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Salvo NM, Olsen GH, Berg T, Janssen K. Biogeographical Ancestry Analyses Using the ForenSeq TM DNA Signature Prep Kit and Multiple Prediction Tools. Genes (Basel) 2024; 15:510. [PMID: 38674444 PMCID: PMC11050699 DOI: 10.3390/genes15040510] [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: 03/17/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The inference of biogeographical ancestry (BGA) can assist in police investigations of serious crime cases and help to identify missing people and victims of mass disasters. In this study, we evaluated the typing performance of 56 ancestry-informative SNPs in 177 samples using the ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx system. Furthermore, we compared the prediction accuracy of the tools Universal Analysis Software v1.2 (UAS), the FROG-kb, and GenoGeographer when inferring the ancestry of 503 Europeans, 22 non-Europeans, and 5 individuals with co-ancestry. The kit was highly sensitive with complete aiSNP profiles in samples with as low as 250pg input DNA. However, in line with others, we observed low read depth and occasional drop-out in some SNPs. Therefore, we suggest not using less than the recommended 1ng of input DNA. FROG-kb and GenoGeographer accurately predicted both Europeans (99.6% and 91.8% correct, respectively) and non-Europeans (95.4% and 90.9% correct, respectively). The UAS was highly accurate when predicting Europeans (96.0% correct) but performed poorer when predicting non-Europeans (40.9% correct). None of the tools were able to correctly predict individuals with co-ancestry. Our study demonstrates that the use of multiple prediction tools will increase the prediction accuracy of BGA inference in forensic casework.
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Affiliation(s)
- Nina Mjølsnes Salvo
- Centre for Forensic Genetics, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Post Box 6050, 9037 Tromsø, Norway
| | | | | | - Kirstin Janssen
- Centre for Forensic Genetics, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Post Box 6050, 9037 Tromsø, Norway
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Lai L, Liu L, Wang Y, Liu S, Zhang J, Zheng X. QR code technology in individual identification training provides an introduction in hands-on forensic DNA genotyping to medical students. BMC MEDICAL EDUCATION 2023; 23:314. [PMID: 37147637 PMCID: PMC10161171 DOI: 10.1186/s12909-023-04284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Forensic biology is a subject in the field of forensic science that stresses practical teaching and training in laboratory skills. Visualization of deoxyribonucleic acid (DNA) profiles is important in individual identification and is easily performed by well-trained examiners. Therefore, developing a novel training project for obtaining individual DNA profiles can improve the quality of teaching for medical students or trainees. DNA profiles based on quick response (QR) codes can also be applied to practical teaching and operation training for individual identification. METHODS A novel training project was developed through an experimental course in forensic biology. Blood samples and buccal swabs with oral epithelial cells, as used in the forensic DNA laboratory, were obtained from medical students at Fujian Medical University. DNA was isolated, and a number of short tandem repeat (STR) loci were used as genetic markers to generate DNA profiles. The students converted DNA profiles and individual information into a QR code. The QR code could then be scanned by a mobile phone for consulting and retrieval. Gene identity cards with QR codes were produced and provided to every student. The participation rate and passing rate of students who participated in the novel training project were calculated and compared with those of students in the traditional experimental course, and a chi-square test was carried out by SPSS 23.0 software to evaluate the teaching effectiveness. p < 0.05 indicated significant differences. In addition, a survey was conducted to investigate the likelihood of using of gene identity cards with QR codes in the future. RESULTS A total of 54 of 91 medical students who studied forensic biology participated in the novel training project in 2021. Only 31 of 78 students who studied forensic biology participated in the traditional experimental course in 2020. The participation rate in the novel training project was 24% higher than that of the traditional experimental course. The participants in the novel training project showed better performance in forensic biological handling techniques. The passing rate of the students in the forensic biology course with the novel training project was approximately 17% higher than that of the students in the former course. The participation rates and passing rates of the two groups were significantly different (χ = 6.452, p = 0.008 and χ = 11.043, p = 0.001). In the novel training project, all participants made 54 gene identity cards with QR codes. Furthermore, in the DNA profiles of four African students who participated, we found two rare alleles that were not discovered in Asians. The survey showed that the use of gene identity cards with QR codes was accepted by most participants, and the likelihood of future utilization was 78%. CONCLUSION We established a novel training project to promote the learning activities of medical students in experimental forensic biology courses. The participants showed great interest in using gene identity cards with QR codes to store general individual identity information and DNA profiles. They also examined the genetic population differences between different races based on DNA profiles. Hence, the novel training project could be useful for training workshops, forensic experimental courses, and medical big data research.
