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Hu W, Zhou H, Li J, Yuan P, Zhang L, Liu X, Yan J. Visual identification for species and sex derived from bloodstain based on phosphate-mediated isothermal amplification colorimetric system. Talanta 2024; 275:126149. [PMID: 38678926 DOI: 10.1016/j.talanta.2024.126149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Species and sex confirmation of the biological specimen play a crucial role in crime investigation. However, the specimen found in the scene is always trace quantity, which is hard to be analyzed by current methods. Moreover, the time-consuming DNA extraction, sophisticated apparatus, and complex data processing make it difficult to satisfy the demand of speediness and convenience for point-of-care tests. In this study, we first exhibit a phosphate-based visual system for field-based species and sex identification derived from trace bloodstain. By introducing phosphate ion-based colorimetry into loop-mediated isothermal amplification (LAMP) for result interpretation, not only the bloodstain can be directly submitted to mitochondrial variant amplification owing to the enhanced amplification efficiency by pyrophosphate ion hydrolyzation, but also the colorimetric signal can be recognized by the naked eye for result output within 30 min through molybdophosphate generation. Aerosol contamination, the major conflict of LAMP, has been solved once and for all by integrating uracil-DNA glycosylase into this system that still holds on a constant temperature. As a demonstration, cytochrome b and Y-chromosomal amelogenin are employed to identify species and sex respectively, which has achieved a highly sensitive and specific distinguishability under a strong interferential background. Accurate results can be obtained from both the simulative degraded and dated specimen, which indicates that this novel system may serve as a promising tool in forensic practice.
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Affiliation(s)
- Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Huyun Zhou
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Xiaonan Liu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China.
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Pedroza Matute S, Turvey K, Iyavoo S. Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study. Forensic Sci Int Genet 2024; 71:103049. [PMID: 38653142 DOI: 10.1016/j.fsigen.2024.103049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel's performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.
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Affiliation(s)
| | - Kiera Turvey
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom
| | - Sasitaran Iyavoo
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom; School of Chemistry, College of Health and Science, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, United Kingdom.
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Rogers LM, Halcrow SE, Kleffmann T, King CL. Comparing Walker's (2008) skull trait sex estimation standard to proteomic sex estimation for a group of South Asian individuals. Forensic Sci Int Synerg 2024; 8:100450. [PMID: 38314398 PMCID: PMC10837481 DOI: 10.1016/j.fsisyn.2023.100450] [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: 10/19/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 02/06/2024]
Abstract
This research assesses the potential for misidentification of sex in individuals of South Asian ancestry using the Walker (2008) morphological skull sex estimation standard [1]. Chromosomal sex was assessed using proteomic analysis targeting sex chromosome-specific amylogenic peptides. Results showed that the Walker method produced incorrect classification for 36.7 % of individuals. Overwhelmingly, those incorrectly assigned were chromosomally male. Misidentification was due to males within the group having lower trait scores (i.e., more gracile traits) than the standard would predict. There was also a high level of overlap in trait scores between male and females indicating reduced expression of sexual dimorphism. The use of established multivariate statistical techniques improved accuracy of sex estimation in some cases, but larger osteological data sets from South Asian individuals are required to develop population-specific standards. We suggest that peptide analysis may provide a useful tool for the forensic anthropologist when assessing sex in populations without population specific osteological standards.
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Affiliation(s)
- Laura M Rogers
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Siân E Halcrow
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Charlotte L King
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Lai L, Huang XL, Mei DR, Li Y, Wu YC. Analysis of a Yp11.2 region deletion in a Chinese female with Turner syndrome: A case report. Heliyon 2023; 9:e15162. [PMID: 37089332 PMCID: PMC10113852 DOI: 10.1016/j.heliyon.2023.e15162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
In recent years, an increasing number of abnormal DNA genotypes caused by chromosomal abnormalities have been revealed in cases of individual identification and sex-typing analysis, especially analyses of the amelogenin and short tandem repeat (STR) loci on the sex chromosomes. Here, we report a 17-year-old female with Turner syndrome typed as male due to the presence of the amelogenin Y allele. The Y-STR haplotype showed allele dropout of three Y-STR loci (DYS549, DYS392 and DYS448). Further examination showed that the proband's karyotype was 45,X/46,X,del(Y) (q11.23), and the deletion of the Yp11.2 region was confirmed to encompass the observed microdeletion of the azoospermia factor (AZF)b + c region. One challenge in forensics is inaccurate sex typing of individuals at the molecular level, particularly for individuals with chromosomal abnormalities. This case suggests that various medical evaluations, including the examination of sex-related manifestations, karyotypes, and clinical phenotypes of individuals, along with the detection of sex-typing gene markers will be beneficial to overcome the issues caused by cytogenetic disorders of the sex chromosomes.
