1
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Horschitz S, Frank J, Koch P. Generation of three induced pluripotent stem cell lines carrying different variants of the BDNF (Val66Met) polymorphism. Stem Cell Res 2023; 66:102989. [PMID: 36473250 DOI: 10.1016/j.scr.2022.102989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has been implicated in a multitude of neurodevelopmental processes including neuronal differentiation, axonal outgrowth, synaptic plasticity, or survival. One human-specific single nucleotide polymorphism (rs6265) in the BDNF gene causes a substitution of valine (Val) to methionine (Met) at codon 66 in the pro domain of the protein (Val66Met). This substitution is associated to reduced hippocampal volumes, poor performance on hippocampal-dependent memory tasks, and some mental disorders such as schizophrenia, depression or Alzheimer's disease. Here we generated three iPSC lines from healthy donors, either homozygous (Val/Val and Met/Met) or heterozygous (Val/Met) for the polymorphism.
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Affiliation(s)
- Sandra Horschitz
- Hector Institute for Translational Brain Research, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Germany; German Cancer Research Center, Heidelberg, Germany.
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Germany
| | - Philipp Koch
- Hector Institute for Translational Brain Research, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Germany; German Cancer Research Center, Heidelberg, Germany
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2
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Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M. An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. NAR Genom Bioinform 2022; 4:lqac009. [PMID: 35178516 PMCID: PMC8846365 DOI: 10.1093/nargab/lqac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics.
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Affiliation(s)
- P Prakrithi
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vigneshwar Senthilvel
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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3
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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4
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Tang W, Liang P. Alu master copies serve as the drivers of differential SINE transposition in recent primate genomes. Anal Biochem 2020; 606:113825. [PMID: 32712063 DOI: 10.1016/j.ab.2020.113825] [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: 02/19/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022]
Abstract
Alu elements, averaging ~300bp in length, are a family of primate-specific short intersperse nuclear elements (SINEs) with more than one million copies and contributing to ~11% of primate genomes. Despite mostly being shared among primates, our recent study revealed highly differential recent Alu transposition among the genomes of primates from Hominidae and Cercopithecidae families. To understand the underlying mechanism, we analyzed six primate genomes and revealed species- and lineage-specific Alu profile exclusively defined by AluY composition. Among all Alus from the 6 genomes, we identified 5401 Alu master copies with 99% being from the AluY subfamily. The numbers of Alu master copies are positively correlated to the number of AluY elements in the genomes with the baboon genome having the largest number of most recent Alu master copies at high activities, while the crab-eating macaque genome having a low number of Alu master copies with low activity. Furthermore, the expression level of Alu master copies is positively correlated with their transposition activity. Our results support the concept that Alu transposition in primate genomes is driven by a small number of master copies, the number and relative activity of which contribute to the differential Alu transposition in recent primate genomes.
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Affiliation(s)
- Wanxiangfu Tang
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada.
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5
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Xu J, Sun L, Wang X, Wang X, Xing W, Zhou P, Li S. Population data for 20 insertion-null allele markers in the Li ethnic minority from Hainan Province. Int J Legal Med 2020; 134:2075-2077. [PMID: 32935145 DOI: 10.1007/s00414-020-02424-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Insertion/null polymorphisms (INNULs) can be used as an alternative marker of STRs to detect the highly degraded samples in forensic cases. In this study, we evaluated the genetic data of 20 INNUL markers in the Innotyper® 21 Human DNA Analysis Kit (InnoGenomics) for Hainan Li population, including allele frequencies and forensic parameters. No significant deviation from Hardy-Weinberg equilibrium and linkage disequilibrium was found in all loci after Bonferroni correction. The combined power of discrimination (CPD) was 0.99999891, the combined power of exclusion for duo paternity testing (CPEduo) was 0.75274389, and the combined power of exclusion for trio paternity testing (CPEtrio) was 0.94766143. These data would be useful for the application of the kit in practice and the research of the kit used in molecular anthropology studies.
