151
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Gadkar V, Rillig MC. Application of Phi29 DNA polymerase mediated whole genome amplification on single spores of arbuscular mycorrhizal (AM) fungi. FEMS Microbiol Lett 2005; 242:65-71. [PMID: 15621421 DOI: 10.1016/j.femsle.2004.10.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 10/11/2004] [Accepted: 10/21/2004] [Indexed: 11/30/2022] Open
Abstract
Genetic analysis of arbuscular mycorrhizal (AM) fungi relies on analysis of single spores. The low DNA content makes it difficult to perform large scale molecular analysis. We present the application of Phi29 DNA polymerase mediated strand displacement amplification (SDA) to genomic DNA extracted from single spores of Glomus and Gigaspora species to address this problem. The genome coverage of the SDA process was evaluated by PCR amplification of the beta-tubulin1 gene and part of the rDNA cluster present in AM fungi. The fidelity of SDA was evaluated further by sequencing the Glomus intraradices ITS1 variants to detect the four ITS1 variants previously identified for this fungus.
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Affiliation(s)
- Vijay Gadkar
- Microbial Ecology Program, Division of Biological Sciences, 32 Campus Drive # 4824, University of Montana, Missoula, MT 59812, USA.
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152
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Jiang Z, Zhang X, Deka R, Jin L. Genome amplification of single sperm using multiple displacement amplification. Nucleic Acids Res 2005; 33:e91. [PMID: 15942023 PMCID: PMC1143700 DOI: 10.1093/nar/gni089] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.
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Affiliation(s)
- Zhengwen Jiang
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
| | - Xingqi Zhang
- Department of Obstetrics and Gynecology, Northwestern University Medical SchoolChicago, IL, USA
| | - Ranjan Deka
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
| | - Li Jin
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
- State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences and Morgan-Tan International Center for Life Sciences, Fudan UniversityShanghai, China
- To whom correspondence should be addressed at Liren Biology Building, Room 220, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China. Tel: +86 21 65642800; Fax: +86 21 55664388;
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153
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Roper MG, Easley CJ, Landers JP. Advances in Polymerase Chain Reaction on Microfluidic Chips. Anal Chem 2005; 77:3887-93. [PMID: 15952761 DOI: 10.1021/ac050756m] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael G Roper
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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154
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Foster SJ, Monahan BJ. Whole genome amplification from filamentous fungi using Phi29-mediated multiple displacement amplification. Fungal Genet Biol 2005; 42:367-75. [PMID: 15809002 DOI: 10.1016/j.fgb.2005.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 01/06/2005] [Accepted: 01/26/2005] [Indexed: 11/18/2022]
Abstract
The availability of genomic DNA of sufficient quality and quantity is fundamental to molecular genetic analysis. Many filamentous fungi are slow growing or even unculturable and current DNA isolation methods are often unsatisfactory. We have used multiple displacement amplification (MDA) to amplify whole genomes for two fungal species, Penicillium paxilli and the slow growing endophyte of grasses Epichloe festucae. Up to 10 microg of high molecular weight DNA was routinely amplified from less than 10 ng of template DNA obtained using glass bead-mediated disruption of fungal spores or alkaline lysis of mycelium. PCR was possible from MDA-generated DNA and amplicons up to 10 kb were successfully amplified. RFLP analysis was successful, with bands of up to 5 kb routinely detected. Hybridization of MDA-amplified DNA to a cosmid library illustrated that the MDA product amplified from E. festucae is representative of the genome. MDA is a reliable method that could be applied to applications ranging from high-throughput screening of deletion mutants to genomic library construction.
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Affiliation(s)
- Simon J Foster
- Centre for Functional Genomics, Institute of Molecular BioSciences, Massey University, Private Bag 11 222, Palmerston North 5321, New Zealand.
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155
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Shao W, Tang J, Dorak MT, Song W, Lobashevsky E, Cobbs CS, Wrensch MR, Kaslow RA. Molecular typing of human leukocyte antigen and related polymorphisms following whole genome amplification. ACTA ACUST UNITED AC 2005; 64:286-92. [PMID: 15304010 DOI: 10.1111/j.0001-2815.2004.00295.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Reliable, high-resolution genotyping of human leukocyte antigen (HLA) polymorphisms is often compromised by DNA samples of suboptimal quality or limited quantity. We tested the feasibility of molecular typing for variants at HLA and neighboring loci using whole genome amplification (WGA) strategy facilitated by the Phi29 DNA polymerase. With little (5-100 ng) starting genomic DNA of varying quality and source materials, WGA was deemed successful in 167 of 169 DNA from 47 cell lines, 100 European Americans, and 22 native Africans. The Phi29-processed DNA provided adequate templates for polymerase chain reaction (PCR)-based analyses of several HLA (A, B, C, DRB1, and DQB1) and related loci (HFE, MICA, and 10 microsatellites) in the 6p24.3-6p21.3 region, with PCR amplicons ranging from 92 to 2200 bp. Five different genotyping techniques resolved and confirmed 364 genotypes when both original and Phi29-processed DNA worked in PCRs. General population genetic analyses provided additional evidence that WGA may represent a reliable and simple approach to securing ample genomic DNA for typing HLA, MICA, and related variants.
