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Abstract
Modern molecular biology relies on large amounts of high-quality genomic DNA. However, in a number of clinical or biological applications this requirement cannot be met, as starting material is either limited (e.g., preimplantation genetic diagnosis (PGD) or analysis of minimal residual cancer) or of insufficient quality (e.g., formalin-fixed paraffin-embedded tissue samples or forensics). As a consequence, in order to obtain sufficient amounts of material to analyze these demanding samples by state-of-the-art modern molecular assays, genomic DNA has to be amplified. This chapter summarizes available technologies for whole-genome amplification (WGA), bridging the last 25 years from the first developments to currently applied methods. We will especially elaborate on research application, as well as inherent advantages and limitations of various WGA technologies.
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Affiliation(s)
- Zbigniew Tadeusz Czyz
- Project Group, Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Josef-Engert-Straße 9, 93053, Regensburg, Germany
| | - Stefan Kirsch
- Project Group, Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Josef-Engert-Straße 9, 93053, Regensburg, Germany
| | - Bernhard Polzer
- Project Group, Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Josef-Engert-Straße 9, 93053, Regensburg, Germany.
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Orjuela-Sánchez P, Brandi MC, Ferreira MU. Microsatellite analysis of malaria parasites. Methods Mol Biol 2013; 1006:247-58. [PMID: 23546796 DOI: 10.1007/978-1-62703-389-3_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Microsatellites have been increasingly used to investigate the population structure of malaria parasites, to map genetic loci contributing to phenotypes such as drug resistance and virulence in laboratory crosses and genome-wide association studies and to distinguish between treatment failures and new infections in clinical trials. Here, we provide optimized protocols for genotyping highly polymorphic microsatellites sampled from across the genomes of the human malaria parasites Plasmodium falciparum and P. vivax that have been extensively used in research laboratories worldwide.
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Affiliation(s)
- Pamela Orjuela-Sánchez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Digital transcriptome profiling from attomole-level RNA samples. Genome Res 2010; 20:519-25. [PMID: 20133332 DOI: 10.1101/gr.102129.109] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Accurate profiling of minute quantities of RNA in a global manner can enable key advances in many scientific and clinical disciplines. Here, we present low-quantity RNA sequencing (LQ-RNAseq), a high-throughput sequencing-based technique allowing whole transcriptome surveys from subnanogram RNA quantities in an amplification/ligation-free manner. LQ-RNAseq involves first-strand cDNA synthesis from RNA templates, followed by 3' polyA tailing of the single-stranded cDNA products and direct single molecule sequencing. We applied LQ-RNAseq to profile S. cerevisiae polyA+ transcripts, demonstrate the reproducibility of the approach across different sample preparations and independent instrument runs, and establish the absolute quantitative power of this method through comparisons with other reported transcript profiling techniques and through utilization of RNA spike-in experiments. We demonstrate the practical application of this approach to define the transcriptional landscape of mouse embryonic and induced pluripotent stem cells, observing transcriptional differences, including over 100 genes exhibiting differential expression between these otherwise very similar stem cell populations. This amplification-independent technology, which utilizes small quantities of nucleic acid and provides quantitative measurements of cellular transcripts, enables global gene expression measurements from minute amounts of materials and offers broad utility in both basic research and translational biology for characterization of rare cells.
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Affiliation(s)
- Fatih Ozsolak
- Helicos BioSciences Corporation, Cambridge, MA 02139, USA.
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Rana BK, Wessel J, Mahboubi V, Rao F, Haeller J, Gayen JR, Eskin E, Valle AM, Das M, Mahata SK, Taupenot L, Stridsberg M, Talley TT, Ziegler MG, Smith DW, Schork NJ, O'Connor DT, Taylor P. Natural variation within the neuronal nicotinic acetylcholine receptor cluster on human chromosome 15q24: influence on heritable autonomic traits in twin pairs. J Pharmacol Exp Ther 2009; 331:419-28. [PMID: 19671882 PMCID: PMC2775266 DOI: 10.1124/jpet.109.157271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 08/06/2009] [Indexed: 01/18/2023] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are combinations of subunits arranged as pentamers encircling a central cation channel. At least nine alpha and four beta subunits are expressed in the central and peripheral nervous systems; their presence in autonomic ganglia, the adrenal medulla, and central nervous system, with accompanying responses elicited by nicotinic agonists, point to their involvement in cardiovascular homeostasis. nAChRs formed by alpha3, alpha5, and beta4 subunits may regulate blood pressure (BP) by mediating release of catestatin, the endogenous nicotinic antagonist fragment of chromogranin A (CHGA) and potent inhibitor of catecholamine secretion. Genes encoding these subunits (CHRNA3, CHRNA5, and CHRNB4) are clustered on human chromosome 15q24. Because variation in this cluster may alter autonomic regulation of BP, we sequenced approximately 15 kilobase pairs in 15q24 containing their coding and 5'- and 3'-untranslated regions in 80 individuals. We identified 63 variants: 25 in coding regions of CHRNA3, CHRNA5, and CHRNB4 and 48 noncoding single-nucleotide polymorphisms (SNPs). Haplotype frequencies varied across ethnic populations. We assessed the contribution of six SNPs in the putative catestatin binding region of CHRNA3 and CHRNB4 to autonomic traits. In twins, catestatin and BP were heritable. CHRNA3 SNPs and haplotypes containing K95K (G285A) associated with circulating plasma catestatin, epinephrine levels, as well as systolic BP, suggesting altered coupling of the nAChRs to BP. Studies of chromaffin cells in vitro reveal that nicotinic agonist stimulation releases catecholamines and CHGA, a process augmented by overexpression of CHRNA3 and blocked by catestatin. These cellular events suggest a homeostatic mechanism underlying the pleiotropic actions of CHRNA3 genetic variation on autonomic function observed in twins.