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Affiliation(s)
- Jie Xu
- Criminal Technology Detachment of Haikou Public Security Bureau, Haikou, China
| | - Lijuan Sun
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xianwen Wang
- Criminal Technology Detachment of Haikou Public Security Bureau, Haikou, China
| | - Xiehong Wang
- Criminal Technology Detachment of Haikou Public Security Bureau, Haikou, China
| | - Weisheng Xing
- Criminal Technology Detachment of Haikou Public Security Bureau, Haikou, China
| | - Pingmei Zhou
- Criminal Technology Detachment of Haikou Public Security Bureau, Haikou, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China.
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6
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Kim GH, Kwon SY, Lee SY, Seong KM, Kim J, Lim SK. Evaluation of the InnoTyper21® system for the applications into trace and degraded DNA in the Korean population. Int J Legal Med 2020; 134:2053-2059. [PMID: 32929592 DOI: 10.1007/s00414-020-02429-3] [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: 06/23/2020] [Accepted: 09/10/2020] [Indexed: 11/25/2022]
Abstract
The InnoTyper 21® Human Identification kit consists of amelogenin and 20 bi-allelic Alus, retrotransposon markers existing abundantly in human genome. The InnoTyper 21® kit produces shorter amplicons (60-125 bp) than conventional short tandem repeat (STR) genotyping kit, then it is effective on the analysis of challengeable forensic samples including insufficient or highly degraded DNAs. Also, as the genotyping with InnoTyper21® kit is compatible with PCR and capillary electrophoresis, it is easy to incorporate into the workflow in forensic laboratories. In the internal validation of InnoTyper21® kit on sensitivity, degradation, and mixture studies for the evaluation in this study, we acquired full profiles on analyzing small concentration DNA (as low as 25 pg) and highly degraded DNA (up to 105 degradation index value). Through the Korean population study, forensic statistical parameters were investigated and a specific variant of T insertion in NBC51 was confirmed in six samples. Comparison of Korean population with five populations or 1000 Genomes Project data show Korean specific substructure. It is expected that the InnoTyper 21® kit will be used into the actual forensic cases, utilizing the population study investigated through this research.
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Affiliation(s)
- Gyeong Hyeon Kim
- Forensic DNA Division, National Forensic Service, Wonju-si, Republic of Korea
| | - So Yeun Kwon
- Forensic DNA Division, National Forensic Service, Wonju-si, Republic of Korea
| | - So-Yeon Lee
- Forensic DNA Division, National Forensic Service, Dae-gu, Republic of Korea
| | - Ki Min Seong
- Forensic DNA Division, National Forensic Service, Wonju-si, Republic of Korea
| | - Jeongyong Kim
- Forensic DNA Division, National Forensic Service, Wonju-si, Republic of Korea
| | - Si-Keun Lim
- Department of Forensic Sciences, Graduate School of Sungkyunkwan University, Suwon, Republic of Korea.
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7
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Transcriptome variation in human populations and its potential application in forensics. J Appl Genet 2019; 60:319-328. [PMID: 31401728 PMCID: PMC6803616 DOI: 10.1007/s13353-019-00510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/04/2022]
Abstract
This review presents the state-of-the-art in the forensic application of genetic methods driven by the research in population transcriptomics. In the first part of the review, the constraints of using classical genomic markers are shortly reviewed. In the second part, the developments in the field of inter-population diversity at the transcriptomic level are presented. Subsequently, a potential of population-specific transcriptomic markers in forensic science applications, including ascertaining population affiliation of human samples and cell mixtures separation, are presented.
