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Patterson EC, Lall GM, Neumann R, Ottolini B, Sacchini F, Foster AP, Jobling MA, Wetton JH. Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 2023; 67:102944. [PMID: 37820546 DOI: 10.1016/j.fsigen.2023.102944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.r.l., Via Guglielmo Silva, 36-20149 Milano (MI), Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, North Somerset BS40 5DU, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
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2
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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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3
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Harper CK. Poaching Forensics: Animal Victims in the Courtroom. Annu Rev Anim Biosci 2023; 11:269-286. [PMID: 36790886 DOI: 10.1146/annurev-animal-070722-084803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.
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Affiliation(s)
- Cindy K Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa;
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de Groot M, Anderson H, Bauer H, Bauguil C, Bellone RR, Brugidou R, Buckley RM, Dovč P, Forman O, Grahn RA, Kock L, Longeri M, Mouysset‐Geniez S, Qiu J, Sofronidis G, van der Goor LHP, Lyons LA. Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus). Anim Genet 2021; 52:675-682. [PMID: 34143521 PMCID: PMC8519126 DOI: 10.1111/age.13100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 01/02/2023]
Abstract
The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university-based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping-by-sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo-autosomal sexing marker (zinc-finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.
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Affiliation(s)
- M. de Groot
- MolGenTraverse 2VeenendaalUtrecht3905NLThe Netherlands
| | | | - H. Bauer
- Laboklin GMBH & Co. KGBad Kissingen97688Germany
| | | | - R. R. Bellone
- Veterinary Genetics LaboratorySchool of Veterinary MedicineUniversity of CaliforniaDavisCA95616USA
- Population Health and ReproductionSchool of Veterinary MedicineUniversity of CaliforniaDavisCA95616USA
| | | | - R. M. Buckley
- Department of Veterinary Medicine and SurgeryCollege of Veterinary MedicineUniversity of MissouriColumbiaMO65211USA
| | - P. Dovč
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaLjubljana1000Slovenia
| | | | - R. A. Grahn
- Veterinary Genetics LaboratorySchool of Veterinary MedicineUniversity of CaliforniaDavisCA95616USA
| | - L. Kock
- Neogen GenomicsLincolnNE68504USA
| | - M. Longeri
- Department of Veterinary MedicineUniversity of MilanMilan20133Italy
| | | | - J. Qiu
- Neogen GenomicsLincolnNE68504USA
| | - G. Sofronidis
- Orivet Genetic Pet CareSuite St. KildaMelbourneVic.3182Australia
| | | | - L. A. Lyons
- Department of Veterinary Medicine and SurgeryCollege of Veterinary MedicineUniversity of MissouriColumbiaMO65211USA
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Seo D, Cho S, Manjula P, Choi N, Kim YK, Koh YJ, Lee SH, Kim HY, Lee JH. Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs. Animals (Basel) 2021; 11:ani11010241. [PMID: 33477975 PMCID: PMC7835996 DOI: 10.3390/ani11010241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.
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Affiliation(s)
- Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (D.S.); (S.C.); (P.M.); (S.H.L.)
- Bio-AI Convergence Research Center, Chungnam National University, Daejeon 34134, Korea; (Y.-K.K.); (Y.J.K.)
| | - Sunghyun Cho
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (D.S.); (S.C.); (P.M.); (S.H.L.)
- Bio-AI Convergence Research Center, Chungnam National University, Daejeon 34134, Korea; (Y.-K.K.); (Y.J.K.)
| | - Prabuddha Manjula
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (D.S.); (S.C.); (P.M.); (S.H.L.)
| | - Nuri Choi
- SELS Center, Division of Biotechnology, Advanced Institute of Environment and Bioscience, Chonbuk National University, Iksan 54596, Korea;
| | - Young-Kuk Kim
- Bio-AI Convergence Research Center, Chungnam National University, Daejeon 34134, Korea; (Y.-K.K.); (Y.J.K.)
- Department of Computer Science and Engineering, Chungnam National University, Daejeon 34134, Korea
| | - Yeong Jun Koh
- Bio-AI Convergence Research Center, Chungnam National University, Daejeon 34134, Korea; (Y.-K.K.); (Y.J.K.)
- Department of Computer Science and Engineering, Chungnam National University, Daejeon 34134, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (D.S.); (S.C.); (P.M.); (S.H.L.)
- Bio-AI Convergence Research Center, Chungnam National University, Daejeon 34134, Korea; (Y.-K.K.); (Y.J.K.)
| | - Hyung-Yong Kim
- Insilicogen Inc., Yongin 16954, Korea
- Correspondence: (H.-Y.K.); (J.H.L.); Tel.: +82-42-821-5779 (J.H.L.)
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (D.S.); (S.C.); (P.M.); (S.H.L.)
- Bio-AI Convergence Research Center, Chungnam National University, Daejeon 34134, Korea; (Y.-K.K.); (Y.J.K.)
- Correspondence: (H.-Y.K.); (J.H.L.); Tel.: +82-42-821-5779 (J.H.L.)
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Zhang B, Zhao N, Peng K, He X, Chen CX, Liu H, Liu K, Jia L, Bao B. A combination of genome-wide association study screening and SNaPshot for detecting sex-related SNPs and genes in Cynoglossus semilaevis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100711. [PMID: 32683285 DOI: 10.1016/j.cbd.2020.100711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/16/2022]
Abstract
Chinese tongue sole (Cynoglossus semilaevis) males and females exhibit great differences in growth rate and appearance. The species is heterogametic (ZW/ZZ) and has sex-reversed "pseudomales" that are genetically female and physiologically male. In this study, we identified eight sex-specific single nucleotide polymorphism (SNP) markers for the sex identification of C. semilaevis by using a combination of genome-wide association study (GWAS) screening and SnaPshot validation. Candidate SNPs were screened using genotyping by sequencing to perform GWAS of the differential SNPs between the sexes of C. semilaevis. The SNP loci were amplified using a multiplex PCR system and detected via SNaPshot, which enables multiplexing of up to 30-40 SNPs in a single assay and ensures high accuracy of the results. The molecular markers detected in our study were used to successfully identify normal males and pseudomales from 45 caught and 40 cultured C. semilaevis specimens. Linkage disequilibrium analysis showed that the eight SNP loci were related to each other, with a strong linkage. Moreover, we investigated the expression of prdm6 mRNA containing a missense SNP and confirmed that the gene is differentially expressed in the gonads of the different sexes of C. semilaevis; the expression of prdm6 mRNA was significantly higher in the males than in the females and pseudomales. This means prdm6 may be related to sex differentiation in C. semilaevis.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Medicine Biotechnology Co, Ltd, Tianjin, China
| | - Kangkang Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Chun Xiu Chen
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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7
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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