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Burgos G, Barrionuevo-Pérez K, Restrepo T, Tejera E, de Waard JH, Garzón-Salazar A, Gusmão L. High-performance LAMP-based method for human sex identification using Y chromosome-specific genetic markers. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Cranial and Odontological Methods for Sex Estimation—A Scoping Review. Medicina (B Aires) 2022; 58:medicina58091273. [PMID: 36143950 PMCID: PMC9505889 DOI: 10.3390/medicina58091273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
The estimation of sex from osteological and dental records has long been an interdisciplinary field of dentistry, forensic medicine and anthropology alike, as it concerns all the above mentioned specialties. The aim of this article is to review the current literature regarding methods used for sex estimation based on the skull and the teeth, covering articles published between January 2015 and July 2022. New methods and new approaches to old methods are constantly emerging in this field, therefore resulting in the need to summarize the large amount of data available. Morphometric, morphologic and biochemical analysis were reviewed in living populations, autopsy cases and archaeological records. The cranial and odontological sex estimation methods are highly population-specific and there is a great need for these methods to be applied to and verified on more populations. Except for DNA analysis, which has a prediction accuracy of 100%, there is no other single method that can achieve such accuracy in predicting sex from cranial or odontological records.
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Fujimoto K, Fujii G, Shojo H, Nakanishi H, Kanzawa-Kiriyama H, Saitoh M, Yoshizawa K, Aono T, Horita T, Takada A, Saito K, Ueki K, Adachi N. Highly sensitive sex determination method using the exon 1 region of the amelogenin gene. Leg Med (Tokyo) 2022; 59:102136. [PMID: 36049424 DOI: 10.1016/j.legalmed.2022.102136] [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: 05/26/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Sex determination is a crucial factor in the identification of unidentified human remains. Sex determination by DNA analysis is particularly useful because it can be applied to samples for which morphological characteristics are unavailable. Because samples handled in forensic DNA typing are easily degraded by environmental factors and microorganisms, there is a need for a method that can accurately determine sex even in highly decayed samples. Previous studies mainly used sex differences in an intron of the amelogenin gene. However, this region is highly polymorphic, and there are cases where accurate sexing cannot be performed because of genetic mutations in the target region. Thus, for reliable sex determination, it is desirable to select loci with as few non-sexual polymorphisms as possible. In this study, we focused on the exon 1 region of the amelogenin gene, which has very little polymorphism other than sex differences. We developed a primer set for sex determination and compared it with the GlobalFiler™ PCR Amplification Kit (GF), which is widely used for forensic DNA typing. The results showed that the amount of DNA required for accurate sex determination was 25 pg for both methods, achieving equivalent sensitivity. Next, we compared the two methods using ancient human skeletons and found that the present method with its shorter amplicon was considerably superior to GF. The present method is simple, rapid, inexpensive, and suitable for analyzing highly degraded samples. Therefore, this method is expected to contribute to forensic sciences and physical anthropology.
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Affiliation(s)
- Kana Fujimoto
- Department of Oral and Maxillofacial Surgery, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan; Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
| | - Gento Fujii
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan; Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 272-8562, Japan.
| | - Hideki Shojo
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
| | - Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan.
| | - Hideaki Kanzawa-Kiriyama
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Ibaraki 305-0005, Japan.
| | - Masao Saitoh
- Center for Medical Education and Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
| | - Kunio Yoshizawa
- Department of Oral and Maxillofacial Surgery, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
| | - Tomoya Aono
- Department of Historic Heritage (archaeology), Faculty of Arts, Tohoku University of Art and Design, 3-4-5, Kamisakurada, Yamagata, Yamagata 990-9530, Japan.
| | - Tetsuya Horita
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan.
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan.
| | - Koichiro Ueki
- Department of Oral and Maxillofacial Surgery, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
| | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi. 1110 Shimo-kato, Chuo, Yamanashi 409-3898, Japan.
