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Zeng K, Du J, Chen YZ, Wang DY, Sun ML, Li YZ, Wang DY, Liu SH, Zhu XM, Lv P, Du Z, Liu K, Yao J. Metabolomics efficiently discriminates monozygotic twins in peripheral blood. Int J Legal Med 2024:10.1007/s00414-024-03269-1. [PMID: 38858273 DOI: 10.1007/s00414-024-03269-1] [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: 11/15/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Monozygotic (MZ) twins cannot be distinguished using conventional forensic STR typing because they present identical STR genotypings. However, MZ twins do not always live in the same environment and often have different dietary and other lifestyle habits. Metabolic profiles are deyermined by individual characteristics and are also influenced by the environment in which they live. Therefore, they are potential markers capable of identifying MZ twins. Moreover, the production of proteins varies from organism to organism and is influenced by both the physiological state of the body and the external environment. Hence, we used metabolomics and proteomics to identify metabolites and proteins in peripheral blood to discriminate MZ twins. We identified 1749 known metabolites and 622 proteins in proteomic analysis. The metabolic profiles of four pairs of MZ twins revealed minor differences in intra-MZ twins and major differences in inter-MZ twins. Each pair of MZ twins exhibited distinct characteristics, and four metabolites-methyl picolinate, acesulfame, paraxanthine, and phenylbenzimidazole sulfonic acid-were observed in all four MZ twin pairs. These four differential exogenous metabolites conincidently show that the different external environments and life styles can be well distinguished by metabolites, considering that twins do not all have the same eating habits and living environments. Moreover, MZ twins showed different protein profiles in serum but not in whole blood. Thus, our results indicate that differential metabolites provide potential biomarkers for the personal identification of MZ twins in forensic medicine.
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Affiliation(s)
- Kuo Zeng
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Jiang Du
- Department of Pathology, School of Basic Medicine, China Medical University, Shenyang, P.R. China
| | - Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dan-Yang Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Mao-Ling Sun
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dong-Yi Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Shu-Han Liu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Kun Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, P.R. China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China.
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China.
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Segal NL. Twins Standing in for Co-Twins: Explanation and Speculation/Twin Research Reviews: Single v. Multiple Embryo Transfer; Neurimaging of Twins with Periventricular Nodular Heterotopia; Twin Dietary Study; New Hungarian Text on Twins/Human Interest: Valedictorian and Salutatorian Twins; Twin Mother at Age Seventy; Twins Reunited by Tiktok; New Film on Twins with Selective Mutism; Becoming Twin Doctors. Twin Res Hum Genet 2024:1-5. [PMID: 38738462 DOI: 10.1017/thg.2024.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
An overview of circumstances in which twins take the place of their co-twin is presented. Various explanations and speculations are proposed for understanding twins' willingness to do so in certain situations. This section is followed by reviews of timely twin research, namely single versus multiple embryo transfer; neurimaging of twins with periventricular nodular heterotopia; a twin dietary comparison; and a new book of twin-related readings from Hungary. The final portion of this article concerns human interest stories that both inform and entertain. They involve valedictorian and salutatorian twins; a mother delivering twins at age seventy; twins reunited by TikTok; a new film about twins with selective mutism; and twins becoming doctors.
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Affiliation(s)
- Nancy L Segal
- Department of Psychology, California State University, Fullerton, California, USA
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3
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Sun W, Wang Z, Wen S, Huang A, Li H, Jiang L, Feng Q, Fan D, Tian Q, Han D, Liu X. Technical strategy for monozygotic twin discrimination by single-nucleotide variants. Int J Legal Med 2024; 138:767-779. [PMID: 38197923 DOI: 10.1007/s00414-023-03150-7] [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: 03/08/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Monozygotic (MZ) twins are theoretically genetically identical. Although they are revealed to accumulate mutations after the zygote splits, discriminating between twin genomes remains a formidable challenge in the field of forensic genetics. Single-nucleotide variants (SNVs) are responsible for a substantial portion of genetic variation, thus potentially serving as promising biomarkers for the identification of MZ twins. In this study, we sequenced the whole genome of a pair of female MZ twins when they were 27 and 33 years old to approximately 30 × coverage using peripheral blood on an Illumina NovaSeq 6000 Sequencing System. Potentially discordant SNVs supported by whole-genome sequencing were validated extensively by amplicon-based targeted deep sequencing and Sanger sequencing. In total, we found nine bona fide post-twinning SNVs, all of which were identified in the younger genomes and found in the older genomes. None of the SNVs occurred within coding exons, three of which were observed in introns, supported by whole-exome sequencing results. A double-blind test was employed, and the reliability of MZ twin discrimination by discordant SNVs was endorsed. All SNVs were successfully detected when input DNA amounts decreased to 0.25 ng, and reliable detection was limited to seven SNVs below 0.075 ng input. This comprehensive analysis confirms that SNVs could serve as cost-effective biomarkers for MZ twin discrimination.
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Affiliation(s)
- Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
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Hwa HL, Lin CY, Yu YJ, Linacre A, Lee JCI. DNA identification of monozygotic twins. Forensic Sci Int Genet 2024; 69:102998. [PMID: 38100853 DOI: 10.1016/j.fsigen.2023.102998] [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: 08/23/2023] [Revised: 11/14/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
This study details the differentiation of identical twins based on single mutational base differences. There were three pairs of male monozygotic (MZ) twins in this study. DNA samples from blood, a buccal swab or saliva from each individual were all initially genotyped using 22 autosomal STR and 27 Y-STR loci. Preliminary screening confirmed there were no differences in the STR data between each pair of MZ twins. Whole Genome Sequence (WGS) data were generated from DNA extracted from the three body fluids from each individual. Kinship coefficients with 0.4254, 0.4557 and 0.4543 from 3 twins were generated based on WGS data to further confirm that their relationship was that of MZ twins. The fastq data generated by the Illumina Hiseq 2000 between MZ twins were then treated as "normal" as opposed to "tumor" using commercially available software tools to identify mutational single base changes. Sanger DNA sequencing confirmed there were 1, 5 and 9 single base changes found in WGS data from each of the three MZ twin sets. There was individual variation in the mutational base changes when comparing data from the three body fluids. The methods used in this study to differentiate MZ twins based on WGS data can readily be performed in many operational forensic DNA laboratories using user friendly software.
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Affiliation(s)
- Hsiao-Lin Hwa
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan
| | - Chun-Yen Lin
- Institute of Forensic Medicine, Ministry of Justice, New Taipei City 23016, Taiwan
| | - Yu-Jen Yu
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide 5001, Australia
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan.
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Tuazon OM, Wickenheiser RA, Ansell R, Guerrini CJ, Zwenne GJ, Custers B. Law enforcement use of genetic genealogy databases in criminal investigations: Nomenclature, definition and scope. Forensic Sci Int Synerg 2024; 8:100460. [PMID: 38380276 PMCID: PMC10876674 DOI: 10.1016/j.fsisyn.2024.100460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Although law enforcement use of commercial genetic genealogy databases has gained prominence since the arrest of the Golden State Killer in 2018, and it has been used in hundreds of cases in the United States and more recently in Europe and Australia, it does not have a standard nomenclature and scope. We analyzed the more common terms currently being used and propose a common nomenclature: investigative forensic genetic genealogy (iFGG). We define iFGG as the use by law enforcement of genetic genealogy combined with traditional genealogy to generate suspect investigational leads from forensic samples in criminal investigations. We describe iFGG as a proper subset of forensic genetic genealogy, that is, FGG as applied by law enforcement to criminal investigations; hence, investigative FGG or iFGG. We delineate its steps, compare and contrast it with other investigative techniques involving genetic evidence, and contextualize its use within criminal investigations. This characterization is a critical input to future studies regarding the legal status of iFGG and its implications on the right to genetic privacy.