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Affiliation(s)
- Li Lai
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China.
- Central Laboratory of Fujian Provincial Hospital, No.134 East Road, Fujian, Fuzhou, 350001, China.
| | - Li Liu
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Yaochen Wang
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
- Central Laboratory of Fujian Provincial Hospital, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Shanlong Liu
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
- Central Laboratory of Fujian Provincial Hospital, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Jiancheng Zhang
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Xiaochun Zheng
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
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3
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Frégeau CJ. A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2021. [DOI: 10.1080/00085030.2021.2016206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chantal J. Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, Ottawa, ON, Canada
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Weisz NA, Roberts KA, Hardy WR. Reliability of phenotype estimation and extended classification of ancestry using decedent samples. Int J Legal Med 2021; 135:2221-2233. [PMID: 34436656 DOI: 10.1007/s00414-021-02631-x] [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: 12/16/2020] [Accepted: 06/04/2021] [Indexed: 11/30/2022]
Abstract
The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both markers have been validated for use in forensic biology, there is little data to determine the practical utility of these estimations to assist in identifying missing persons using decedent casework samples. The accuracy and utility of phenotypic and ancestral estimations were investigated for 300 samples received by the Los Angeles County Department of Medical Examiner-Coroner. piSNP genotypes were translated into hair and eye colors using the Forenseq™ Universal Analysis Software (UAS) on the MiSeq FGx™ and the HIrisPlex System, and statistical accuracy was evaluated in context with the reported decedent characteristics. Similarly, estimates of each decedent's biogeographical ancestry were compared to assess the efficacy of these markers to predict ancestry correctly. The average UAS and the HIrisPlex system prediction accuracy for brown and blue eyes were 95.3% and 96.2%, respectively. Intermediate eye color could not be predicted with high accuracy using either system. Other than the black hair phenotype reporting an accuracy that exceeded 90% using either system, hair color was also too variable to be predicted with high accuracy. The FROG-kb database distinguishes decedents adequately beyond the Asian, African, European, and Admixed American global ancestries provided by the MiSeq FGx™ UAS PCA plots. FROG-kb correctly identified Middle Eastern, Pacific Islander, Latin American, or Jewish ancestries with accuracies of 70.0%, 81.8%, 73.8%, and 86.7%, respectively.
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Affiliation(s)
- Naomi A Weisz
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA
| | - Katherine A Roberts
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA. .,California Forensic Science Institute, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA.
| | - W Reef Hardy
- Human Genomics Unit, Los Angeles County Department of Medical Examiner-Coroner, 1104 N Mission Road, Los Angeles, CA, 90033, USA
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Frégeau CJ. Validation of the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B for phenotypic and biogeographical ancestry predictions using the Micro MiSeq® Flow Cells. Forensic Sci Int Genet 2021; 53:102533. [PMID: 34058534 DOI: 10.1016/j.fsigen.2021.102533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
In anticipation of offering phenotypic and biogeographical ancestry predictions to help resolve cases, the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B was evaluated in the context of Micro MiSeq® Flow Cells. These flow cells were determined as the best format for a quick turnaround time response and cost effective approach compared to standard flow cells. The phenotype informative SNPs (piSNPs) and ancestry informative SNPs (aiSNPs) were thoroughly examined through sensitivity, reproducibility and repeatability, concordance, robustness (mock casework) and low level DNA mixture studies purposely selecting individuals with different phenotypes (hair and eye color) when possible and different biogeographical ancestry. SNP locus-specific interpretation thresholds were established for the Universal Analysis Software (UAS) based on surviving alleles and SNP predictor rank to minimize false homozygous genotypes and maximize the information that can be derived from an unknown sample. Dropin alleles' intensity determined an appropriate threshold to minimize false heterozygous SNP genotypes. The selection of inappropriate interpretation thresholds was shown to have major consequences on phenotypic predictions. A 3.2% and 4.8% minor DNA component contribution to a DNA mixture had no impact on ancestry predictions whereas a 9.1% contribution did. The multi-locus SNP genotypes generated using the ForenSeq™ DNA Signature Prep kit/Primer Mix B were shown to be reliable, reproducible, concordant and resulted in predictions that were also reliable, reproducible and concordant based on the limited number of donors (N = 19) used in this study.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