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Affiliation(s)
- Brinda K Rana
- Departments of Psychiatry, University of California at San Diego, La Jolla, California 92093-0657, USA
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Mengel-From J, Børsting C, Sanchez JJ, Eiberg H, Morling N. Determination of cis/trans phase of variations in the MC1R gene with allele-specific PCR and single base extension. Electrophoresis 2009; 29:4780-7. [PMID: 19016241 DOI: 10.1002/elps.200800107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The MC1R gene encodes a protein with key regulatory functions in the melanin synthesis. A multiplex PCR and a multiplex single base extension protocol were established for genotyping six exonic MC1R variations highly penetrant for red hair (R), four exonic MC1R variations weakly penetrant for red hair (r), two frameshift variations highly penetrant for red hair (R) and three variations in the promoter region. We genotyped 600 individuals from Denmark using either CE or MALDI-TOF MS as the detection platform. A total of 62 individuals were genotyped R/R and among the 62 individuals, 57 had red hair and five had blond hair colour. Two different R alleles may be located in cis (RR/-) position or trans (R/R) position, and the phenotype associated with RR/- and R/R may be different. Two allele-specific PCRs were established with primers targeting the -G445A variation in the MC1R promoter and the allele-specific PCR products were used in the multiplex single base extension assay. In all 62 individuals, the MC1R variants were situated in trans position. Another 18 individuals with red hair colour were either genotyped R/- or R/r, suggesting that other genes influence hair colour.
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Affiliation(s)
- Jonas Mengel-From
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Whole genome amplification of the rust Puccinia striiformis f. sp. tritici from single spores. J Microbiol Methods 2009; 77:229-34. [PMID: 19233233 DOI: 10.1016/j.mimet.2009.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 02/11/2009] [Indexed: 11/24/2022]
Abstract
Rust fungi are obligate parasites and cannot be routinely cultured to obtain sufficient biomass for DNA extractions. Multiple displacement amplification (MDA) was demonstrated in this study for whole genome amplification from single spores of the rust fungus, Puccinia striiformis. The genomic DNA coverage and fidelity of this method was evaluated by PCR amplification and sequencing of two genetic markers: portions of the multi-copy nuclear ribosomal DNA internal transcribed spacer region (ITS) and the single copy beta-tubulin gene from two geographical diverse isolates. Our results show that MDA is a valuable tool for whole genome amplification from single spores, and we propose that MDA-amplified DNA can be used for molecular genetic analysis of the wheat yellow rust fungus.
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Havryliuk T, Orjuela-Sánchez P, Ferreira MU. Plasmodium vivax: Microsatellite analysis of multiple-clone infections. Exp Parasitol 2008; 120:330-6. [DOI: 10.1016/j.exppara.2008.08.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/13/2008] [Accepted: 08/21/2008] [Indexed: 11/17/2022]
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Cho MH, Ciulla D, Klanderman BJ, Raby BA, Silverman EK. High-Resolution Melting Curve Analysis of Genomic and Whole-Genome Amplified DNA. Clin Chem 2008; 54:2055-8. [DOI: 10.1373/clinchem.2008.109744] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Abstract
Background: High-resolution melting curve analysis is an accurate method for mutation detection in genomic DNA. Few studies have compared the performance of high-resolution DNA melting curve analysis (HRM) in genomic and whole-genome amplified (WGA) DNA.
Methods: In 39 paired genomic and WGA samples, 23 amplicons from 9 genes were PCR amplified and analyzed by high-resolution melting curve analysis using the 96-well LightScanner (Idaho Technology). We used genotyping and bidirectional resequencing to verify melting curve results.
Results: Melting patterns were concordant between the genomic and WGA samples in 823 of 863 (95%) analyzed sample pairs. Of the discordant patterns, there was an overrepresentation of alternate melting curve patterns in the WGA samples, suggesting the presence of a mutation (false positives). Targeted resequencing in 135 genomic and 136 WGA samples revealed 43 single nucleotide polymorphisms (SNPs). All SNPs detected in genomic samples were also detected in WGA. Additional genotyping and sequencing allowed the classification of 628 genomic and 614 WGA amplicon samples. Heterozygous variants were identified by non–wild-type melting pattern in 98% of genomic and 97% of WGA samples (P = 0.11). Wild types were correctly classified in 99% of genomic and 91% of WGA samples (P < 0.001).