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Affiliation(s)
- Oliver M. Tuazon
- Center for Law and Digital Technologies (eLaw), Institute for the Interdisciplinary Study of the Law, Leiden Law School, Leiden University, Kamerlingh Onnes Building, Steenschuur 25, 2311 ES, Leiden, the Netherlands
| | - Ray A. Wickenheiser
- New York State Police Crime Laboratory System, Forensic Investigation Center, 1220 Washington Avenue, Building #30, Albany, NY, 12226-3000, USA
| | - Ricky Ansell
- Swedish Police Authority, National Forensic Centre, SE-581 94, Linköping, Sweden
- Department of Physics, Chemistry and Biology, Linköping University, Sweden
| | - Christi J. Guerrini
- Baylor College of Medicine, Center for Medical Ethics and Health Policy, Houston, TX, 77030, USA
| | - Gerrit-Jan Zwenne
- Center for Law and Digital Technologies (eLaw), Institute for the Interdisciplinary Study of the Law, Leiden Law School, Leiden University, Kamerlingh Onnes Building, Steenschuur 25, 2311 ES, Leiden, the Netherlands
| | - Bart Custers
- Center for Law and Digital Technologies (eLaw), Institute for the Interdisciplinary Study of the Law, Leiden Law School, Leiden University, Kamerlingh Onnes Building, Steenschuur 25, 2311 ES, Leiden, the Netherlands
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Kim JY, Lee HY, Lee SY, Kim SY, Park JL, Lee SD. DNA methylome profiling of blood to identify individuals in a pair of monozygotic twins. Genes Genomics 2023; 45:1273-1279. [PMID: 37198375 PMCID: PMC10504115 DOI: 10.1007/s13258-023-01396-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/30/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Short tandem repeat (STR) markers cannot be used to distinguish between genetically identical monozygotic (MZ) twins, causing problems in a case with an MZ twin as a suspect. Many studies have shown that in older MZ twins, there are significant differences in overall content and genomic distribution of methylation. OBJECTIVE In this study, we analyzed the DNA methylome profile of blood to identify recurrent differentially methylated CpG sites (DMCs) to discriminate between MZ twins. METHODS Blood samples were collected from 47 paired MZ twins. We performed the DNA methylation profiling using the HumanMethylation EPIC BeadChip platform and identified recurrent DMCs between MZ twins. Then, Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and motif enrichment analyses were performed to reveal the biological functions of recurrent DMCs. We collected DNA methylome data from the Gene Expression Omnibus (GEO) public database to verify the recurrent DMCs between MZ twins. RESULTS We identified recurrent DMCs between MZ twin samples and observed that they were enriched in immune-related genes. In addition, we verified our DMCs in a public dataset. CONCLUSION Our results suggest that the methylation level at recurrent DMCs between MZ twins may serve as a valuable biomarker for identification of individuals in a pair of MZ twins.
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Affiliation(s)
- Jae-Yoon Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, 03080, Korea
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - So-Yeon Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jong-Lyul Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea.
- Aging Convergence Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea.
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, 03080, Korea.
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7
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Mikolicz A, Simon B, Gáspár O, Shahbazi A, Vag J. Reproducibility of the digital palate in forensic investigations, a two-year retrospective cohort study of twins. J Dent 2023:104562. [PMID: 37230239 DOI: 10.1016/j.jdent.2023.104562] [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: 12/18/2022] [Revised: 05/09/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023] Open
Abstract
OBJECTIVES The palatal scans of the same individuals were compared after two years to assess forensic reproducibility. The effect of orthodontic treatment, the comparison area and the digitization approach were investigated. METHODS The palate was scanned in 20 pairs of monozygotic twins by an intraoral scanner (IOS) three times to assess repeatability. They were rescanned two years later by two different IOSs. An elastic impression and a plaster model were also made and scanned by a laboratory scanner (indirect digitization). Mean absolute distance between scans was compared after best-fit alignment. Scans from the two sessions were compared to evaluate the combined effect of aging, orthodontic treatment and different digitization methods (forensic reproducibility). Additionally, the scans of different digitization methods from the second session were compared (technical reproducibility). The between-siblings difference was compared in the two sessions to evaluate the effect of aging on palatal morphology. RESULTS The anterior palatal area showed significantly better repeatability and forensic reproducibility than the whole palate (p<0.001), but orthodontic treatment had no effect. Indirect digitization produced lower forensic and technical reproducibility than IOSs. For IOSs, repeatability (22 µm) was significantly (p<0.001) better than either forensic (75-77 µm) or technical reproducibility (37 µm). No significant changes were observed from the first to the second session in the between-sibling comparison. The closest between-sibling value (239 µm) considerably exceeded the highest forensic reproducibility value (141 µm). CONCLUSIONS Reproducibility is acceptable between the different IOSs, even two years apart, but is poor between IOS and indirect digitization. The anterior palate is relatively stable in young adults. CLINICAL SIGNIFICANCE Intraoral scanning of the anterior palatal area has superior reproducibility, regardless of the IOS brand. Therefore, the IOS method could be suitable for identifying humans through anterior palatal morphology. However, the digitization of elastic impressions or plaster models had low reproducibility, preventing their application for forensic purposes.
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Affiliation(s)
- Akos Mikolicz
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
| | - Botond Simon
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
| | - Orsolya Gáspár
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
| | - Arvin Shahbazi
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary; Department of Anatomy, Histology and Embryology (Oral Morphology Group), Semmelweis University, Budapest, Hungary; Department of Periodontology, Semmelweis University, Budapest, Hungary
| | - Janos Vag
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary.
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Xue J, Tan M, Zhang R, Chen D, Liu G, Zheng Y, Wu Q, Xiao Y, Liao M, Qu S, Liang W. Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 2023; 65:102887. [PMID: 37209601 DOI: 10.1016/j.fsigen.2023.102887] [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: 11/28/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/22/2023]
Abstract
In recent years, microhaplotypes (MHs) have become a research hotspot within the field of forensic genetics. Traditional MHs contain only SNPs that are closely linked within short fragments. Herein, we broaden the concept of general MHs to include short InDels. Complex kinship identification plays an important role in disaster victim identification and criminal investigations. For distant relatives (e.g., 3rd-degree), many genetic markers are required to enhance power of kinship testing. We performed genome-wide screening for new MH markers composed of two or more variants (InDel or SNP) within 220 bp based on the Chinese Southern Han from the 1000 Genomes Project. An NGS-based 67plex MH panel (Panel B) was successfully developed, and 124 unrelated individual samples were sequenced to obtain population genetic data, including alleles and allele frequencies. Of the 67 genetic markers, 65 MHs were, as far as we know, newly discovered, and 32 MHs had effective number of allele (Ae) values greater than 5.0. The average Ae and heterozygosity of the panel were 5.34 and 0.7352, respectively. Next, 53 MHs from a previous study were collected as Panel A (average Ae of 7.43), and Panel C with 87 MHs (average Ae of 7.02) was formed by combining Panels A and B. We investigated the utility of these three panels in kinship analysis (parent-child, full siblings, 2nd-degree, 3rd-degree, 4th-degree, and 5th-degree relatives), with Panel C exhibiting better performance than the two other panels. Panel C was able to separate parent-child, full-sibling, and 2nd-degree relative duos from unrelated controls in real pedigree data, with a small false testing level (FTL) of 0.11% in simulated 2nd-degree duos. For more distant relationships, the FTL was much higher: 8.99% for 3rd-degree, 35.46% for 4th-degree, and 61.55% for 5th-degree. When a carefully chosen extra relative was known, this may enhance the testing power for distant kinship analysis. Two twins from the Q family (2-5 and 2-7) and W family (3-18 and 3-19) shared the same genotypes in all tested MHs, which led to the incorrect conclusion that an uncle-nephew duo was classified as a parent-child duo. In addition, Panel C showed great capacity for excluding close relatives (2nd-degree and 3rd-degree relatives) during paternity tests. Among 18,246 real and 10,000 simulated unrelated pairs, none were misinterpreted as a relative within 2nd-degree at a log10(LR) cutoff of 4. The panels presented herein could provide supplementary power for the analysis of complex kinship.