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8
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Badache H, Boussetta S, Elgaaeid AB, Cherni L, El-khil HK. Investigation of the genetic structure of Kabyle and Chaouia Algerian populations through the polymorphism of Alu insertion markers. Ann Hum Biol 2019; 46:150-159. [DOI: 10.1080/03014460.2019.1588994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hocine Badache
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Amel Benammar Elgaaeid
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
| | - Houssein Khodjet El-khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
- Department of Biomedical Sciences, College of Health Sciences Qatar University, Doha, Qatar
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9
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Moura-Neto RS, Mello ICT, Silva R, Maette APC, Bottino CG, Woerner A, King J, Wendt F, Budowle B. Evaluation of InnoTyper® 21 in a sample of Rio de Janeiro population as an alternative forensic panel. Int J Legal Med 2017; 132:149-151. [PMID: 28748403 DOI: 10.1007/s00414-017-1642-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/04/2017] [Indexed: 10/19/2022]
Abstract
The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of short tandem repeat (STR) loci in typing forensic biological evidence. This study investigated the efficiency of the InnoTyper® 21 Innul markers in an urban admixed population sample in Rio de Janeiro (n = 40) and one highly compromised sample collected as evidence by the Rio de Janeiro police. No significant departures from Hardy-Weinberg equilibrium were detected after the Bonferroni correction (α' ≈ 0.05/20, p < 0.0025), and no significant linkage disequilibrium was observed between markers. Assuming loci independence, the cumulative random match probability (RMP) was 2.3 × 10-8. A lower mean Fis value was obtained for this sample population compared with those of three North American populations (African-American, Southwest Hispanic, US Caucasian). Principal component analysis with the three North American populations and one from 21 East Asian population showed that African Americans segregated as an independent group while US Caucasian, Southwest Hispanic, East Asian, and Rio de Janeiro populations are in a single large heterogeneous group. Also, a full Innuls profile was produced from an evidence sample, despite the DNA being highly degraded. In conclusion, this system is a useful complement to standard STR kits.
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Affiliation(s)
- R S Moura-Neto
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - I C T Mello
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - R Silva
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - A P C Maette
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - C G Bottino
- Policia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense, Rio de Janeiro, RJ, Brazil
| | - A Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - J King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - F Wendt
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - B Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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10
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Brown H, Thompson R, Murphy G, Peters D, La Rue B, King J, Montgomery AH, Carroll M, Baus J, Sinha S, Wendt FR, Song B, Chakraborty R, Budowle B, Sinha SK. Development and validation of a novel multiplexed DNA analysis system, InnoTyper® 21. Forensic Sci Int Genet 2017; 29:80-99. [DOI: 10.1016/j.fsigen.2017.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/08/2017] [Accepted: 03/15/2017] [Indexed: 01/21/2023]
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González-Giraldo Y, Rodríguez-Dueñas M, Forero DA. Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92). Mol Biotechnol 2016; 58:197-201. [PMID: 26843017 DOI: 10.1007/s12033-016-9915-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Insertion/Deletion polymorphisms (InDels) are a common type of genetic variation, with a growing role in population genetics and applied genomics. There is the need for the development of novel cost-effective assays for genotyping InDels of high importance. The main objective of this study was to develop high-resolution melting-based assays for genotyping two commonly studied Alu insertion polymorphisms: FXIIIB and PV92 (rs70942849 and rs3138523). Three primers (two forward and one reverse) were designed for each marker, and high-resolution melting (HRM) analyses in a qPCR platform were performed, using EvaGreen fluorescent dye. For each one of the two Alu insertion polymorphisms, HRM analyses identified distinguishable peaks for the three genotypes, allowing a robust genotyping. Results were validated using 96 DNA samples previously genotyped and the assays worked with different DNA concentrations. In this study, we developed novel cost-effective assays, using qPCR, for genotyping two Alu insertion polymorphisms (widely used as ancestry markers). Our results highlight the feasibility of using HRM analyses for genotyping InDel polymorphisms of medical and biotechnological importance.
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Affiliation(s)
- Yeimy González-Giraldo
- Department of Nutrition and Biochemistry, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia.,Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Marisol Rodríguez-Dueñas
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,Faculty of Science, Universidad Antonio Nariño, Bogotá, Colombia
| | - Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.
