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Seyoum S, Adams DH, Matheson RE, Whittington JA, Alvarez AC, Sheridan NE, Panzner K, Puchulutegui C. Genetic relationships and hybridization among three western Atlantic sparid species: sheepshead (Archosargus probatocephalus), sea bream (A. rhomboidalis) and pinfish (Lagodon rhomboides). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01244-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractThree species of sparids in the western Atlantic, sheepshead (Archosargus probatocephalus), sea bream (A. rhomboidalis), and pinfish (Lagodon rhomboides), share overlapping habitats, spawning seasons, and spawning grounds, providing opportunities for interaction among these species. Three regions of mitochondrial DNA and three nuclear DNA intron sequences were used to construct the genetic relationships among these species. The results showed that these species are closely related, suggesting the presence of soft polytomy with sheepshead and western Atlantic sea bream as sister species. However, western Atlantic sea bream and pinfish are equally divergent from sheepshead. We used a suite of 18 microsatellite markers to verify the occurrence of hybridization, identify the parental types, and evaluate the filial-generation status of 36 individuals morphologically identified as hybrids from the Indian River Lagoon system, in Florida. The 36 putative hybrids were analyzed with a reference group of 172 western Atlantic sea bream, 232 pinfish, and 157 sheepsheads and were all genetically determined to be F1 of sheepshead and western Atlantic sea bream with very little indication or no introgressive hybridization among the 172 reference specimens of western Atlantic sea bream. Hybridization was asymmetric, with western Atlantic sea bream males crossing with sheepshead females. Hybrids were first observed in the Indian River Lagoon in 2005, after the western Atlantic sea bream had become common there, in the 1990s. Their occurrence could be associated with unique features of the Indian River Lagoon that bring the two species together or with recent anthropogenic changes in this system. Further study is needed to determine the causes and long-term effects of the recurrent production of F1 hybrids and the degree of their sterility in the Indian River Lagoon.
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von Kohn C, Conrad K, Kramer M, Pooler M. Genetic diversity of Magnolia ashei characterized by SSR markers. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Gomes-Pereira M, Monckton DG. Ethidium Bromide Modifies The Agarose Electrophoretic Mobility of CAG•CTG Alternative DNA Structures Generated by PCR. Front Cell Neurosci 2017; 11:153. [PMID: 28611596 PMCID: PMC5447772 DOI: 10.3389/fncel.2017.00153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/10/2017] [Indexed: 12/21/2022] Open
Abstract
The abnormal expansion of unstable simple sequence DNA repeats can cause human disease through a variety of mechanisms, including gene loss-of-function, toxic gain-of-function of the encoded protein and toxicity of the repeat-containing RNA transcript. Disease-associated unstable DNA repeats display unusual biophysical properties, including the ability to adopt non-B-DNA structures. CAG•CTG trinucleotide sequences, in particular, have been most extensively studied and they can fold into slipped-stranded DNA structures, which have been proposed as mutation intermediates in repeat size expansion. Here, we describe a simple assay to detect unusual DNA structures generated by PCR amplification, based on their slow electrophoretic migration in agarose and on the effects of ethidium bromide on the mobility of structural isoforms through agarose gels. Notably, the inclusion of ethidium bromide in agarose gels and running buffer eliminates the detection of additional slow-migrating DNA species, which are detected in the absence of the intercalating dye and may be incorrectly classified as mutant alleles with larger than actual expansion sizes. Denaturing and re-annealing experiments confirmed the slipped-stranded nature of the additional DNA species observed in agarose gels. Thus, we have shown that genuine non-B-DNA conformations are generated during standard PCR amplification of CAG•CTG sequences and detected by agarose gel electrophoresis. In contrast, ethidium bromide does not change the multi-band electrophoretic profiles of repeat-containing PCR products through native polyacrylamide gels. These data have implications for the analysis of trinucleotide repeat DNA and possibly other types of unstable repetitive DNA sequences by standard agarose gel electrophoresis in diagnostic and research protocols. We suggest that proper sizing of CAG•CTG PCR products in agarose gels should be performed in the presence of ethidium bromide.