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8
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Dash HR, Kaitholia K, Kumawat RK, Singh AK, Shrivastava P, Chaubey G, Das S. Sequence variations, flanking region mutations, and allele frequency at 31 autosomal STRs in the central Indian population by next generation sequencing (NGS). Sci Rep 2021; 11:23238. [PMID: 34853383 PMCID: PMC8636586 DOI: 10.1038/s41598-021-02690-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/18/2021] [Indexed: 02/05/2023] Open
Abstract
Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India.
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, Madhya Pradesh, 769001, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 470001, India
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Thornton R, Hutchinson E, Edkins A. PCR based method for sex estimation from bone samples of unidentified South African fetal remains. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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10
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Genetic characterization of a collection of Tsantsas from Ecuadorian museums. Forensic Sci Int 2021; 325:110879. [PMID: 34174769 DOI: 10.1016/j.forsciint.2021.110879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/17/2021] [Accepted: 06/11/2021] [Indexed: 11/22/2022]
Abstract
Tsantsas are shrunken human heads originally made for ceremonial purposes by Amazonian indigenous groups of the Shuar and Achuar family, previously called Jivaroan tribes. A significant demand of these objects during the first half of the 20th century led to the manufacture of counterfeit shrunken heads for commercial purposes. For museums where these collections are held, as well as for the indigenous groups who claim their ownership, it is important to identify the origin and authenticity of these tsantsas. We hypothesized that a collection of 14 tsantsas from 3 different museum collections in Ecuador are human and aimed to characterize their sex and potential origin. We amplified the amelogenin gene and performed a high resolution melting analysis to determine their human origin and characterize their sex. We also analyzed a fragment (16209-16402) from the HVR-1 region to identify the mtDNA haplogroups present in the tsantsa collection. Our exploratory results show that all the tsantsas are human and that the collection is comprised of 13 males and 1 female. A total of seven mtDNA haplogroups were found among the tsantsa collection using the mtDNA EMPOP database. These results show a predominance of the Amerindian mtDNA haplogroups B, C and D. Additional principal component analysis, genetic distance tree and haplotype network analyses suggest a relationship between the tsantsa specimens and Native American groups.
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Lai L, Huang XL, Wang YC, Liu SL, Lin SM, Chen D, Han LL, Yu H, Shen XL. Detection and analysis of null alleles of amelogenin in gender identification. Leg Med (Tokyo) 2021; 52:101899. [PMID: 34052679 DOI: 10.1016/j.legalmed.2021.101899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 11/17/2022]
Abstract
In this study, we located eight samples with null alleles of amelogenin out of 10,750 cases, and discussed the influence in gender identification and forensic personal identification. Amelogenin was detected and retested by several autosomal STR kits and sex chromosomal STR kits, and the causes were analyzed by chromosome karyotype analysis and Y chromosome microdeletion detection if necessary. Suspected AMEL-X loss was observed in five samples, but no abnormality was detected in the X-STR loci. AMEL-X was recovered when samples were retested by other detection systems designed with different primers. One sample had AMEL-X and X-STR loci loss, and the karyotype was chimeric 45,X0[70]/46,X,+mar[13].Two male samples lost AMEL-Y fragment, and both of them lost DYS522-DYS570-DYS576 loci, but no abnormalities were found in the STS loci of SRY and AZF regions. Therefore, when carrying out gender identification by using amelogenin, it is essential to focus on null alleles of amelogenin. In especially, deal with the samples collected from the individuals who had chromosomal hereditary disorders(e.g. Turner Syndrome and Oligospermia / Azoospermia). In order to achieve this, laboratories should have various techniques to verify the null alleles of amelogenin and ensure accurate genotyping. Accurate genotyping of amelogenin and DNA database establishment are vital for personal identification.