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Affiliation(s)
- Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
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Liu J, Zhang S, Wen Y, Su Y, Jiang L, Li S, Shen J, Zheng X, Li X, Chen X, Wang Z. Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing. Forensic Sci Int 2023; 348:111708. [PMID: 37119662 DOI: 10.1016/j.forsciint.2023.111708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuyuan Zhang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Shen
- Anhui Hopegenerich Biotechnology, Hefei 230031, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xingrui Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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11
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Distinguishing between monozygotic twins' blood samples through immune repertoire sequencing. Forensic Sci Int Genet 2023; 64:102828. [PMID: 36682099 DOI: 10.1016/j.fsigen.2023.102828] [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: 10/11/2022] [Revised: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Monozygotic (MZ) twins with highly similar genomic DNA sequences can not be distinguished by conventional forensic DNA testing. The immune repertoire (IR) reflects an individual's immune history, which is unique between individuals, has been applied to individualized treatment in precision medicine. However, the application of IR in forensic genetics has not been reported to date. In this study, the diversity in the complementary determining region 3 (CDR3) of both the T-cell receptor β chain (TCRβ) and B-cell receptor heavy chain (also known as immunoglobulin heavy chain, IGH) in four pairs of MZ twins were analyzed. The results showed that the amino acid sequences length distribution frequency of TCRβ CDR3 had 4-10 differences, and the nucleic acid sequences length distribution frequency of TCRβ CDR3 had 2-7 differences between MZ twins. The shared difference of four pairs of MZ twins focused on the length distribution frequency of 34 bp nucleotide sequences in TCRβ. By analyzing the usage frequency of V and J genes in TCRβ and IGH CDR3 DNA sequence rearrangements, we also found that there were biases between each pair of MZ twins, and the usage frequency of TRBJ2-3 showed common differences between each pair of MZ twins. Furthermore, each pair of MZ twins had its own unique V-J genes combination mode in TCRβ and IGH CDR3 DNA sequences. This study, for the first time, suggested that IR can be used as a potential biological marker to distinguish MZ twins.
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [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: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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Fonseca RI, Fridman C. Analysis of isoalleles and flanking SNPs of STR markers by NGS to distinguish monozygotic twins. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.064] [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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14
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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15
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Gutierrez R, Roman MG, Harrel M, Hughes S, LaRue B, Houston R. Assessment of the ForenSeq mtDNA control region kit and comparison of orthogonal technologies. Forensic Sci Int Genet 2022; 59:102721. [DOI: 10.1016/j.fsigen.2022.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/13/2022] [Accepted: 05/08/2022] [Indexed: 11/04/2022]
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16
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Gorden EM, Sturk-Andreaggi K, Marshall C. Capture enrichment and massively parallel sequencing for human identification. Forensic Sci Int Genet 2021; 53:102496. [PMID: 33770700 DOI: 10.1016/j.fsigen.2021.102496] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/07/2023]
Abstract
In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and high-throughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.
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Affiliation(s)
- Erin M Gorden
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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Baggett JP, Tillett RL, Cooper EA, Yerka MK. De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity. PLoS One 2021; 16:e0248213. [PMID: 33684158 PMCID: PMC7939377 DOI: 10.1371/journal.pone.0248213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance into trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeats) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized. An analysis of published sorghum genomes selected to represent its five main races (bicolor, caudatum, durra, kafir, and guinea; 75 accessions total) identified 130,120 SSR motifs. Average lengths were 23.8 bp and 95% were between 10 and 92 bp, making them suitable for NGS. Validation through targeted sequencing amplified 188 of 192 assayed SSR loci. Results highlighted the distinctness of accessions from the guinea sub-group margaritiferum from all other sorghum accessions, consistent with previous studies of nuclear and mitochondrial DNA. SSRs that efficiently fingerprinted margaritiferum individuals (Xgma1 -Xgma6) are presented. Developing similar fingerprints of other sub-populations (Xunr1 -Xunr182) was not possible due to the extensive admixture between them in the data set analyzed. In summary, these methods were able to fingerprint specific sub-populations when rates of admixture between them are low.
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Affiliation(s)
- John P. Baggett
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States of America
| | - Richard L. Tillett
- Nevada Center for Bioinformatics, University of Nevada, Reno, NV, United States of America
| | - Elizabeth A. Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Melinda K. Yerka
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, Reno, NV, United States of America
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Romanos P, Borjac J. Epigenetic Discrimination of Lebanese Monozygotic Twins as a Promising Forensic Approach. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee JH, Kim J, Kim H, Kim HS, Kim E. Massively parallel sequencing of 25 short tandem repeat loci including the SE33 marker in Koreans. Genes Genomics 2021; 43:133-140. [PMID: 33481226 DOI: 10.1007/s13258-020-01033-4] [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: 09/29/2020] [Accepted: 12/19/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Massively parallel sequencing (MPS) technology has recently been introduced in research, clinical diagnostics, and forensics. MPS enables determination of the genotypes of multiple short tandem repeat (STR) markers and to determine nucleotide sequence variations, additionally. OBJECTIVE To improve STR analysis and a paternity index, a new, smaller-sized STR panel was designed that includes the SE33 locus. METHODS This study performed MPS using an STR panel including the SE33 marker in 101 Koreans. The concordance study was conducted by comparing the data obtained from the MPS assay with the results of a capillary electrophoresis (CE)-based method. RESULTS In this study, an in-house MPS panel is designed that incorporates the 20 Combined DNA Index System (CODIS) loci and the Penta D, Penta E, and SE33 markers for enhanced discriminatory ability. The data obtained via MPS analysis were compared with CE data to confirm concordance. Fifty previously unreported alleles were detected through the MPS analysis. Three new SNP variations in the flanking region were also identified. Statistical analysis demonstrated that the SE33 marker was most effectively determined the match probability (PM) and typical paternity index (TPI). In the sensitivity study, concentrations as low as 80 pg could be used to obtain full and concordant profiles. CONCLUSIONS We designed a new, smaller-sized STR panel that includes the SE33 locus to improve STR analysis and the paternity index. Various new alleles were identified in SE33, indicating a high degree of polymorphism. The panel is expected to provide valid data for discrimination of unidentified bodies.
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Affiliation(s)
- Ja Hyun Lee
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Korea
| | - Jeongyong Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Korea
| | - Hyojeong Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Korea
| | - Hyo Sook Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Korea
| | - Eungsoo Kim
- DNA Analysis Division, National Forensic Service Seoul Institute, Seoul, 08036, Korea.
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Turrina S, Bortoletto E, Giannini G, De Leo D. Monozygotic twins: Identical or distinguishable for science and law? MEDICINE, SCIENCE, AND THE LAW 2021; 61:62-66. [PMID: 33591870 DOI: 10.1177/0025802420922335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Monozygotic twins, also known as monovular twins, share an identical genetic heritage because they are two individuals who derive from the same zygote. For this reason, they have been considered indistinguishable. They represent a limit for the application of markers and analytical methods that are routinely used in forensic science because analyses of DNA fragments (short tandem repeats analysed by capillary electrophoresis) are unable to distinguish monozygotic twins. The recent introduction of ultra-deep next generation sequencing in forensic genetics, also known as massively parallel sequencing, has made it possible to identify a number of genetic variations through genome sequencing (such as copy number variations, single nucleotide polymorphisms and DNA methylation) that make it possible to distinguish monozygotic twins. Here, we present a case of ascertaining biological paternity, in which the alleged father had a monozygotic twin brother. This case led to the examination of international law in similar cases in which the only available biological evidence derives from classical forensic genetic analysis, performed with short tandem repeat (autosomal and/or gonosomal) capillary electrophoresis and the probative value, if recognised, of the next generation sequencing technology in the courtroom.