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Affiliation(s)
- Mário Gomes-Pereira
- Laboratory CTGDM, INSERM UMR1163Paris, France.,Institut Imagine, Université Paris Descartes-Sorbonne Paris CitéParis, France
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, United Kingdom
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Kulibaba RA, Liashenko YV. Influence of the PCR artifacts on the genotyping efficiency by the microsatellite loci using native polyacrylamide gel electrophoresis. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716030087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pinto-Carrasco D, Košnar J, López-González N, Koutecký P, Těšitel J, Rico E, Martínez-Ortega MM. Development of 14 microsatellite markers in Odontites vernus s.l. (Orobanchaceae) and cross-amplification in related taxa. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1500111. [PMID: 27011897 PMCID: PMC4795918 DOI: 10.3732/apps.1500111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Microsatellite primers were developed for the first time in the root hemiparasite herb Odontites vernus (Orobanchaceae). These markers will be useful to investigate the role of polyploidization in the evolution of this diploid-tetraploid complex, as well as the extent of gene flow between different ploidy levels. METHODS AND RESULTS Fourteen polymorphic and reproducible loci were identified and optimized from O. vernus using a microsatellite-enriched library and 454 Junior sequencing. The set of primers amplified di- to pentanucleotide repeats and showed two to 13 alleles per locus. Transferability was tested in 30 taxa (19 belonging to Odontites and 11 from eight other genera of Orobanchaceae tribe Rhinantheae). CONCLUSIONS The results indicate the utility of the newly developed microsatellites in O. vernus and several other species, which will be useful for taxon delimitation and conservation genetics studies.
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Affiliation(s)
- Daniel Pinto-Carrasco
- Departamento de Botánica, Universidad de Salamanca, E-37007 Salamanca, Spain
- Biobanco de ADN Vegetal, Banco Nacional de ADN, Edificio Multiusos I+D+I, E-37007 Salamanca, Spain
| | - Jiří Košnar
- Faculty of Science, University of South Bohemia, CZ-370 05 České Budějovice, Czech Republic
| | - Noemí López-González
- Departamento de Botánica, Universidad de Salamanca, E-37007 Salamanca, Spain
- Biobanco de ADN Vegetal, Banco Nacional de ADN, Edificio Multiusos I+D+I, E-37007 Salamanca, Spain
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, CZ-370 05 České Budějovice, Czech Republic
| | - Jakub Těšitel
- Faculty of Science, University of South Bohemia, CZ-370 05 České Budějovice, Czech Republic
| | - Enrique Rico
- Departamento de Botánica, Universidad de Salamanca, E-37007 Salamanca, Spain
- Biobanco de ADN Vegetal, Banco Nacional de ADN, Edificio Multiusos I+D+I, E-37007 Salamanca, Spain
| | - M. Montserrat Martínez-Ortega
- Departamento de Botánica, Universidad de Salamanca, E-37007 Salamanca, Spain
- Biobanco de ADN Vegetal, Banco Nacional de ADN, Edificio Multiusos I+D+I, E-37007 Salamanca, Spain
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Lau CH, Zhu H, Tay JCK, Li Z, Tay FC, Chen C, Tan WK, Du S, Sia VK, Phang RZ, Tang SY, Yang C, Chi Z, Liang CC, Ning E, Wang S. Genetic rearrangements of variable di-residue (RVD)-containing repeat arrays in a baculoviral TALEN system. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2014; 1:14050. [PMID: 26015987 PMCID: PMC4362386 DOI: 10.1038/mtm.2014.50] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 08/17/2014] [Indexed: 01/24/2023]
Abstract
Virus-derived gene transfer vectors have been successfully employed to express the transcription activator-like effector nucleases (TALENs) in mammalian cells. Since the DNA-binding domains of TALENs consist of the variable di-residue (RVD)-containing tandem repeat modules and virus genome with repeated sequences is susceptible to genetic recombination, we investigated several factors that might affect TALEN cleavage efficiency of baculoviral vectors. Using a TALEN system designed to target the AAVS1 locus, we observed increased sequence instability of the TALE repeat arrays when a higher multiplicity of infection (MOI) of recombinant viruses was used to produce the baculoviral vectors. We also detected more deleterious mutations in the TALE DNA-binding domains when both left and right TALEN arms were placed into a single expression cassette as compared to the viruses containing one arm only. The DNA sequence changes in the domains included deletion, addition, substitution, and DNA strand exchange between the left and right TALEN arms. Based on these observations, we have developed a protocol using a low MOI to produce baculoviral vectors expressing TALEN left and right arms separately. Cotransduction of the viruses produced by this optimal protocol provided an improved TALEN cleavage efficiency and enabled effective site-specific transgene integration in human cells.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Haibao Zhu
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Johan Chin-Kang Tay
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Zhendong Li
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Felix Chang Tay
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Can Chen
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Wee-Kiat Tan
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Shouhui Du
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Vic-Ki Sia
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Rui-Zhe Phang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Shin-Yi Tang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Chiyun Yang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Zhixia Chi
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Chieh-Ching Liang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Er Ning
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Shu Wang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore ; Institute of Bioengineering and Nanotechnology , Singapore, Singapore
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Analysis of post-transplant chimerism by using a single amplification reaction of 38 Indel polymorphic loci. Bone Marrow Transplant 2014; 49:1432-5. [PMID: 25111510 DOI: 10.1038/bmt.2014.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/11/2014] [Accepted: 06/22/2014] [Indexed: 11/08/2022]
Abstract
In order to detect chimerism after allogeneic hematopoietic SCT (HSCT), several methods have been developed. In this study we describe the use of a set of insertion/deletion (Indel) polymorphic loci to determine the level of donor cell engraftment. We analyzed 50 DNA samples from patients who had undergone HSCT, and also several artificial chimeric samples created by mixing different DNA specimens from non-transplanted donors in various proportions. A specific set of 38 autosomic Indel polymorphisms were analyzed. For comparison purposes, a set of 15 short tandem repeats (STRs) were analyzed using the Identifiler Plus Amplification Kit. Our results suggest that Indel-based and STR-based procedures behave similarly in most cases. However, Indel analysis may provide additional information in some cases with a small minor chimeric component or when the presence of stutter bands complicates chimerism estimation.
