more contributors. Here, we give recommendations on how to estimate probabilities considering drop-out, Pr(D), and drop-in, Pr(C). For reasons of clarity, we have deliberately restricted the current recommendations considering drop-out and/or drop-in at only one locus. Furthermore, we offer recommendations on how to use Pr(D) and Pr(C) with the likelihood ratio principles that are generally recommended by the International Society of Forensic Genetics (ISFG) as measure of the weight of the evidence in forensic genetics. Examples of calculations are included. An Excel spreadsheet is provided so that scientists and laboratories may explore the models and input their own data.
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Affiliation(s)
- P Gill
- Norwegian Institute of Public Health, Oslo, Norway.
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Geserick G, Wirth I. Genetic Kinship Investigation from Blood Groups to DNA Markers. Transfus Med Hemother 2012; 39:163-175. [PMID: 22851931 PMCID: PMC3375130 DOI: 10.1159/000338850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 04/03/2012] [Indexed: 11/19/2022] Open
Abstract
The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation.
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Affiliation(s)
- Gunther Geserick
- Berlin, Police Academy of the State of Brandenburg, Oranienburg, Germany
| | - Ingo Wirth
- Police Academy of the State of Brandenburg, Oranienburg, Germany
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Schneider PM. Beyond STRs: The Role of Diallelic Markers in Forensic Genetics. ACTA ACUST UNITED AC 2012; 39:176-180. [PMID: 22851932 DOI: 10.1159/000339139] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 04/17/2012] [Indexed: 11/19/2022]
Abstract
Short tandem repeat (STR) polymorphisms have been firmly established as standard DNA marker systems since more than 15 years both in forensic stain typing as well as in paternity and kinship testing. However, when analyzing genetic relationships in deficiency cases, STRs have a couple of disadvantages due to the sometimes poor biostatistical efficiency as well as the possibility to observe one or more genetic inconsistencies that could also be explained by mutational events. In such situations, additional robust markers with negligible mutations rates such as single nucleotide polymorphisms (SNPs) and insertion/deletion markers (indels) can be used as adjuncts to provide decisive genetic information in favor for or against the assumed relationship. Both SNPs and indels can now be typed more easily using multiplexes of up to 50 loci based on fragment length analysis on instruments available in all routine forensic and paternity testing laboratories, thus making it possible to extend the range of markers beyond the currently used STRs.
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Affiliation(s)
- Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Germany
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Børsting C, Tomas C, Morling N. Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing. Methods Mol Biol 2012; 830:87-107. [PMID: 22139655 DOI: 10.1007/978-1-61779-461-2_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
We describe a method for simultaneous amplification of 49 autosomal single nucleotide polymorphisms (SNPs) by multiplex PCR and detection of the SNP alleles by single base extension (SBE) and capillary electrophoresis. All the SNPs may be amplified from only 100 pg of genomic DNA and the length of the amplicons range from 65 to 115 bp. The high sensitivity and the short amplicon sizes make the assay very suitable for typing of degraded DNA samples, and the low mutation rate of SNPs makes the assay very useful for relationship testing. Combined, these advantages make the assay well suited for disaster victim identifications, where the DNA from the victims may be highly degraded and the victims are identified via investigation of their relatives. The assay was validated according to the ISO 17025 standard and used for routine case work in our laboratory.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
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Yuan L, Ge J, Lu D, Yang X. Population data of 21 non-CODIS STR loci in Han population of northern China. Int J Legal Med 2012; 126:659-64. [DOI: 10.1007/s00414-011-0664-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/27/2011] [Indexed: 11/29/2022]
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Abstract
Genetic testing holds many promises in movement disorders, but also pitfalls that require careful consideration for meaningful results. These include the primary indication for testing in the first place, concerns regarding the implications of symptomatic, presymptomatic, and susceptibility testing, the mutation frequency in the gene of interest, the general lack of neuroprotective treatment options for neurodegenerative movement disorders, the prognosis of the condition diagnosed, and patient confidentiality concerns. Furthermore, new technical achievements and the available technical expertise, feasibility of specific gene testing, and its coverage through a health insurance carrier should be considered. Guidelines for testing have been established by some disease societies to advise clinicians and in parallel legal regulations are being adjusted at a national and international level. We review these and other critical points and recent developments regarding genetic testing in the field of movement disorders.
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Monies D, Abu Al Saud N, Sahar N, Meyer BF. Population studies and parentage testing for Arabian horses using 15 microsatellite markers. Anim Genet 2011; 42:225-6. [PMID: 24725232 DOI: 10.1111/j.1365-2052.2010.02103.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- D Monies
- Department of Genetics, KFSH&RC, Riyadh, Saudi Arabia.Biostatistics, Epidemiology & Scientific Computing, KFSH&RC, Riyadh, Saudi Arabia
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Linacre A, Gusmão L, Hecht W, Hellmann AP, Mayr WR, Parson W, Prinz M, Schneider PM, Morling N. ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. Forensic Sci Int Genet 2010; 5:501-5. [PMID: 21106449 DOI: 10.1016/j.fsigen.2010.10.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/30/2010] [Indexed: 10/18/2022]
Abstract
The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only.
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Affiliation(s)
- A Linacre
- School of Biology, Flinders University, Adelaide, Australia.
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49
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Børsting C, Rockenbauer E, Morling N. Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard. Forensic Sci Int Genet 2009; 4:34-42. [DOI: 10.1016/j.fsigen.2009.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 04/03/2009] [Accepted: 04/09/2009] [Indexed: 11/25/2022]
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50
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Lancia M, Coletti A, Dobosz M, Carnevali E, Massetti S, Merigioli S, Carlini L. Analysis of complex family cases with probabilistic expert systems. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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