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Affiliation(s)
- Stefania Turrina
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Elena Bortoletto
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Giacomo Giannini
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Domenico De Leo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
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MicroRNAs: An Update of Applications in Forensic Science. Diagnostics (Basel) 2020; 11:diagnostics11010032. [PMID: 33375374 PMCID: PMC7823886 DOI: 10.3390/diagnostics11010032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs containing 18–24 nucleotides that are involved in the regulation of many biochemical mechanisms in the human body. The level of miRNAs in body fluids and tissues increases because of altered pathophysiological mechanisms, thus they are employed as biomarkers for various diseases and conditions. In recent years, miRNAs obtained a great interest in many fields of forensic medicine given their stability and specificity. Several specific miRNAs have been studied in body fluid identification, in wound vitality in time of death determination, in drowning, in the anti-doping field, and other forensic fields. However, the major problems are (1) lack of universal protocols for diagnostic expression testing and (2) low reproducibility of independent studies. This review is an update on the application of these molecular markers in forensic biology.
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Rolf B, Krawczak M. The germlines of male monozygotic (MZ) twins: Very similar, but not identical. Forensic Sci Int Genet 2020; 50:102408. [PMID: 33157386 DOI: 10.1016/j.fsigen.2020.102408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 11/19/2022]
Abstract
In 2012, a thought experiment in this journal suggested that paternity cases involving monozygotic (MZ) twins as putative fathers could be solved by means of whole genome sequencing (WGS). Although arising from a single fertilization event, MZ twins nevertheless continue to acquire somatic mutations during their development, including those that occur in the germline. Provided that paternity had been narrowed down to the twin pair beforehand by classical DNA analysis, one post-zygotic mutation would suffice to assign the paternal compartment of an offspring genome unambiguously to either twin if that mutation is found in the offspring and one twin, but not in the other twin. Since the publication of a proof-of-principle report in 2014, we have worked up five additional cases of MZ twin germline discrimination in real life, four paternity disputes and one criminal case requiring the identification of a sperm trace donor among a pair of MZ twin brothers. In this opinion paper, we report on the experiences made in the course of our work and take a look at possibilities for further development of the approach.
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Affiliation(s)
- Burkhard Rolf
- Eurofins Medigenomix Forensik GmbH, Anzinger Str. 7a, 85560, Ebersberg, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Brunswiker Strasse 10, 24105, Kiel, Germany.
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23
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Application of intraoral scanner to identify monozygotic twins. BMC Oral Health 2020; 20:268. [PMID: 33008463 PMCID: PMC7532102 DOI: 10.1186/s12903-020-01261-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA base identification is a proper and high specificity method. However, identification could be challenged in a situation where there is no database or the DNA sequence is almost identical, as in the case of monozygotic (MZ) twins. The aim of this study was to introduce a novel forensic method for distinguishing between almost identical MZ twins by means of an intraoral scanner using the 3D digital pattern of the human palate. METHODS The palatal area of 64 MZ twins and 33 same-sex dizygotic (DZ) twins (DZSS) and seven opposite-sex dizygotic twins (DZOS) were scanned three times with an intraoral scanner. From the scanned data, an STL file was created and exported into the GOM Inspect® inspection software. All scans within a twin pair were superimposed on each other. The average deviation between scans of the same subject (intra-subject deviation, ISD) and between scans of the two siblings within a twin pair (intra-twin deviation, ITD) was measured. One-sided tolerance interval covering 99% of the population with 99% confidence was calculated for the ISD (upper limit) and the ITD (lower limit). RESULTS The mean ISD of the palatal scan was 35.3 μm ± 0.78 μm. The calculated upper tolerance limit was 95 μm. The mean ITD of MZ twins (406 μm ± 15 μm) was significantly (p < 0.001) higher than the ISD, and it was significantly lower than the ITD of DZSS twins (594 μm ± 53 μm, p < 0.01) and the ITD of DZOS twins (853 μm ± 202 μm, p < 0.05). CONCLUSION The reproducibility of palatal intraoral scans proved to be excellent. The morphology of the palate shows differences between members of MZ twins despite their almost identical DNA, indicating that this method could be useful in forensic odontology.
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25
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Exploring of rare differences in mtGenomes between MZ twins using massively parallel sequencing. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Zhang M, Dilliott AA, Khallaf R, Robinson JF, Hegele RA, Comishen M, Sato C, Tosto G, Reitz C, Mayeux R, George-Hyslop PS, Freedman M, Rogaeva E. Genetic and epigenetic study of an Alzheimer's disease family with monozygotic triplets. Brain 2019; 142:3375-3381. [PMID: 31580390 PMCID: PMC6821163 DOI: 10.1093/brain/awz289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/26/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022] Open
Abstract
Age at onset of Alzheimer's disease is highly variable, and its modifiers (genetic or environmental) could act through epigenetic changes, such as DNA methylation at CpG sites. DNA methylation is also linked to ageing-the strongest Alzheimer's disease risk factor. DNA methylation age can be calculated using age-related CpGs and might reflect biological ageing. We conducted a clinical, genetic and epigenetic investigation of a unique Ashkenazi Jewish family with monozygotic triplets, two of whom developed Alzheimer's disease at ages 73 and 76, while the third at age 85 has no cognitive complaints or deficits in daily activities. One of their offspring developed Alzheimer's disease at age 50. Targeted sequencing of 80 genes associated with neurodegeneration revealed that the triplets and the affected offspring are heterozygous carriers of the risk APOE ε4 allele, as well as rare substitutions in APP (p.S198P), NOTCH3 (p.H1235L) and SORL1 (p.W1563C). In addition, we catalogued 52 possibly damaging rare variants detected by NeuroX array in affected individuals. Analysis of family members on a genome-wide DNA methylation chip revealed that the DNA methylation age of the triplets was 6-10 years younger than chronological age, while it was 9 years older in the offspring with early-onset Alzheimer's disease, suggesting accelerated ageing.
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Affiliation(s)
- Ming Zhang
- First Rehabilitation Hospital, School of Medicine, Tongji University, Shanghai, China
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, China
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
| | - Allison A Dilliott
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Roaa Khallaf
- Department of Medicine, Division of Neurology, Baycrest Health Sciences, and University of Toronto, Toronto, ON, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael Comishen
- Department of Medicine, Division of Neurology, Baycrest Health Sciences, and University of Toronto, Toronto, ON, Canada
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, USA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University. 1051 Riverside Drive, New York, NY, USA
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
| | - Morris Freedman
- Department of Medicine, Division of Neurology, Baycrest Health Sciences, Mt. Sinai Hospital, and University of Toronto, Toronto, ON, Canada
- Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
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Mateen RM, Tariq A. Increasing acceptability of forensic DNA analysis in Pakistan. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2019. [DOI: 10.1186/s41935-019-0162-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Yuan L, Chen X, Liu Z, Liu Q, Song A, Bao G, Wei G, Zhang S, Lu J, Wu Y. Identification of the perpetrator among identical twins using next-generation sequencing technology: A case report. Forensic Sci Int Genet 2019; 44:102167. [PMID: 31605960 DOI: 10.1016/j.fsigen.2019.102167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/12/2019] [Accepted: 09/26/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Monozygotic (MZ) twins, considered genetically identical, cannot be distinguished using regular short tandem repeats (STR) typing, thus presenting a challenge for forensic geneticists. In paternity testing, single nucleotide polymorphisms (SNPs) in nuclear DNA can help distinguish MZ twins. However, the unique features of the mitochondrial genome, such as high copy number, small genome size, and high substitution rate, make it a promising source for applications in forensic science. METHODS Whole-genome sequencing (WGS) was performed on blood samples, and bioinformatic analysis was used to distinguish between MZ twins. Amplification refractory mutation system polymerase chain reaction (ARMS-PCR) was used to confirm the WGS results. This methodology was further applied to forensic samples from criminal cases. Amplicon sequencing was also performed to further exclude the innocent twin. RESULTS The monozygosity of the twins was confirmed using STR typing. Only one potential somatic mutation, m.6903 T > C (2.6%), in the mitochondrial genome of one of the twins was verified when the sequence depth was set to 2000-fold, while no other distinguishing locus in the nuclear genome was identified. By dividing the number of C-reads by total reads, WGS data confirmed the amount of the minor component C to be 2.6%, which was further confirmed by ARMS-PCR. In addition, the heterogeneous locus was used to identify samples obtained from four criminal cases for forensic testing. Two heterogeneous loci in the sperm DNA of the other twin were identified by amplicon sequencing, and the amount of minor component T in m.6935C > T and m.6938C > T was estimated to be 17.91% and 18.79%, respectively. CONCLUSION The biological samples taken from the MZ twins were distinguished using a combination of WGS, allele-specific PCR, and deep-amplicon sequencing. Compared with nuclear DNA, mitochondrial DNA exhibited a higher potential for distinguishing between the MZ twins. The distinguishing feature of the mitochondrial DNA was the heterogeneous SNPs that occurred in only one twin. One SNP was further verified in the samples from the criminal cases and helped identify the perpetrator in case 1 and case 2. Furthermore, two heterogeneous SNPs found by amplicon sequencing helped to exclude the innocent twin in all four cases. Our findings demonstrated that a combination of deep sequencing and molecular analysis can be an effective way to distinguish between identical twins and can be used to analyze samples from criminal cases.