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A polymorphic microsatellite repeat within the ECE-1c promoter is involved in transcriptional start site determination, human evolution, and Alzheimer's disease. J Neurosci 2013; 32:16807-20. [PMID: 23175834 DOI: 10.1523/jneurosci.2636-12.2012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Genetic factors strongly contribute to the pathogenesis of sporadic Alzheimer's disease (AD). Nevertheless, genome-wide association studies only yielded single nucleotide polymorphism loci of moderate importance. In contrast, microsatellite repeats are functionally less characterized structures within our genomes. Previous work has shown that endothelin-converting enzyme-1 (ECE-1) is able to reduce amyloid β content. Here we demonstrate that a CpG-CA repeat within the human ECE-1c promoter is highly polymorphic, harbors transcriptional start sites, is able to recruit the transcription factors poly(ADP-ribose) polymerase-1 and splicing factor proline and glutamine-rich, and is functional regarding haplotype-specific promoter activity. Furthermore, genotyping of 403 AD patients and 444 controls for CpG-CA repeat length indicated shifted allelic frequency distributions. Sequencing of 245 haplotype clones demonstrated that the overall CpG-CA repeat composition of AD patients and controls is distinct. Finally, we show that human and chimpanzee [CpG](m)-[CA](n) ECE-1c promoter repeats are genetically and functionally distinct. Our data indicate that a short genomic repeat structure constitutes a novel core promoter element, coincides with human evolution, and contributes to the pathogenesis of AD.
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Abstract
Microsatellites have been utilized for decades for genotyping individuals in various types of research. Automated scoring of microsatellite loci has allowed for rapid interpretation of large datasets. Although the use of software produces an automated process to score or genotype samples, several sources of error have to be taken into account to produce accurate genotypes. A variety of problems (from extracting DNA to entering a genotype into a database) which can arise throughout this process might result in erroneous genotype assignment to one or more samples, potentially confounding the conclusions of your study. Correctly assigning a genotype to a sample requires knowledge of the chemistry you use to generate the data as well as the software you use to analyze these results. In this chapter we describe the critical and more common points that researchers experience when scoring microsatellite loci. More importantly we provide insight from an experienced perspective for these challenges.
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Affiliation(s)
- Lluvia Flores-Rentería
- Department of Biological Sciences, Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, USA
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Capillary electrophoretic genotyping of epidermal growth factor receptor for pharmacogenomic assay of lung cancer therapy. J Chromatogr A 2012; 1256:276-9. [PMID: 22901298 DOI: 10.1016/j.chroma.2012.07.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/19/2012] [Accepted: 07/26/2012] [Indexed: 11/21/2022]
Abstract
In this research, a universal multiplex PCR method combining capillary gel electrophoresis was established for simultaneous analysis of mutations in exons 18-21 of EGFR kinase domain gene. After rinsing of the gel solution (1 × TBE buffer containing 2% HEC and 1.5% HPC), the diluted PCR sample was electrokinetically injected and separated at 35°C. Several parameters were investigated for method optimization, including the kinds of polymer, capillary temperature and separation voltage. Under optimal conditions, time taken for analyzing mutations of EGFR kinase domain gene in lung cancer patients was short (within 15 min). A total of 50 lung cancer patients' tumor tissues were analyzed, and two frequent mutations associated with therapeutic efficiency of lung cancer were identified, including deletion of exon 19 (8/50) and L858R point mutation in exon 21 (12/50). This method is feasible for application in pharmacogenomic assay of lung cancer therapy. By applying this simple and effective method for genotyping of lung cancer patients, the information of pharmacogenomics was supplied for lung cancer therapy and to assist diagnosis to prolong patients' lives.