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Progress in the implementation of massively parallel sequencing for forensic genetics: results of a European-wide survey among professional users. Int J Legal Med 2021; 135:1425-1432. [PMID: 33847802 PMCID: PMC8205868 DOI: 10.1007/s00414-021-02569-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/10/2021] [Indexed: 01/21/2023]
Abstract
A European-wide online survey was conducted to generate an overview on the state-of-the-art using massively parallel sequencing (MPS) platforms for forensic DNA analysis and DNA phenotyping among forensic practitioners in Europe. The survey was part of the dissemination activities of the “VISible Attributes through GEnomics – VISAGE” Horizon 2020 funded European research project [30], in preparation of a series of educational training activities. A total of 105 replies from 32 European countries representing participants from police, governmental, academic, and private laboratories providing professional services in the field of forensic genetics were included in the final analysis. Of these, 73% already own an MPS platform or are planning to acquire one within the next 1–2 years. One-third of the participants have already carried out MPS-based STR sequencing, identity, or ancestry SNP typing. A total of 23–40% of participants are planning to explore all FDP applications showing the overall very high interest in using MPS for the whole range of forensic MPS markers and applications. About 50% of the participants have previously gathered experience using forensic DNA phenotyping (FDP) markers based on conventional (i.e., not MPS-based) DNA typing methods. A total of 55% of the participants have attended training on the general use of MPS technology, but 36% have received no training whatsoever. Accordingly, 90% have expressed high or medium interest to attend training on the analysis and interpretation of DNA phenotyping data for predicting appearance, ancestry, and age. The results of our survey will provide valuable information for organizing relevant training workshops on all aspects of MPS-based DNA phenotyping for the forensic genetics scientific community.
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Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes (Basel) 2020; 11:genes11121398. [PMID: 33255693 PMCID: PMC7760956 DOI: 10.3390/genes11121398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/21/2022] Open
Abstract
As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.
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8
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Barrio PA, García Ó, Phillips C, Prieto L, Gusmão L, Fernández C, Casals F, Freitas JM, González-Albo MDC, Martín P, Mosquera A, Navarro-Vera I, Paredes M, Pérez JA, Pinzón A, Rasal R, Ruiz-Ramírez J, Trindade BR, Alonso A. The first GHEP-ISFG collaborative exercise on forensic applications of massively parallel sequencing. Forensic Sci Int Genet 2020; 49:102391. [PMID: 32957016 DOI: 10.1016/j.fsigen.2020.102391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/17/2023]
Abstract
One of the main goals of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. The GHEP-ISFG supports several Working Commissions which develop different scientific activities. One of them, the Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications", organized its first collaborative exercise on forensic applications of MPS technology in 2019. The aim of this exercise was to assess the concordance between the MPS results and those obtained with conventional technologies (capillary electrophoresis and Sanger sequencing), as well as to compare the results obtained within the different MPS platforms and/or the different kits/panels and analysis software packages (commercial and open-access) available on the market. The seven participating laboratories analyzed some samples of the annual GHEP-ISFG proficiency test (EIADN No. 27 (2019)), using Ion Torrent™ or MiSeq FGx® platforms. Six of them sent autosomal STR sequence data, five laboratories performed MPS analysis of individual identification SNPs, four laboratories reported MPS data of Y-chromosomal STRs, and X-chromosomal STRs, three laboratories performed MPS analysis of ancestry informative SNPs and phenotype informative SNPs, two labs performed MPS analysis of the mitochondrial DNA control region, and only one lab produced MPS data of lineage informative SNPs. Autosomal STR sequencing results were highly concordant to the consensus obtained by capillary electrophoresis in the EIADN No. 27 (2019) exercise. Furthermore, in general, a high level of concordance was observed between the results of the participating laboratories, regardless of the platform used. The main discordances were due to errors during the analysis process or from sequence data obtained with low depth of coverage. In this paper we highlight some issues that still arise, such as standardization of the nomenclature for STRs analyzed by sequencing with MPS, the universal uptake of a nomenclature framework by the analysis software, and well established validation and accreditation of the new MPS platforms for use in routine forensic case-work.