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Affiliation(s)
- Lijuan Yuan
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China; Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Xihui Chen
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Ziyu Liu
- Department of Microbiology, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Qingbo Liu
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - An Song
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Guoqiang Bao
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Gang Wei
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Sijia Zhang
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Jianguo Lu
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China.
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China.
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Hyun CH, Kim H, Ryu S, Kim W. Preliminary study on microeukaryotic community analysis using NGS technology to determine postmortem submersion interval (PMSI) in the drowned pig. J Microbiol 2019; 57:1003-1011. [PMID: 31555993 DOI: 10.1007/s12275-019-9198-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/29/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
Abstract
while several methods for determining postmortem submersion interval (PMSI) in drowning cases have been suggested, the estimation of PMSI remains difficult. Next-generation sequencing (NGS) technology enables simultaneous identification of multiple taxa from environmental samples. Although NGS has been applied to estimate time since death, this application has been mainly focused on terrestrial cases. As a case study, we investigated microeukaryotic biodiversity and community structures in submerged car bonnet and drowned pig using NGS technology. NGS analysis showed that the microeukaryotic biodiversity in pig carcass was relevantly lower than that in car bonnet. NGS results also revealed that water molds and algae were related to decomposition. Relative abundances of Filobasidium, Achlya, Saprolegnia, Hydrodicton, Lobosphaera, and Scenedesmus varied with decomposition period. This data indicated that these taxa might be useful as good indicators to estimate PMSI. This study showed microeukaryotic community analysis using NGS technology may help solve drowning cases in forensic investigation.
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Affiliation(s)
- Cheol-Ho Hyun
- Department of forensic investigation, Jeonbuk Provincial Police Agency, Jeonju zip-code, Republic of Korea
| | - Heesoo Kim
- School of Biological Sciences, Seoul National University, Seoul zip-code, Republic of Korea
| | - Seongho Ryu
- Soonchunhyang Institute of Med-Bio Sciences (SIMS), Soonchunhyang University, Cheonan zip-code, Republic of Korea.
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul zip-code, Republic of Korea.
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Cho Y, Lee S, Hong JH, Kim BJ, Hong WY, Jung J, Lee HB, Sung J, Kim HN, Kim HL, Jung J. Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins. Nucleic Acids Res 2019; 46:e92. [PMID: 29873758 PMCID: PMC6125643 DOI: 10.1093/nar/gky445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 05/15/2018] [Indexed: 12/30/2022] Open
Abstract
Calling variants from next-generation sequencing (NGS) data or discovering discordant sequences between two NGS data sets is challenging. We developed a computer algorithm, ADIScan1, to call variants by comparing the fractions of allelic reads in a tester to the universal reference genome. We then created ADIScan2 by modifying the algorithm to directly compare two sets of NGS data and predict discordant sequences between two testers. ADIScan1 detected >99.7% of variants called by GATK with an additional 724 393 SNVs. ADIScan2 identified ∼500 candidates of discordant sequences in each of two pairs of the monozygotic twins. About 200 of these candidates were included in the ∼2800 predicted by VarScan2. We verified 66 true discordant sequences among the candidates that ADIScan2 and VarScan2 exclusively predicted. ADIScan2 detected many discordant sequences overlooked by VarScan2 and Mutect, which specialize in detecting low frequency mutations in genetically heterogeneous cancerous tissues. Numbers of verified sequences alone were >5 times more than expected based on recently estimated mutation rates from whole genome sequences. Estimated post-zygotic mutation rates were 1.68 × 10−7 in this study. ADIScan1 and 2 would complement existing tools in screening causative mutations of diverse genetic diseases and comparing two sets of genome sequences, respectively.
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Affiliation(s)
- Yangrae Cho
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea.,DFTBA, CALS, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sunho Lee
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea.,School of Computer Science and Engineering, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Jong Hui Hong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Byong Joon Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea
| | - Woon-Young Hong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea
| | - Jongcheol Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea
| | - Hyang Burm Lee
- DFTBA, CALS, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Joohon Sung
- Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Han-Na Kim
- Department of Biochemistry, School of Medicine, Ewha Woman's University, Seoul 07985, Republic of Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Woman's University, Seoul 07985, Republic of Korea
| | - Jongsun Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon 34025, Republic of Korea
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Co-Twin Control Studies: Natural Events, Experimental Interventions and Rare Happenings/Twin Research: Cancer Risk in Overweight Twins; Prognosis After Fetal Loss of One Twin; Twin Concordance for Parkinson's Disease; Neuroanatomy of Musically Discordant MZ Twins/News Articles: Twin Birth with Two Wombs; Twins' Prenatal Interactions; Switched-at-Birth Twins; Fetus-in-Fetu; Unsolved Paternity. Twin Res Hum Genet 2019; 22:272-276. [PMID: 31284890 DOI: 10.1017/thg.2019.29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Co-twin control is a well-known methodological twin research design, but its variations and complexities are less well known. Various issues and illustrations are presented with reference to studies involving natural events, experimental interventions and rare happenings that underlie monozygotic (MZ) twins' environmental differences. This discussion is followed by summaries of recent twin research pertaining to cancer risk in overweight twins, the physical risk to surviving twins after fetal loss of a co-twin, a 20-year update of twin concordance for Parkinson's disease, and neuroanatomical differences in musically discordant MZ twin pairs. Several twin-related items that have attracted attention in the news are also summarized.
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Kasbekar DP. A cross-eyed geneticist’s view. J Biosci 2019. [DOI: 10.1007/s12038-019-9869-3] [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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33
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The New Sesquizygotic Twins and More: Exotic Twin Types/Twin Research Reviews: Parental Affection and Co-Twins’ Personality; Prenatal Demise in Twin Pregnancies; Heteropaternal Superfecundation; Selective Feticide in Dichorionic Twins/In the News: Identical Twin Oscar Winner; ‘Superfecundated’ Twins with Gay Fathers; Partly Living Apart; Which Twin Committed the Crime? Twin Res Hum Genet 2019; 22:195-198. [DOI: 10.1017/thg.2019.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractThe second recorded case of sesquizygotic (SQZ) twins is summarized. It is suspected that SQZ twins result from the fertilization of an egg by two separate spermatozoa, followed by division of the fertilized ovum. Next, recent studies examining how differences in parental affection affect co-twins’ personality profiles, the prenatal demise of fetuses during twin pregnancy, a forensic case of heteropaternal superfecundation and selective feticide in dichorionic twins are reviewed. Finally, summaries of newsworthy items featuring an identical twin Oscar winner, a case of ‘superfecundated’ twins born to a gay couple, identical twins who try partly living apart and new molecular techniques to distinguish an innocent identical twin from his or her guilty co-twin are presented.