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Rapid and cost-effective screening of newly identified microsatellite loci by high-resolution melting analysis. Mol Genet Genomics 2011; 286:225-35. [PMID: 21847526 DOI: 10.1007/s00438-011-0641-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 08/04/2011] [Indexed: 12/13/2022]
Abstract
This study describes a new method for identifying microsatellite loci that will reliably amplify and show high degree of polymorphism in a given species. Microsatellites are the most powerful codominant markers available today, but the development of novel loci remains a labour-intensive and expensive process. In de novo isolation, approaches using next generation sequencing (NGS) are gradually replacing ones using Escherichia coli libraries, resulting in unparalleled numbers of candidate loci available. We present a systematic review of published microsatellite primer notes and show that, on average, about half of all candidate loci are lost due to insufficient PCR amplification, monomorphism or multicopy status in the genome, no matter what isolation strategy is used. Thus, the screening of candidate loci remains a major step in marker development. Re-assessing capillary-electrophoresis genotyped loci via high-resolution melting analysis (HRM), we evaluate the usefulness of HRM for this step. We demonstrate its applicability in a genotyping case study and introduce a fast, HRM-based workflow for the screening of microsatellite loci. This workflow may readily be applied to NGS-based marker development and has the potential to cut the costs of traditional testing by half to three quarters.
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Axford MM, López-Castel A, Nakamori M, Thornton CA, Pearson CE. Replacement of the myotonic dystrophy type 1 CTG repeat with 'non-CTG repeat' insertions in specific tissues. J Med Genet 2011; 48:438-43. [PMID: 21622935 DOI: 10.1136/jmg.2010.085944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Recently, curious mutations have been reported to occur within the (CTG)n repeat tract of the myotonic dystrophy type 1 (DM1) locus. For example, the repeat, long presumed to be a pure repeat sequence, has now been revealed to often contain interruption motifs in a proportion of cases with expansions. Similarly, a few de novo somatic CTG expansions have been reported to arise from non-expanded DM1 alleles with 5-37 units, thought to be genetically stable. AIMS AND METHODS This study has characterised a novel mutation configuration at the DM1 CTG repeat that arose as somatic mosaicism in a juvenile onset DM1 patient with a non-expanded allele of (CTG)12 and tissue specific expansions ranging from (CTG)1100 to 6000. RESULTS The mutation configuration replaced the CTG tract with a non-CTG repeat insertion of 43 or 60 nucleotides, precisely placed in the position of the CTG tract with proper flanking sequences. The inserts appeared to arise from a longer human sequence on chromosome 4q12, and may have arisen through DNA structure mediated somatic inter-gene recombination or replication/repair template switching errors. De novo insertions were detected in cerebral cortex and skeletal muscle, but not in heart or liver. Repeat tracts with -1 or -2 CTG units were also detected in cerebellum, which may have arisen by contractions of the short (CTG)12 allele. CONCLUSION This non-CTG configuration expands current understanding of the sequence variations that can arise at this hypermutable site.
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Affiliation(s)
- Michelle M Axford
- Genetics and Genome Biology, The Hospital for Sick Children, TMDT Building 101 College Street, 15th Floor, Rm 15-312 East Tower, Toronto, ON M5G 1L7, Canada
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Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ. Current trends in microsatellite genotyping. Mol Ecol Resour 2011; 11:591-611. [PMID: 21565126 DOI: 10.1111/j.1755-0998.2011.03014.x] [Citation(s) in RCA: 427] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.