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Laybourn S, Akam EC, Cox N, Singh P, Mastana SS. Genetic analysis of novel Alu insertion polymorphisms in selected indian populations. Am J Hum Biol 2016; 28:941-944. [PMID: 27292586 DOI: 10.1002/ajhb.22881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 05/03/2016] [Accepted: 05/10/2016] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Indian subpopulations (Chenchu, Koya, and Lobana Sikh) were analyzed at the genetic level for 12 Alu polymorphisms. These markers were then utilized to establish levels of genetic identity between the Indian populations and more widely between the Indian populations and a European population. METHODS Previously collected blood samples were extracted using the phenol-chloroform method. The samples were utilized as templates for PCR using Alu specific primers and then analyzed by agarose gel electrophoresis for the presence and absence of the approximately 300 bp insertions. Allele frequencies were calculated by the gene counting method and were tested for Hardy-Weinberg equilibrium, heterozygosities, inbreeding coefficient, and GST to assess the level of genetic differentiation. RESULTS All of the Alu loci were polymorphic in the three Indian populations studied and their average observed heterozygosity ranged from 0.294 (Lobana Sikh) to 0.357 (Koya). Allele and genotype frequency variation at the 2b, 9a, and ACE loci led to statistically significant pairwise differences among the three study populations. Overall population heterogeneity was observed for 7 out of 12 Alu polymorphisms. CONCLUSION The overall results show that these Indian samples, though displaying significant genetic variation and differences among themselves, form an Indian cluster, which as expected, is distinct from the European sample (Russian). As Alus are easily analyzed and quantified by standard and cost-effective methodologies, this finding further reinforces their utility as effective population genetic markers. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:941-944, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Susie Laybourn
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Elizabeth Claire Akam
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Nick Cox
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, Punjab, India
| | - Sarabjit S Mastana
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
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Asari M, Oka K, Omura T, Maseda C, Tasaki Y, Shiono H, Matsubara K, Matsuda M, Shimizu K. Universal fluorescent labeling of amplification products using locked nucleic acids. Electrophoresis 2013; 34:448-55. [PMID: 23161600 DOI: 10.1002/elps.201200215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 09/16/2012] [Accepted: 09/25/2012] [Indexed: 12/15/2022]
Abstract
Amplification/hybridization-based genetic analyses using primers containing locked nucleic acids (LNAs) present many benefits. Here, we developed a novel design for universal fluorescent PCR using LNAs. Universal fluorescent PCR generates intermediate nonlabeled fragments and final fluorescent fragments in a two-step amplification process that uses locus-specific primers with universal tails and universal fluorescent primers. In this study, a few standard nucleotides were replaced with LNAs only in the fluorescent universal primers. The sequence of the fluorescent universal primer significantly affected the amplification efficiency. For primers with three LNAs, the fluorescent primers with stable M13(-47) sequences provided the most efficient signal (approximately tenfold higher than the primers with M13(-21) sequences at lower Tm values). Moreover, AT-rich LNA substitutions in the fluorescent primers produced much lower amplification efficiencies than GC-rich substitutions. GC-rich LNAs produced greater differences in Tm values among primers, and resulted in the preferential production of fluorescently labeled amplicons. The specificity and sensitivity of LNA-containing fluorescent primers were assessed by genotyping eight STRs in Japanese individuals, and full STR profiles could be generated using as little as 0.25 ng of genomic DNA. The method permitted clear discrimination of alleles and represents sensitive STR genotyping at a reduced cost.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
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14
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Komkov AI, Maschan MA, Shvets VI, Lebedev IB. [The functional analysis of polymorphic insertions of Alu retroelements at acute lymphoblastic leukemia]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 38:351-64. [PMID: 22997707 DOI: 10.1134/s1068162012030089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Human genome variability observed within patient cohorts is considered as a goal of functional genomics essential for personalized medicine progress. In the current research we implement functional analysis of 31 polymorphic Alu insertions located within gene introns for individual genomes of patients with acute lymphoblastic leukemia (ALL). As a result we demonstrated a decrease of the primary transcripts content for 21 Alu-containing alleles. The most strong inhibitory effect of 10 Alu insertions was observed in both mononuclear blood cells of healthy donors and B-lymphoblasts of ALL patients. Allele frequencies of three Alu insertions that are located in MEF2C (two of them) and TAX1BP1 genes significantly differ (p-value 0.027. 0.052. 0.014 accordingly) between cohorts of healthy donors and ALL patients. Prolong influence of the Alu insertions on intracellular content of mature mRNA was studied for corresponding allele of TARBP1 gene.