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Affiliation(s)
- Pedro A Barrio
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain.
| | - Óscar García
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - Christopher Phillips
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - Lourdes Prieto
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Genetics Unit, University of Santiago de Compostela, Spain; Comisaría General de Policía Científica, Madrid, Spain
| | - Leonor Gusmão
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; DNA Diagnostics Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Coro Fernández
- Quality Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jorge M Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brazil
| | | | - Pablo Martín
- Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
| | - Ana Mosquera
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | | | - Manuel Paredes
- Subdirección de Investigación Científica, Instituto Nacional de Medicina Legal y Ciencias Forenses, Colombia
| | - Juan Antonio Pérez
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - Andrea Pinzón
- Grupo Nacional de Ciencias Forenses, Instituto Nacional de Medicina Legal y Ciencias Forenses, Colombia
| | - Raquel Rasal
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | - Antonio Alonso
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
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9
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Pereira V, Santangelo R, Børsting C, Tvedebrink T, Almeida APF, Carvalho EF, Morling N, Gusmão L. Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations. Front Genet 2020; 11:966. [PMID: 32973885 PMCID: PMC7472784 DOI: 10.3389/fgene.2020.00966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect's BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.
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Affiliation(s)
- Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roberta Santangelo
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Ana Paula F Almeida
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizeu F Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto de Investigação e Inovação em Saúde, i3S, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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Elsaid HH, El-Hefnawy KA, Elalawi SM. C677T MTHFR Gene Polymorphism is Contributing Factor in Development of Renal Impairment in Young Hypertensive Patients. Indian J Clin Biochem 2020; 36:213-220. [PMID: 33867713 DOI: 10.1007/s12291-020-00890-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/01/2020] [Indexed: 12/27/2022]
Abstract
Homocysteine concentration affected by the activities of the enzymes methylene tetra-hyrdofolate reductase (MTHFR). Polymorphisms in MTHFR gene associated with an impairment of MTHFR activity. Hyperhomocysteinemia is a result of single nucleotide polymorphisms (SNPs) in MTHFR 677 C>T that can cause homocysteine levels in the blood to increase. The purpose of this study is to investigate the relationships between MTHFR C677T (rs1801133) gene polymorphism, changes in homocysteine concentrations and progress of renal impairment in young adult hypertensive patients. Two hundred young hypertensive patients (age 21-24 years) were involved in this study; they were classified into patients with and without renal impairment in addition to 200 age and sex matched healthy controls. All participants were submitted to laboratory investigations as assay of MTHFR gene polymorphism C677T (rs1801133) by PCR/RFLP, determination of lipid profile, homocysteine and folic acid concentrations in addition to urinary albumin creatinine ratio (UACR). The levels of both homocysteine and UACR in the TT genotype patients were higher than those in the CC genotype group. Individuals who carry the T allele were more risky to hypertension and progress to early renal impairment in young age compared with those carrying the C allele [OR 2.02 (1.33-3.08), P < 0.001]. Genetic variants of C677T MTHFR gene and hyperhomocysteinemia may be responsible for rapid progress of renal impairment in Egyptian young age hypertensive patients. TT genotype or T allele may be considered as a predisposing factor for both elevated Hcy levels and the development of renal impairment. This study believed that lowering of homocysteine level can reduce renal impairment of hypertensive patients.