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Xiao C, Pan C, Liu E, He H, Liu C, Huang Y, Yi S, Huang D. Differences of microRNA expression profiles between monozygotic twins' blood samples. Forensic Sci Int Genet 2019; 41:152-158. [PMID: 31132533 DOI: 10.1016/j.fsigen.2019.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022]
Abstract
Monozygotic (MZ) twins are widely regarded as genetically identical, and traditional DNA typing methods are insufficient in identifying MZ twins. So the discrimination of MZ twins become a forensic problem. MicroRNAs (miRNAs) are a class of small, endogenous, non-protein-coding RNA molecules of approximately 22 nucleotides in length, and exist extensively in a variety of eukaryotic cells. MiRNAs regulate gene expression and play fundamental roles in multiple biological processes, including cell differentiation, proliferation and apoptosis as well as aging and disease processes. The goal of this study is to explore the differential expression of miRNAs within MZ twin pairs, and aimed to find new biomarkers for distinguishing MZ twins. Thus, the miRNA expression profiles of seven pairs of healthy MZ twins of different sex and age were analyzed by miRNA microarray. A total of 545 miRNAs were found to be differentially expressed in these MZ twin pairs, and 2, 5, 22, 53 and 132 differentially expressed miRNAs were shared across six, five, four, three and two pairs of MZ twins respectively. These findings had been confirmed by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays on select miRNAs, including miR-151a-3p, miR-3653-3p, miR-142-3p, miR-4325, miR-16-5p, let-7i-5p, miR-222-3p, miR-550b-3p, miR-4791 and miR-27a-3p. The results demonstrated that there are differences in the expression of miRNAs within MZ twin pairs, suggesting a role of miRNAs in identifying MZ twins.
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Affiliation(s)
- Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Chao Pan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Erliang Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Tianjin Municipal Public Security Bureau Wuqing Branch, Tianjin, PR China
| | - Huayu He
- Xiaogan Municipal Public Security Bureau, Xiaogan, PR China
| | - Chunfeng Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yujie Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
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Distinguishing genetically between the germlines of male monozygotic twins. PLoS Genet 2018; 14:e1007756. [PMID: 30571769 PMCID: PMC6301568 DOI: 10.1371/journal.pgen.1007756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/10/2018] [Indexed: 11/19/2022] Open
Abstract
Identification of the potential donor(s) of human germline-derived cells is an issue in many criminal investigations and in paternity testing. The experimental and statistical methodology necessary to work up such cases is well established but may be more challenging if monozygotic (MZ) twins are involved. Then, elaborate genome-wide searches are required for the detection of early somatic mutations that distinguish the cell sample and its donor from the other twin, usually relying upon reference material other than semen (e.g. saliva). The first such cases, involving either criminal sexual offenses or paternity disputes, have been processed successfully by Eurofins Genomics and Forensics Campus. However, when presenting the experimental results in court, common forensic genetic practice requires that the residual uncertainty about donorship is quantified in the form of a likelihood ratio (LR). Hence, we developed a general mathematical framework for LR calculation, presented herein, which allows quantification of the evidence in favour of the true donor in the respective cases, based upon observed DNA sequencing read counts. In many instances of practical forensic casework, particularly when connected to sexual assault, genetic analysis is carried out to identify the likely donor of a sperm sample left at the crime scene. The experimental and statistical methodology for such investigations is well established. In cases involving monozygotic (MZ) twin suspects, however, the procedure is hampered by the fact that the two individuals usually coincide for the genetic markers tested. One way to overcome this problem is to use the latest DNA sequencing technology to undertake a genome-wide search for those few mutations that occur during early embryonic development and hence allow distinguishing between MZ twins in later life. Following this approach, the first cases of criminal sexual offense have been worked on successfully by Eurofins Genomics and Forensics Campus, leading to the identification of sperm sample donors from saliva reference samples taken from MZ twin suspects. As a matter of principle, however, the residual uncertainty of the experimental results needs to be evaluated and reported as well. Therefore, we developed a novel mathematical framework to quantify the evidential power of the genetic data in cases attempting to identify MZ twin donors, based upon comprehensive DNA sequencing. Moreover, we demonstrate that the same mathematical method can be used to resolve paternity disputes involving alleged fathers who have MZ twin brothers.
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Wisch JK, Farrell E, Siegel M, Freyermuth S. Misconceptions and persistence: resources for targeting student alternative conceptions in biotechnology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:602-611. [PMID: 30414242 DOI: 10.1002/bmb.21176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
Conceptual understanding and reasoning of nonscience major students enrolled in a course on biotechnology were evaluated before and after instruction. The instrument for analysis of student understanding was the Biotechnology Instrument for Knowledge Elicitation (BIKE). The BIKE targets 11 key concepts, as determined by experts in the field. A statistically significant score improvement was observed in each of the 11 concept areas after completion of the course, Biotechnology in Society (N = 117). Student responses to both the pretest and posttest were highly informative and revealed several common misconceptions that could have been overlooked in a closed form testing scenario. These alternative conceptions and recommended clarifications have been presented here. Our goal in documenting and distributing these is to better equip educators in biology and biochemistry to anticipate student preconceptions, design targeted interventions, and improve student conceptual reasoning in topics pertaining to biology and biotechnology. © 2018 International Union of Biochemistry and Molecular Biology, 46(6):602-611, 2018.
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Affiliation(s)
- Julie K Wisch
- Department of Neurology, Washington University, St. Louis, Missouri
| | - Emma Farrell
- School of Math and Natural Sciences, Arizona State University, Tempe, Arizona
| | - Marcelle Siegel
- Department of Biochemistry, Science Education Center, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Sharyn Freyermuth
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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Bruijns B, Tiggelaar R, Gardeniers H. Massively parallel sequencing techniques for forensics: A review. Electrophoresis 2018; 39:2642-2654. [PMID: 30101986 PMCID: PMC6282972 DOI: 10.1002/elps.201800082] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/07/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology, and medical diagnostics. Reflected by the growing number of articles published over the last 2-3 years, these techniques have also gained attention in the forensic field. This review contains a brief description of first, second, and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field. Relevance to the forensic analysis is that besides generation of standard STR-profiles, DNA repeats can also be sequenced to look for polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage analysis. These developments clearly demonstrate that the use of NGS will grow into an indispensable tool for forensic science.
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Affiliation(s)
- Brigitte Bruijns
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
- Life ScienceEngineering & DesignSaxion University of Applied SciencesEnschedeThe Netherlands
| | - Roald Tiggelaar
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
- NanoLab cleanroom, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
| | - Han Gardeniers
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
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DNA methylation-based age prediction using massively parallel sequencing data and multiple machine learning models. Forensic Sci Int Genet 2018; 37:215-226. [DOI: 10.1016/j.fsigen.2018.09.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/06/2018] [Indexed: 01/09/2023]
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Fang C, Zhao J, Liu X, Zhang J, Cao Y, Yang Y, Yu C, Zhang X, Qian J, Liu W, Wu H, Yan J. MicroRNA profile analysis for discrimination of monozygotic twins using massively parallel sequencing and real-time PCR. Forensic Sci Int Genet 2018; 38:23-31. [PMID: 30321748 DOI: 10.1016/j.fsigen.2018.09.011] [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: 02/12/2018] [Revised: 07/22/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022]
Abstract
In general, it is extremely problematic to discriminate between monozygotic twins (MZTs), who share the same genomic DNA sequence, using traditional DNA-based identification methods such as short tandem repeat profiling. MicroRNAs (miRNAs) have shown potential in forensic applications owing to their low molecular weight, abundant and tissue-specific expression. In this study, we utilized massively parallel sequencing technology to perform genome-wide profiling of miRNAs in the blood from four pairs of healthy MZTs. On average, 158 miRNAs were detected in each individual and 14% of which were differentially expressed within each pair of MZTs. The miRNAs with the most significant differences in expression between the twins were confirmed using real-time polymerase chain reaction. Our results demonstrated that miRNAs have potential for use as molecular markers in MZTs discrimination.