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Affiliation(s)
- W Shao
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
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156
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Tzvetkov MV, Becker C, Kulle B, Nürnberg P, Brockmöller J, Wojnowski L. Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification. Electrophoresis 2005; 26:710-5. [PMID: 15690424 DOI: 10.1002/elps.200410121] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Whole-genome DNA amplification by multiple displacement (MD-WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD-WGA. We observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra-assay reproducibility of the genotyping technique used. However, MD-WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3-fold reduction of noncalled SNPs by combining the results from two independent MD-WGA reactions. This indicated that inter-reaction variations rather than specific chromosomal loci reduced the efficiency of MD-WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD-WGA appears to be the current method of choice to amplify genomic DNA for array-based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.
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Affiliation(s)
- Mladen V Tzvetkov
- Department of Clinical Pharmacology, Georg-August-University Göttingen, Göttingen, Germany
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157
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Abstract
A substantial contribution of genetic factors to the risk of psychiatric disorders such as schizophrenia, bipolar disorder, autism, and drug and alcohol dependence has already been established. However, the familial transmission of these disorders cannot be explained by simple Mendelian models of inheritance, and non-genetic factors must also play a substantial role in their etiologies. Furthermore, the prevalence of any major psychiatric disorder is a great deal higher than that of Mendelian disorders. It has been suggested that evolutionary forces would rapidly eliminate large gene effects, which would suggest that mental disorders, which are highly prevalent, are associated with minor gene effects (Risch, 1994). The current paradigm is that genes with small interacting genetic effects, in conjunction with environmental factors, affect the risk for psychiatric disease. New laboratory and statistical methodology and database tools, and the availability of large clinical samples for the study of linkage and association sustain optimism that genes involved with these diseases will be characterized in the near future. This accomplishment should in turn lead not only to a better understanding of the primary molecular pathophysiology and to more specific and effective therapies, but also to a better understanding of non-genetic risk factors that could be targets for preventive strategies.
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Affiliation(s)
- A R Sanders
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare Research Institute, Northwestern University, Illinois 60201, USA.
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158
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Handyside AH, Robinson MD, Simpson RJ, Omar MB, Shaw MA, Grudzinskas JG, Rutherford A. Isothermal whole genome amplification from single and small numbers of cells: a new era for preimplantation genetic diagnosis of inherited disease. Mol Hum Reprod 2004; 10:767-72. [PMID: 15322224 DOI: 10.1093/molehr/gah101] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Preimplantation genetic diagnosis (PGD) of single gene defects following assisted conception typically involves removal of single cells from preimplantation embryos and analysis using highly sensitive PCR amplification methods taking stringent precautions to prevent contamination from foreign or previously amplified DNA. Recently, whole genome amplification has been achieved from small quantities of genomic DNA by isothermal amplification with bacteriophage 29 DNA polymerase- and exonuclease-resistant random hexamer primers. Here we report that isothermal whole genome amplification from single and small numbers of lymphocytes and blastomeres isolated from cleavage stage embryos yielded microgram quantities of amplified DNA, and allowed analysis of 20 different loci, including the DeltaF508 deletion causing cystic fibrosis and polymorphic repeat sequences used in DNA fingerprinting. As with analysis by PCR-based methods, some preferential amplification or allele drop-out at heterozygous loci was detected with single cells. With 2-5 cells, amplification was more consistent and with 10 or 20 cells results were indistinguishable from genomic DNA. The use of isothermal whole genome amplification as a universal first step marks a new era for PGD since, unlike previous PCR-based methods, sufficient DNA is amplified for diagnosis of any known single gene defect by standard methods and conditions.
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Affiliation(s)
- Alan H Handyside
- Leeds PGD Centre, Assisted Conception Unit, Clarendon Wing, Leeds General Infirmary, Leeds, UK
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159
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Pask R, Rance HE, Barratt BJ, Nutland S, Smyth DJ, Sebastian M, Twells RCJ, Smith A, Lam AC, Smink LJ, Walker NM, Todd JA. Investigating the utility of combining phi29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray genotyping. BMC Biotechnol 2004; 4:15. [PMID: 15279678 PMCID: PMC514612 DOI: 10.1186/1472-6750-4-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Accepted: 07/27/2004] [Indexed: 12/03/2022] Open
Abstract
Background Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated Φ29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray™ genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates. Results Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray sample exclusion rate, blind to sample type, was 10.5% for MDA product compared to 5.8% for gDNA. Conclusions We conclude that the BeadArray technology successfully produces high quality genotyping data from MDA product. The combination of these technologies improves the feasibility and efficiency of mapping common disease susceptibility genes despite limited stocks of gDNA samples.
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Affiliation(s)
- Rebecca Pask
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Helen E Rance
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Bryan J Barratt
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Sarah Nutland
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Deborah J Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Meera Sebastian
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Rebecca CJ Twells
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Anne Smith
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Alex C Lam
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Luc J Smink
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - Neil M Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
| | - John A Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK
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