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Affiliation(s)
- Hanaa H Elsaid
- Clinical Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Khaled A El-Hefnawy
- Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Saffaa M Elalawi
- Clinical Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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11
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FrogAncestryCalc: A standalone batch likelihood computation tool for ancestry inference panels catalogued in FROG-kb. Forensic Sci Int Genet 2020; 46:102237. [DOI: 10.1016/j.fsigen.2020.102237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/11/2019] [Accepted: 01/12/2020] [Indexed: 01/06/2023]
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12
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Guo Y, Jin X, Xia Z, Chen C, Cui W, Zhu B. A small NGS–SNP panel of ancestry inference designed to distinguish African, European, East, and South Asian populations. Electrophoresis 2020; 41:649-656. [DOI: 10.1002/elps.201900231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/09/2020] [Accepted: 01/15/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Yu‐Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Xiao‐Ye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Zhi‐Yu Xia
- Department of EpidemiologyUniversity of Washington Seattle WA USA
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Bo‐Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of Stomatology, Xi'an Jiaotong University Xi'an P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center Xi'an P. R. China
- Department of Forensic GeneticsSchool of Forensic Medicine, Southern Medical University Guangzhou P. R. China
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13
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Ambers A, Bus MM, King JL, Jones B, Durst J, Bruseth JE, Gill-King H, Budowle B. Forensic genetic investigation of human skeletal remains recovered from the La Belle shipwreck. Forensic Sci Int 2020; 306:110050. [DOI: 10.1016/j.forsciint.2019.110050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 10/25/2022]
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14
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England R, Harbison S. A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ryan England
- Forensic Science Program, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Sallyann Harbison
- Institute of Environmental Science and Research Ltd Auckland New Zealand
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15
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Sharma V, Jani K, Khosla P, Butler E, Siegel D, Wurmbach E. Evaluation of ForenSeq™ Signature Prep Kit B on predicting eye and hair coloration as well as biogeographical ancestry by using Universal Analysis Software (UAS) and available web‐tools. Electrophoresis 2019; 40:1353-1364. [DOI: 10.1002/elps.201800344] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 12/07/2018] [Accepted: 01/14/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Vishakha Sharma
- Office of Chief Medical ExaminerDepartment of Forensic Biology New York NY USA
| | - Krupa Jani
- Office of Chief Medical ExaminerDepartment of Forensic Biology New York NY USA
| | - Pavan Khosla
- Office of Chief Medical ExaminerDepartment of Forensic Biology New York NY USA
| | - Erin Butler
- Office of Chief Medical ExaminerDepartment of Forensic Biology New York NY USA
| | - Donald Siegel
- Office of Chief Medical ExaminerDepartment of Forensic Biology New York NY USA
| | - Elisa Wurmbach
- Office of Chief Medical ExaminerDepartment of Forensic Biology New York NY USA
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16
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Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Sci Int Genet 2018; 38:54-69. [PMID: 30347322 DOI: 10.1016/j.fsigen.2018.09.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/28/2023]
Abstract
Microhaplotype loci (microhaps, MHs) are a novel type of molecular marker of less than 300 nucleotides, defined by two or more closely linked SNPs associated in multiple allelic combinations. The value of these markers is enhanced by massively parallel sequencing (MPS), which allows the sequencing of both parental haplotypes at each of the many multiplexed loci. This review describes the features of these multi-SNP markers and documents their value in forensic genetics, focusing on individualization, biogeographic ancestry inference, and mixture deconvolution. Foreseeable applications also include missing person identification, relationship testing, and medical diagnostic applications. The technique is not restricted to humans.
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Affiliation(s)
- Fabio Oldoni
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States
| | - Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Daniele Podini
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States.
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17
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King JL, Churchill JD, Novroski NM, Zeng X, Warshauer DH, Seah LH, Budowle B. Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet 2018; 36:60-76. [DOI: 10.1016/j.fsigen.2018.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/03/2018] [Accepted: 06/05/2018] [Indexed: 11/26/2022]
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18
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Bulbul O, Filoglu G. Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing. Electrophoresis 2018; 39:2743-2751. [DOI: 10.1002/elps.201800243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
| | - Gonul Filoglu
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
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19
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Improving ancestry distinctions among Southwest Asian populations. Forensic Sci Int Genet 2018; 35:14-20. [DOI: 10.1016/j.fsigen.2018.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/10/2018] [Accepted: 03/22/2018] [Indexed: 12/20/2022]
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20
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Kidd KK, Soundararajan U, Rajeevan H, Pakstis AJ, Moore KN, Ropero-Miller JD. The redesigned Forensic Research/Reference on Genetics-knowledge base, FROG-kb. Forensic Sci Int Genet 2018; 33:33-37. [DOI: 10.1016/j.fsigen.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 01/22/2023]
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21
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A review of bioinformatic methods for forensic DNA analyses. Forensic Sci Int Genet 2017; 33:117-128. [PMID: 29247928 DOI: 10.1016/j.fsigen.2017.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/30/2017] [Accepted: 12/10/2017] [Indexed: 12/20/2022]
Abstract
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used.