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Affiliation(s)
- Chen Fang
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xu Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jingjing Zhang
- Beijing Huayan Judicial Authentication Institute, Beijing 100192, PR China
| | - Yunwang Cao
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yaran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China
| | - Chunrui Yu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Xiaoli Zhang
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jialin Qian
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Wenli Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China; Beijing Gene Medical Laboratory Co., Ltd., Beijing 100094, PR China.
| | - Jiangwei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China.
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Marqueta-Gracia JJ, Álvarez-Álvarez M, Baeta M, Palencia-Madrid L, Prieto-Fernández E, Ordoñana JR, de Pancorbo MM. Differentially methylated CpG regions analyzed by PCR-high resolution melting for monozygotic twin pair discrimination. Forensic Sci Int Genet 2018; 37:e1-e5. [PMID: 30245065 DOI: 10.1016/j.fsigen.2018.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/06/2018] [Accepted: 08/24/2018] [Indexed: 11/28/2022]
Abstract
Discrimination between monozygotic (MZ) twins is a forensic limitation when using conventional DNA profiling techniques for human identification. Recent works based on epigenetics seem to open a new way to solve this issue due to methylation status of MZ twins change during their lifetime. Methylation analysis through BeadChip platforms allows the study up to 850 K CpG sites revealing that numerous differential methylation regions exist between MZ twins. However, this methodology is difficult to implement in forensic laboratories. On the contrary, PCR-HRM (High Resolution Melting) technology is one of the easiest methods for analyzing DNA methylation and it has been capable to discriminate between MZ twins. The purpose of this study is to contribute with new differential methylation regions in MZ twins to those that have been previously studied through PCR-HRM. Here, we have selected 6 CpG regions located at the ITGA2B, ASPA, PDE4C, ZIC5, USP11 and NOP14 loci that have shown methylation status variation during lifetime. The study has been carried out from saliva-derived DNA of 18 MZ twin pairs. The most discriminating regions were those located at ITGA2B, ASPA and ZIC5 loci showing significant within-pair differences in 44.4% of the cases. Non evidences of relation between age and significant differences between MZ twins were found, although the 50% of MZ twin pairs were discrimnated in the oldest age range (59-66 years old). These results support the use of these regions to increase the number of epigenetics age-related markers available to discriminate between MZ twins in a pair by PCR-HRM in forensic laboratories.
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Affiliation(s)
- José Javier Marqueta-Gracia
- BIOMICs Research Group, Centro de Investigación "Lascaray" Ikergunea, Universidad del País Vasco UPV/EHU, Av. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Maite Álvarez-Álvarez
- Proteomics and Genomics General Services: DNA Bank Unit (SGIker) University of Basque Country UPV/EHU, Av. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Centro de Investigación "Lascaray" Ikergunea, Universidad del País Vasco UPV/EHU, Av. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Centro de Investigación "Lascaray" Ikergunea, Universidad del País Vasco UPV/EHU, Av. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Endika Prieto-Fernández
- BIOMICs Research Group, Centro de Investigación "Lascaray" Ikergunea, Universidad del País Vasco UPV/EHU, Av. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Juan Ramón Ordoñana
- Department of Human Anatomy and Psychobiology and Murcia Institute for BioHealth Research (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Centro de Investigación "Lascaray" Ikergunea, Universidad del País Vasco UPV/EHU, Av. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain.
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Misattributed parentage as an unanticipated finding during exome/genome sequencing: current clinical laboratory practices and an opportunity for standardization. Genet Med 2018; 21:861-866. [DOI: 10.1038/s41436-018-0265-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
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42
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Recent progress, methods and perspectives in forensic epigenetics. Forensic Sci Int Genet 2018; 37:180-195. [PMID: 30176440 DOI: 10.1016/j.fsigen.2018.08.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 01/19/2023]
Abstract
Forensic epigenetics, i.e., investigating epigenetics variation to resolve forensically relevant questions unanswerable with standard forensic DNA profiling has been gaining substantial ground over the last few years. Differential DNA methylation among tissues and individuals has been proposed as useful resource for three forensic applications i) determining the tissue type of a human biological trace, ii) estimating the age of an unknown trace donor, and iii) differentiating between monozygotic twins. Thus far, forensic epigenetic investigations have used a wide range of methods for CpG marker discovery, prediction modelling and targeted DNA methylation analysis, all coming with advantages and disadvantages when it comes to forensic trace analysis. In this review, we summarize the most recent literature on these three main topics of current forensic epigenetic investigations and discuss limitations and practical considerations in experimental design and data interpretation, such as technical and biological biases. Moreover, we provide future perspectives with regard to new research questions, new epigenetic markers and recent technological advances that - as we envision - will move the field towards forensic epigenomics in the near future.
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43
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Amorim A, Pinto N. Big data in forensic genetics. Forensic Sci Int Genet 2018; 37:102-105. [PMID: 30142461 DOI: 10.1016/j.fsigen.2018.08.001] [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: 02/28/2018] [Revised: 07/23/2018] [Accepted: 08/01/2018] [Indexed: 12/16/2022]
Abstract
The potential and difficulties of the application of genome wide data in forensics are analyzed. We argue that, besides statistical, computational, ethical, economic and technical validation problems, the state of the art of population genetics theory is insufficient to deal with the forensic use of this type of data. In order to keep the current standards of quantifying and reporting genetic evidence, namely in kinship analyses and identification, substantial improvement in the theoretical framework should be reached, since to obtain genome-wide results is to provide the experts with data that they cannot quantify the corresponding evidentiary value. Therefore, while a satisfactory, generalized theoretical and biostatistical modelling is not achieved, it may well be wiser to improve the already established approaches to a limited, pre-defined number of validated genetic markers, amenable to a consensual handling and reporting. Whole genome population analyses will prove extremely useful in selecting the best suited and most efficient of those markers.
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Affiliation(s)
- António Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, Porto, Portugal; Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, Porto, Portugal; CMUP, Centro de Matemática da Universidade do Porto, Porto, Portugal.
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44
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Vidaki A, Kalamara V, Carnero-Montoro E, Spector TD, Bell JT, Kayser M. Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting. Genes (Basel) 2018; 9:E252. [PMID: 29758014 PMCID: PMC5977192 DOI: 10.3390/genes9050252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 12/28/2022] Open
Abstract
Monozygotic (MZ) twins are typically indistinguishable via forensic DNA profiling. Recently, we demonstrated that epigenetic differentiation of MZ twins is feasible; however, proportions of twin differentially methylated CpG sites (tDMSs) identified in reference-type blood DNA were not replicated in trace-type blood DNA. Here we investigated buccal swabs as typical forensic reference material, and saliva and cigarette butts as commonly encountered forensic trace materials. As an analog to a forensic case, we analyzed one MZ twin pair. Epigenome-wide microarray analysis in reference-type buccal DNA revealed 25 candidate tDMSs with >0.5 twin-to-twin differences. MethyLight quantitative PCR (qPCR) of 22 selected tDMSs in trace-type DNA revealed in saliva DNA that six tDMSs (27.3%) had >0.1 twin-to-twin differences, seven (31.8%) had smaller (<0.1) but robustly detected differences, whereas for nine (40.9%) the differences were in the opposite direction relative to the microarray data; for cigarette butt DNA, results were 50%, 22.7%, and 27.3%, respectively. The discrepancies between reference-type and trace-type DNA outcomes can be explained by cell composition differences, method-to-method variation, and other technical reasons including bisulfite conversion inefficiency. Our study highlights the importance of the DNA source and that careful characterization of biological and technical effects is needed before epigenetic MZ twin differentiation is applicable in forensic casework.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands.
| | - Vivian Kalamara
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands.