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Affiliation(s)
- E Guichoux
- INRA, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
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Cheng HL, Chiou SS, Liao YM, Chen YL, Wu SM. Genotyping of two single nucleotide polymorphisms in 5,10-methylenetetrahydrofolate reductase by multiplex polymerase chain reaction and capillary electrophoresis. J Chromatogr A 2011; 1218:2114-20. [DOI: 10.1016/j.chroma.2010.08.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 08/25/2010] [Accepted: 08/30/2010] [Indexed: 11/25/2022]
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Védrine SM, Vourc'h P, Tabagh R, Mignon L, Höfflin S, Cherpi-Antar C, Mbarek O, Paubel A, Moraine C, Raynaud M, Andres CR. A functional tetranucleotide (AAAT) polymorphism in an Alu element in the NF1 gene is associated with mental retardation. Neurosci Lett 2011; 491:118-21. [PMID: 21236316 DOI: 10.1016/j.neulet.2011.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 12/30/2010] [Accepted: 01/06/2011] [Indexed: 11/29/2022]
Abstract
Mental retardation (MR) is frequent in neurofibromatosis type 1 (NF1). Allele 5 of a tetranucleotide polymorphism in an Alu element (GXAlu) localized in intron 27b of the NF1 gene has previously been associated with autism. We considered that the microsatellite GXAlu could also represent a risk factor in MR without autism. We developed a rapid method for genotyping by non-denaturing HPLC and assayed the allelic variation of GXAlu marker on in vitro gene expression in Cos-7 cells. A French population of 157 individuals (68 non syndromic non familial MR (NS-MR) patients diagnosed in the University Hospital of Tours; 89 controls) was tested in a case-control assay. We observed a significant association (χ(2)=7.96; p=0.005) between alu4 carriers (7 AAAT repeats) and MR (OR: 7.86; 95% C.I.: 2.13-28.9). The relative in vitro expression of a reporter gene encoding chloramphenicol acetyl transferase (CAT) was higher for alu4 and alu5, suggesting a regulation effect for these alleles on gene expression in vivo. Our results showed an association with a polymorphism regulating the NF1 gene or other genes during brain development.
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Wang CC, Chang JG, Jong YJ, Wu SM. Universal multiplex PCR and CE for quantification ofSMN1/SMN2genes in spinal muscular atrophy. Electrophoresis 2009; 30:1102-10. [DOI: 10.1002/elps.200800375] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
In this study we present a quick and easy method for counting trinucleotide repeats by de-oxyadenosine overhang (A-overhang)–dependent repeat expansion determination (ADRED). During standard Taq DNA polymerase–based sequencing reactions, the unterminated sequencing products of short PCR fragments are tagged with a 3′-end A-overhang that is visible as an intense peak in an electropherogram; this allows for easy and precise determination of the fragment length and thus the extent of repeat expansions. ADRED has clear advantages over existing methods, because repeat numbers of both normal and pathogenic (expanded) alleles can be analyzed without using labeled primers or labeled DNA standards. Because ADRED includes a sequencing step, disease-relevant polymorphisms (e.g., CAA interruptions in spinocerebellar ataxia type 2) can simultaneously be detected.
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Bick SL, Bick DP, Wells BE, Roesler MR, Strawn EY, Lau EC. Preimplantation HLA haplotyping using tri-, tetra-, and pentanucleotide short tandem repeats for HLA matching. J Assist Reprod Genet 2008; 25:323-31. [PMID: 18677557 DOI: 10.1007/s10815-008-9233-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 06/11/2008] [Indexed: 11/25/2022] Open
Abstract
PURPOSE To aid couples wishing to conceive children who are HLA matched to a sibling in need of a hematopoietic progenitor cell transplant, we developed a preimplantation HLA haplotype analysis of embryos that utilizes tri-, tetra-, and pentanucleotide STR markers. METHODS For preimplantation HLA genotyping, we use polymorphic STR markers located across the HLA and flanking regions, selecting exclusively tri-, tetra-, and pentanucleotide repeats. These markers can be resolved using either capillary electrophoresis (CE) or polyacrylamide gels. RESULTS We have developed 43 reliable STR markers for preimplantation HLA matching. Selected STR markers enabled unambiguous identification of embryos whose HLA haplotypes were matched with the affected patient using polyacrylamide gel or capillary electrophoresis. CONCLUSIONS The use of tri-, tetra-, and pentanucleotide repeat markers and polyacrylamide gels for STR genotyping in HLA matching is a simple and cost effective approach to clinical testing.
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Affiliation(s)
- Sarah L Bick
- Division of Medical Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Kleibl Z, Havranek O, Prokopcova J. Rapid detection of CAA/CAG repeat polymorphism in the AIB1 gene using DHPLC. ACTA ACUST UNITED AC 2006; 70:511-3. [PMID: 17234271 DOI: 10.1016/j.jbbm.2006.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 10/09/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
Denaturing high-performance liquid chromatography (DHPLC) has been used for rapid and accurate DNA mutation analysis; to extend the DNA fragment lengths analysis. Recently, polymorphism in polyglutamine-coding region of Amplified In Breast cancer gene 1 (AIB1) was analyzed as an independent genetic risk factor influencing breast cancer onset in carriers of mutation in breast cancer predisposing gene 1 (BRCA1). We have implemented efficient, cost-effective and rapid method for analysis of the AIB1 polyglutamine repeat polymorphism based on DHPLC analysis (WAVE system) of unlabeled PCR products. This strategy can be useful for genotyping of other trinucleotide repeat polymorphisms using DHPLC in medium/high throughput settings.
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Affiliation(s)
- Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Czech Republic.
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