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22
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García O, Ajuriagerra J, Alday A, Alonso S, Pérez J, Soto A, Uriarte I, Yurrebaso I. Frequencies of the precision ID ancestry panel markers in Basques using the Ion Torrent PGM TM platform. Forensic Sci Int Genet 2017; 31:e1-e4. [DOI: 10.1016/j.fsigen.2017.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/03/2017] [Accepted: 09/08/2017] [Indexed: 01/13/2023]
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23
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Sun Q, Jiang L, Zhang G, Liu J, Zhao L, Zhao W, Li C. Twenty-seven continental ancestry-informative SNP analysis of bone remains to resolve a forensic case. Forensic Sci Res 2017; 4:364-366. [PMID: 32002497 PMCID: PMC6968571 DOI: 10.1080/20961790.2017.1306431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/22/2017] [Indexed: 12/30/2022] Open
Abstract
We employed our previously developed 27-plex ancestry-informative single nucleotide polymorphism (SNP) panel to infer the ancestral components of bone remains of a possible foreign pilot found in south-western China. For ancestry assignment of this unknown individual, we first obtained the 27-SNP genotype of the individual. Then, based on a reference database of 3081 individuals from 33 populations, we calculated the match probability and likelihood ratio using the self-developed software program Forensic Intelligence. Inferred ancestral components of this individual were calculated by structure at K = 3. A complete profile was obtained for the individual using our multiplexed SNP assay. The European population was within one order of magnitude of the highest likelihood. The major ancestral component of this individual was 97.6% European.
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Affiliation(s)
- Qifan Sun
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Li Jiang
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Guangfeng Zhang
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Jing Liu
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Lei Zhao
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Wenting Zhao
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Caixia Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
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24
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Abd El-Aziz TA, Mohamed RH. Influence of MTHFR C677T gene polymorphism in the development of cardiovascular disease in Egyptian patients with rheumatoid arthritis. Gene 2017; 610:127-132. [PMID: 28215593 DOI: 10.1016/j.gene.2017.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 02/01/2017] [Accepted: 02/09/2017] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To investigate the association between increased carotid intima-media thickness (CIMT), homocysteine level, and MTHFR C677T (rs1801133) gene polymorphism in Egyptian people with rheumatoid arthritis (RA). SUBJECTS AND METHODS 280 Egyptian women (160 RA patients and 120 controls) were included in the study. CIMT was measured using high resolution B-mode ultrasonography and homocysteine levels were measured using enzyme-linked immunosorbent assay. While, MTHFR C677T polymorphism was analyzed by polymerase chain reaction-restriction fragment length polymorphism. RESULTS We found that subjects who carried the TT genotype and T allele were significantly more likely to develop RA with 2.9 and 1.5 fold, respectively. RA patients carrying the T allele presented a statistically significant increased risk of developing atherosclerosis compared with those carrying the C allele. Moreover, MTHFR TT genotype was independent risk factor of thick CIMT. CONCLUSIONS C677T MTHFR gene polymorphism is associated with RA in Egyptians. MTHFR 677TT carriers had higher concentrations of serum Hcy than did subjects harboring the CC and CT genotypes. The presence of 677T allele increases the risk of atherosclerosis in patients with RA. This increased risk of atherosclerosis could be due to hyperhomocysteinemia.
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Affiliation(s)
- Tarek A Abd El-Aziz
- Cardiology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Rasha H Mohamed
- Biochemistry Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt.
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25
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A preliminary assessment of the ForenSeq™ FGx System: next generation sequencing of an STR and SNP multiplex. Int J Legal Med 2016; 131:73-86. [DOI: 10.1007/s00414-016-1457-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
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26
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Fan GY, Ye Y, Hou YP. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome. Sci Rep 2016; 6:32178. [PMID: 27535707 PMCID: PMC4989243 DOI: 10.1038/srep32178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/03/2016] [Indexed: 01/15/2023] Open
Abstract
Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.