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands.
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Nowak J, Nestorowicz K, Graczyk-Pol E, Mika-Witkowska R, Rogatko-Koros M, Jaskula E, Koscinska K, Madej S, Tomaszewska A, Nasilowska-Adamska B, Szczepinski A, Halaburda K, Dybko J, Kuliczkowski K, Czerw T, Giebel S, Holowiecki J, Baranska M, Pieczonka A, Wachowiak J, Czyz A, Gil L, Lojko-Dankowska A, Komarnicki M, Bieniaszewska M, Kucharska A, Hellmann A, Gronkowska A, Jedrzejczak WW, Markiewicz M, Koclega A, Kyrcz-Krzemien S, Mielcarek M, Kalwak K, Styczynski J, Wysocki M, Drabko K, Wojcik B, Kowalczyk J, Gozdzik J, Pawliczak D, Gwozdowicz S, Dziopa J, Szlendak U, Witkowska A, Zubala M, Gawron A, Warzocha K, Lange A. HLA-inferred extended haplotype disparity level is more relevant than the level of HLA mismatch alone for the patients survival and GvHD in T cell-replate hematopoietic stem cell transplantation from unrelated donor. Hum Immunol 2018; 79:403-412. [PMID: 29605688 DOI: 10.1016/j.humimm.2018.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/18/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
Abstract
Serious risks in unrelated hematopoietic stem cell transplantation (HSCT) including graft versus host disease (GvHD) and mortality are associated with HLA disparity between donor and recipient. The increased risks might be dependent on disparity in not-routinely-tested multiple polymorphisms in genetically dense MHC region, being organized in combinations of two extended MHC haplotypes (Ehp). We assessed the clinical role of donor-recipient Ehp disparity levels in N = 889 patients by the population-based detection of HLA allele phase mismatch. We found increased GvHD incidences and mortality rates with increasing Ehp mismatch level even with the same HLA mismatch level. In multivariate analysis HLA mismatch levels were excluded from models and Ehp disparity level remained independent prognostic factor for high grade acute GvHD (p = 0.000037, HR = 10.68, 95%CI 5.50-32.5) and extended chronic GvHD (p < 0.000001, HR = 15.51, CI95% 5.36-44.8). In group with single HLA mismatch, patients with double Ehp disparity had worse 5-year overall survival (45% vs. 56%, p = 0.00065, HR = 4.05, CI95% 1.69-9.71) and non-relapse mortality (40% vs. 31%, p = 0.00037, HR = 5.63, CI95% 2.04-15.5) than patients with single Ehp disparity. We conclude that Ehp-linked factors contribute to the high morbidity and mortality in recipients given HLA-mismatched unrelated transplant and Ehp matching should be considered in clinical HSCT.
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Affiliation(s)
- Jacek Nowak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland.
| | - Klaudia Nestorowicz
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Elzbieta Graczyk-Pol
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Renata Mika-Witkowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marta Rogatko-Koros
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Emilia Jaskula
- Department of Clinical Immunology, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland; Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
| | - Katarzyna Koscinska
- Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
| | - Sylwia Madej
- Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
| | - Agnieszka Tomaszewska
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Barbara Nasilowska-Adamska
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Andrzej Szczepinski
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Kazimierz Halaburda
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Jaroslaw Dybko
- Department of Hematology, Blood Malignancies and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Kazimierz Kuliczkowski
- Department of Hematology, Blood Malignancies and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Tomasz Czerw
- Department of Bone Marrow Transplantation and Oncohematology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Sebastian Giebel
- Department of Bone Marrow Transplantation and Oncohematology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Jerzy Holowiecki
- Department of Bone Marrow Transplantation and Oncohematology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Malgorzata Baranska
- Department of Oncology Hematology and Paediatric Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Pieczonka
- Department of Oncology Hematology and Paediatric Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jacek Wachowiak
- Department of Oncology Hematology and Paediatric Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Czyz
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Lidia Gil
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Lojko-Dankowska
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Mieczyslaw Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Bieniaszewska
- Department of Hematology and Transplantology, Gdansk Medical University Clinical Center, Gdansk, Poland
| | - Agnieszka Kucharska
- Department of Hematology and Transplantology, Gdansk Medical University Clinical Center, Gdansk, Poland
| | - Andrzej Hellmann
- Department of Hematology and Transplantology, Gdansk Medical University Clinical Center, Gdansk, Poland
| | - Anna Gronkowska
- Department of Hematology, Oncology and Internal Medicine, Warsaw Medical University, Warsaw, Poland
| | - Wieslaw W Jedrzejczak
- Department of Hematology, Oncology and Internal Medicine, Warsaw Medical University, Warsaw, Poland
| | - Miroslaw Markiewicz
- Department of Hematology and Bone Marrow Transplantation, Silesian Medical University, Katowice, Poland
| | - Anna Koclega
- Department of Hematology and Bone Marrow Transplantation, Silesian Medical University, Katowice, Poland
| | - Slawomira Kyrcz-Krzemien
- Department of Hematology and Bone Marrow Transplantation, Silesian Medical University, Katowice, Poland
| | - Monika Mielcarek
- Department of Pediatric Hematology Oncology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Krzysztof Kalwak
- Department of Pediatric Hematology Oncology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Jan Styczynski
- Department of Pediatric Hematology and Oncology, Collegium Medicum Nicolaus Copernicus University Hospital, Bydgoszcz, Poland
| | - Mariusz Wysocki
- Department of Pediatric Hematology and Oncology, Collegium Medicum Nicolaus Copernicus University Hospital, Bydgoszcz, Poland
| | - Katarzyna Drabko
- Department of Paediatric Hematology, Oncology and Transplantology, Medical University, Lublin, Poland
| | - Beata Wojcik
- Department of Paediatric Hematology, Oncology and Transplantology, Medical University, Lublin, Poland
| | - Jerzy Kowalczyk
- Department of Paediatric Hematology, Oncology and Transplantology, Medical University, Lublin, Poland
| | - Jolanta Gozdzik
- Department of Transplantation Children's University Hospital, Polish-American Institute of Pediatrics, Jagiellonian University Medical College, Cracow, Poland
| | - Daria Pawliczak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Slawomir Gwozdowicz
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Joanna Dziopa
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Urszula Szlendak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Agnieszka Witkowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marta Zubala
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Agnieszka Gawron
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Krzysztof Warzocha
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Andrzej Lange
- Department of Clinical Immunology, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland; Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
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46
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Yao L, Xu Z, Zhao H, Tu Z, Liu Z, Li W, Hu L, Wan L. Concordance of mitochondrial DNA sequencing methods on bloodstains using Ion PGM™. Leg Med (Tokyo) 2018; 32:27-30. [PMID: 29499472 DOI: 10.1016/j.legalmed.2018.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 12/03/2017] [Accepted: 02/23/2018] [Indexed: 11/28/2022]
Abstract
In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicons. All amplicons were successfully recovered. A phylogenetic analysis was performed to determine the accuracy of the PGM data, and which were compared to partial Sanger-based sequencing data. The average coverage of the PGM data were above 4000× in all case samples, and 99.86% concordance was observed using both sequencing methods. In conclusion, we demonstrate the ability to recover the complete mtGenome from bloodstains with relatively poor DNA quality by PGM. Moreover, the results are concordant with Sanger sequencing data. This new method has potential use in forensic practice.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Hemiao Zhao
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zheng Tu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zhifang Liu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Wanshui Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lan Hu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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47
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Churbanov A, Abrahamyan L. Preventing Common Hereditary Disorders through Time-Separated Twinning. BIONANOSCIENCE 2018. [DOI: 10.1007/s12668-017-0488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018. [DOI: 10.1007/s12038-018-9741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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49
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Crime investigation through DNA methylation analysis: methods and applications in forensics. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0042-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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50
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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