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Affiliation(s)
- Li Lai
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China; Provincial Clinicial College of Fujian Medical University, Fuzhou, Fujian 350001, PR China
| | - Xiao-Li Huang
- Provincial Clinicial College of Fujian Medical University, Fuzhou, Fujian 350001, PR China; Clinical Laboratory of Fujian Provincial Hospital, Fuzhou, Fujian 350001, PR China
| | - Yao-Cheng Wang
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China; Provincial Clinicial College of Fujian Medical University, Fuzhou, Fujian 350001, PR China
| | - Shang-Long Liu
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China; Provincial Clinicial College of Fujian Medical University, Fuzhou, Fujian 350001, PR China
| | - Sai-Mei Lin
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China
| | - Dian Chen
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China
| | - Li-Li Han
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China
| | - Hong Yu
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China
| | - Xiao-Li Shen
- Forensic Science Institute of Fujian Provincial Hospital, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, Fujian 350001, PR China; Provincial Clinicial College of Fujian Medical University, Fuzhou, Fujian 350001, PR China
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12
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Dissanayake DSB, Holleley CE, Hill LK, O'Meally D, Deakin JE, Georges A. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 2020; 21:667. [PMID: 32993477 PMCID: PMC7526180 DOI: 10.1186/s12864-020-07071-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
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Affiliation(s)
- Duminda Sampath Bandara Dissanayake
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Clare Ellen Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Laura Kate Hill
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present Address: Centre for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Janine Eileen Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
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13
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Jusic A, Salgado-Somoza A, Paes AB, Stefanizzi FM, Martínez-Alarcón N, Pinet F, Martelli F, Devaux Y, Robinson EL, Novella S. Approaching Sex Differences in Cardiovascular Non-Coding RNA Research. Int J Mol Sci 2020; 21:E4890. [PMID: 32664454 PMCID: PMC7402336 DOI: 10.3390/ijms21144890] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular disease (CVD) is the biggest cause of sickness and mortality worldwide in both males and females. Clinical statistics demonstrate clear sex differences in risk, prevalence, mortality rates, and response to treatment for different entities of CVD. The reason for this remains poorly understood. Non-coding RNAs (ncRNAs) are emerging as key mediators and biomarkers of CVD. Similarly, current knowledge on differential regulation, expression, and pathology-associated function of ncRNAs between sexes is minimal. Here, we provide a state-of-the-art overview of what is known on sex differences in ncRNA research in CVD as well as discussing the contributing biological factors to this sex dimorphism including genetic and epigenetic factors and sex hormone regulation of transcription. We then focus on the experimental models of CVD and their use in translational ncRNA research in the cardiovascular field. In particular, we want to highlight the importance of considering sex of the cellular and pre-clinical models in clinical studies in ncRNA research and to carefully consider the appropriate experimental models most applicable to human patient populations. Moreover, we aim to identify sex-specific targets for treatment and diagnosis for the biggest socioeconomic health problem globally.
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Affiliation(s)
- Amela Jusic
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina;
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Ana B. Paes
- INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain; (A.B.P.); (N.M.-A.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Núria Martínez-Alarcón
- INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain; (A.B.P.); (N.M.-A.)
| | - Florence Pinet
- INSERM, CHU Lille, Institut Pasteur de Lille, University of Lille, U1167 F-59000 Lille, France;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milan, Italy;
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Emma Louise Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Susana Novella
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, and INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain
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14
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Lucas CG, Spate AM, Samuel MS, Spate LD, Warren WC, Prather RS, Wells KD. A novel swine sex-linked marker and its application across different mammalian species. Transgenic Res 2020; 29:395-407. [PMID: 32607872 DOI: 10.1007/s11248-020-00204-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 01/25/2023]
Abstract
Advances in genome editing tools have reduced barriers to the creation of animal models. Due to their anatomical and physiological similarities to humans, there has been a growing need for pig models to study human diseases, for xenotransplantation and translational research. The ability to determine the sex of genetically modified embryos, cells or fetuses is beneficial for every project involving the production of transgenic animals. This strategy can improve the time-efficiency and lower the production costs. Additionally, sex assessment is very useful for wildlife studies to understand population behavior and structure. Thus, we developed a simple and fast PCR-based protocol for sex determination in pigs by using a unique primer set to amplify either the DDX3X or DDX3Y gene. The sex was 100% correctly assigned when tail genomic DNA, Day-35 fetus and hair samples from pigs were used. For both blastocysts and oocytes (84.6% and 96.5% of efficacy, respectively) the unidentified samples were potentially due to a limitation in sample size. Our assay also worked for domestic sheep (Ovis aries), American bison (Bison bison) and European cattle (Bos taurus) samples and by in silico analysis we confirmed X-Y amplicon length polymorphisms for the DDX3 gene in 12 other mammalian species. This PCR protocol for determining sex in pig tissues and cells showed to be simple, specific, highly reproducible and less time consuming as well as an important tool for other livestock species and wildlife studies.
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Affiliation(s)
- C G Lucas
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - A M Spate
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - M S Samuel
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - L D Spate
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - W C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - R S Prather
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - K D Wells
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA. .,Division of Animal Science, University of Missouri, Columbia, MO, USA.
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