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15
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LaRue BL, Sinha SK, Montgomery AH, Thompson R, Klaskala L, Ge J, King J, Turnbough M, Budowle B. INNULs: A novel design amplification strategy for retrotransposable elements for studying population variation. Hum Hered 2012; 74:27-35. [PMID: 23095285 DOI: 10.1159/000343050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/30/2012] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Retrotransposable elements (REs), consisting of long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), are a group of markers that can be useful for human identity testing. Until now, however, due to the inherent size difference (up to 6 kb in some instances) associated with insertion and null alleles (or INNULs), the use of REs for facilitated population studies has not been sought or practical. The size of the insertion elements (from a few hundred to several thousand bp) has proven to limit their utility as a marker because of the inefficient amplicon yield with PCR. A novel primer design now facilitates INNUL marker testing. A preliminary panel of single-locus markers was developed to evaluate the potential of typing these insertion elements. Nine INNULs (5 Alu and 4 LINEs) were typed in three major North American populations and analyzed for population genetic features. In addition, the variation of each marker among the sample populations provides insight of its potential use as individual identification or ancestral marker. METHODS INNUL markers were developed into fluorescently labeled single-loci PCR. Nine markers were developed with amplicons that were less than 180 bp in length, and, depending on the locus amplicons of the INNULs, alleles varied in size from 50 to 1 bp. This allele size is noteworthy because the insertion alleles of the 9 loci range in size from 297 to 6,195 bp. The allele distribution of the INNULs was assessed and analyzed in three major North American populations. RESULTS Upon observation of the distribution of the alleles in three major North American populations, the markers generally met Hardy-Weinberg expectations, and there was little evidence of detectable levels of linkage disequilibrium. Due to varying distributions of the alleles in the major population groups tested, some of the markers might be better suited for use as an individual identification marker, while others are better suited for bio-ancestral studies. CONCLUSIONS Using the primer design strategy described in our work, SINEs and (for the first time, to our knowledge) LINEs can be utilized as markers for studying population genetic variation that is more amenable to the limitations of the PCR technique. This study lays the foundation for future work of developing a multiplex panel of INNUL markers that can be used as a single-tube assay for human identity testing utilizing small amplicons (<180 bp), which could be useful for ancient or degraded forensic DNA samples.
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Affiliation(s)
- Bobby L LaRue
- Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
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Kee BP, Chua KH, Lee PC, Lian LH. Population data of six Alu insertions in indigenous groups from Sabah, Malaysia. Ann Hum Biol 2012; 39:505-10. [PMID: 22989108 DOI: 10.3109/03014460.2012.719548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Asari M, Omura T, Oka K, Maseda C, Tasaki Y, Shiono H, Matsubara K, Matsuda M, Shimizu K. Multiplex PCR-based Alu insertion polymorphisms genotyping for identifying individuals of Japanese ethnicity. Genomics 2012; 99:227-32. [PMID: 22293435 DOI: 10.1016/j.ygeno.2012.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 12/21/2011] [Accepted: 01/10/2012] [Indexed: 01/06/2023]
Abstract
Discrimination of Alu insertions is a useful tool for geographic ancestry analysis, and is usually performed by Alu element amplification and agarose gel electrophoresis. Here, we have developed a new fluorescence-based method for multiple Alu genotyping in forensic identification. Allele frequencies were determined in 70 Japanese individuals, and we selected 30 polymorphic Alu insertions. Three primers were designed for each Alu locus to discriminate alleles using the 3-6 bp differences in amplicon sizes. Furthermore, we classified the amplification primers for the 30 loci into three different sets, and PCR using each set of primers provided 10 loci fragments ranging from 50 to 137 bp. Based on population data, the probability of incorrectly assigning a match was 3.7×10(-13). Three independent amplifications and subsequent capillary electrophoresis enabled the sensitive genotyping of small amounts of DNA, indicating that this method is suitable for identifying individuals of Japanese ethnicity.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa 078-8510, Japan.
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