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Affiliation(s)
- Guang Yao Fan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
- The Center for Forensic Science Research, Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
| | - Yi Ye
- The Center for Forensic Science Research, Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
- Department of Forensic Analytical Toxicology, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yi Ping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
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27
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Hollard C, Keyser C, Delabarde T, Gonzalez A, Vilela Lamego C, Zvénigorosky V, Ludes B. Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case. Int J Legal Med 2016; 131:351-358. [DOI: 10.1007/s00414-016-1425-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 12/23/2022]
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28
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A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia. Forensic Sci Int Genet 2016; 23:101-110. [DOI: 10.1016/j.fsigen.2016.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/17/2016] [Accepted: 04/01/2016] [Indexed: 02/04/2023]
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29
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Bulbul O, Cherni L, Khodjet-el-khil H, Rajeevan H, Kidd KK. Evaluating a subset of ancestry informative SNPs for discriminating among Southwest Asian and circum-Mediterranean populations. Forensic Sci Int Genet 2016; 23:153-158. [DOI: 10.1016/j.fsigen.2016.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/27/2022]
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30
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Pilli E, Agostino A, Vergani D, Salata E, Ciuna I, Berti A, Caramelli D, Lambiase S. Human identification by lice: A Next Generation Sequencing challenge. Forensic Sci Int 2016; 266:e71-e78. [PMID: 27289564 DOI: 10.1016/j.forsciint.2016.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/13/2016] [Accepted: 05/08/2016] [Indexed: 11/20/2022]
Abstract
Rapid and progressive advances in molecular biology techniques and the advent of Next Generation Sequencing (NGS) have opened new possibilities for analyses also in the identification of entomological matrixes. Insects and other arthropods are widespread in nature and those found at a crime scene can provide a useful contribution to forensic investigations. Entomological evidence is used by experts to define the postmortem interval (PMI), which is essentially based on morphological recognition of the insect and an estimation of its insect life cycle stage. However, molecular genotyping methods can also provide an important support for forensic entomological investigations when the identification of species or human genetic material is required. This case study concerns a collection of insects found in the house of a woman who died from unknown causes. Initially the insects were identified morphologically as belonging to the Pediculidae family, and then, human DNA was extracted and analyzed from their gastrointestinal tract. The application of the latest generation forensic DNA assays, such as the Quantifiler(®) Trio DNA Quantification Kit and the HID-Ion AmpliSeq™ Identity Panel (Applied Biosystems(®)), individuated the presence of human DNA in the samples and determined the genetic profile.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Firenze, Italy.
| | - Alessandro Agostino
- Life Sciences Solutions, Thermo Fisher Scientific, Via Tiepolo 1, 20090 Monza, Italy
| | - Debora Vergani
- Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Viale Forlanini, 12, 27100 Pavia, Italy
| | - Elena Salata
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Roma, Italy
| | - Ignazio Ciuna
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Roma, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Roma, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Firenze, Italy
| | - Simonetta Lambiase
- Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Viale Forlanini, 12, 27100 Pavia, Italy
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31
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Pakstis AJ, Haigh E, Cherni L, ElGaaied ABA, Barton A, Evsanaa B, Togtokh A, Brissenden J, Roscoe J, Bulbul O, Filoglu G, Gurkan C, Meiklejohn KA, Robertson JM, Li CX, Wei YL, Li H, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK. 52 additional reference population samples for the 55 AISNP panel. Forensic Sci Int Genet 2015; 19:269-271. [DOI: 10.1016/j.fsigen.2015.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/16/2015] [Accepted: 08/07/2015] [Indexed: 12/31/2022]
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32
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Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet 2015; 18:49-65. [DOI: 10.1016/j.fsigen.2015.05.012] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/02/2015] [Accepted: 05/14/2015] [Indexed: 01/20/2023]
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33
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Freire-Aradas A, Ruiz Y, Phillips C, Maroñas O, Söchtig J, Tato AG, Dios JÁ, de Cal MC, Silbiger V, Luchessi A, Luchessi A, Chiurillo M, Carracedo Á, Lareu M. Exploring iris colour prediction and ancestry inference in admixed populations of South America. Forensic Sci Int Genet 2014; 13:3-9. [DOI: 10.1016/j.fsigen.2014.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
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34
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Kidd KK, Pakstis AJ, Speed WC, Lagacé R, Chang J, Wootton S, Haigh E, Kidd JR. Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. Forensic Sci Int Genet 2014; 12:215-24. [PMID: 25038325 DOI: 10.1016/j.fsigen.2014.06.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/01/2014] [Accepted: 06/23/2014] [Indexed: 11/24/2022]
Abstract
SNPs that are molecularly very close (<10kb) will generally have extremely low recombination rates, much less than 10(-4). Multiple haplotypes will often exist because of the history of the origins of the variants at the different sites, rare recombinants, and the vagaries of random genetic drift and/or selection. Such multiallelic haplotype loci are potentially important in forensic work for individual identification, for defining ancestry, and for identifying familial relationships. The new DNA sequencing capabilities currently available make possible continuous runs of a few hundred base pairs so that we can now determine the allelic combination of multiple SNPs on each chromosome of an individual, i.e., the phase, for multiple SNPs within a small segment of DNA. Therefore, we have begun to identify regions, encompassing two to four SNPs with an extent of <200bp that define multiallelic haplotype loci. We have identified candidate regions and have collected pilot data on many candidate microhaplotype loci. Here we present 31 microhaplotype loci that have at least three alleles, have high heterozygosity, are globally informative, and are statistically independent at the population level. This study of microhaplotype loci (microhaps) provides proof of principle that such markers exist and validates their usefulness for ancestry inference, lineage-clan-family inference, and individual identification. The true value of microhaplotypes will come with sequencing methods that can establish alleles unambiguously, including disentangling of mixtures, because a single sequencing run on a single strand of DNA will encompass all of the SNPs.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA.
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Joseph Chang
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Sharon Wootton
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Eva Haigh
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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35
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Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 2014; 10:23-32. [DOI: 10.1016/j.fsigen.2014.01.002] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/31/2023]
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36
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Yun L, Gu Y, Rajeevan H, Kidd KK. Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. Int J Legal Med 2014; 128:447-53. [DOI: 10.1007/s00414-013-0953-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022]
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37
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MTHFR C677T and A1298C gene polymorphisms and their relation to homocysteine level in Egyptian children with congenital heart diseases. Gene 2013; 529:119-24. [DOI: 10.1016/j.gene.2013.07.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/08/2013] [Accepted: 07/12/2013] [Indexed: 01/08/2023]
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38
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Nievergelt CM, Maihofer AX, Shekhtman T, Libiger O, Wang X, Kidd KK, Kidd JR. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. INVESTIGATIVE GENETICS 2013; 4:13. [PMID: 23815888 PMCID: PMC3699392 DOI: 10.1186/2041-2223-4-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 05/14/2013] [Indexed: 02/07/2023]
Abstract
Background Accurate determination of genetic ancestry is of high interest for many areas such as biomedical research, personal genomics and forensics. It remains an important topic in genetic association studies, as it has been shown that population stratification, if not appropriately considered, can lead to false-positive and -negative results. While large association studies typically extract ancestry information from available genome-wide SNP genotypes, many important clinical data sets on rare phenotypes and historical collections assembled before the GWAS area are in need of a feasible method (i.e., ease of genotyping, small number of markers) to infer the geographic origin and potential admixture of the study subjects. Here we report on the development, application and limitations of a small, multiplexable ancestry informative marker (AIM) panel of SNPs (or AISNP) developed specifically for this purpose. Results Based on worldwide populations from the HGDP, a 41-AIM AISNP panel for multiplex application with the ABI SNPlex and a subset with 31 AIMs for the Sequenome iPLEX system were selected and found to be highly informative for inferring ancestry among the seven continental regions Africa, the Middle East, Europe, Central/South Asia, East Asia, the Americas and Oceania. The panel was found to be least informative for Eurasian populations, and additional AIMs for a higher resolution are suggested. A large reference set including over 4,000 subjects collected from 120 global populations was assembled to facilitate accurate ancestry determination. We show practical applications of this AIM panel, discuss its limitations for admixed individuals and suggest ways to incorporate ancestry information into genetic association studies. Conclusion We demonstrated the utility of a small AISNP panel specifically developed to discern global ancestry. We believe that it will find wide application because of its feasibility and potential for a wide range of applications.
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Affiliation(s)
- Caroline M Nievergelt
- Department of Psychiatry, School of Medicine, University of San Diego California, La Jolla, CA, 92093, USA.
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