Conclusions: In WGA DNA, high-resolution DNA melting curve analysis is a sensitive tool for SNP discovery through detection of heterozygote variants; however, it may misclassify a greater number of wild-type samples.
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Affiliation(s)
- Michael H Cho
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA; and
- Harvard Medical School, Boston, MA
| | - Dawn Ciulla
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
| | - Barbara J Klanderman
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Benjamin A Raby
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA; and
- Harvard Medical School, Boston, MA
| | - Edwin K Silverman
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA; and
- Harvard Medical School, Boston, MA
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Lamoril J, Ameziane N, Deybach JC, Bouizegarène P, Bogard M. Les techniques de séquençage de l’ADN : une révolution en marche. Première partie. IMMUNO-ANALYSE & BIOLOGIE SPÉCIALISÉE 2008. [PMCID: PMC7147846 DOI: 10.1016/j.immbio.2008.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- J. Lamoril
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
- Auteur correspondant.
| | - N. Ameziane
- Laboratoire de biologie polyvalente, centre hospitalier de Sens, 89100 Sens, France
| | - J.-C. Deybach
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
| | - P. Bouizegarène
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
| | - M. Bogard
- Laboratoire de biochimie et biologie moléculaire, centre hospitalier de Meaux, 77100 Meaux, France
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Talseth-Palmer BA, Bowden NA, Hill A, Meldrum C, Scott RJ. Whole genome amplification and its impact on CGH array profiles. BMC Res Notes 2008; 1:56. [PMID: 18710509 PMCID: PMC2525645 DOI: 10.1186/1756-0500-1-56] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 07/29/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Some array comparative genomic hybridisation (array CGH) platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA) is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of starting material. A range of WGA methods are available and the multiple displacement amplification (MDA) approach has been shown to be highly accurate, although amplification bias has been reported. In the current study, WGA was used to amplify DNA extracted from whole blood. In total, six array CGH experiments were performed to investigate whether the use of whole genome amplified DNA (wgaDNA) produces reliable and reproducible results. Four experiments were conducted on amplified DNA compared to unamplified DNA and two experiments on unamplified DNA compared to unamplified DNA. FINDINGS All the experiments involving wgaDNA resulted in a high proportion of losses and gains of genomic material. Previously, amplification bias has been overcome by using amplified DNA in both the test and reference DNA. Our data suggests that this approach may not be effective, as the gains and losses introduced by WGA appears to be random and are not reproducible between different experiments using the same DNA. CONCLUSION In light of these findings, the use of both amplified test and reference DNA on CGH arrays may not provide an accurate representation of copy number variation in the DNA.
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Affiliation(s)
- Bente A Talseth-Palmer
- School of Biomedical Sciences, Faculty of Health, University of Newcastle and the Hunter Medical Research Institute, NSW, Australia.
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Apter AJ, Schelleman H, Walker A, Addya K, Rebbeck T. Clinical and genetic risk factors of self-reported penicillin allergy. J Allergy Clin Immunol 2008; 122:152-8. [DOI: 10.1016/j.jaci.2008.03.037] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 03/20/2008] [Accepted: 03/28/2008] [Indexed: 12/01/2022]
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Berthier-Schaad Y, Kao WHL, Coresh J, Zhang L, Ingersoll RG, Stephens R, Smith MW. Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies. Electrophoresis 2007; 28:2812-7. [PMID: 17702060 DOI: 10.1002/elps.200600674] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Whole genome amplification (wga) of DNA is being widely implemented in many laboratories to extend the life of samples only available in limited quantities for genetic analysis. We determined the reliability of wgaDNA genotypes in three sets of replicates from the same individuals: (i) 23 pairs of genomic DNA (gDNA), (ii) 43 pairs gDNA versus wgaDNA, and (iii) 29 pairs of independently amplified wgaDNA. Amplification was performed using multiple displacement amplification (MDA). Genotyping was successful for both DNA types for 1268 out of 1534 SNPs from 164 cardiovascular candidate genes assayed in a single Illumina panel. Amplified DNA failed for 77 SNPs (6%) that were genotyped successfully with genomic material. Percent of successful SNP calls, and concordance between pairs and kappa statistics (kappa) were determined. A total of 54 110 genotypes from gDNA-wgaDNA pairs were available for concordance analysis. Mean kappa for gDNA-wgaDNA pairs was 0.99. Concordance between gDNA-wgaDNA pairs was higher than amongst wgaDNA pairs (mean kappa for the 29 independently amplified pairs of wgaDNA was 0.95; interquartile range: 0.93-1.00). A statistical analysis of those SNPs which failed to genotype from amplified DNA only revealed that those loci were more likely to be closer to the telomeres and in locally GC-rich sequences. In summary, the MDA method produces wgaDNA samples that can be genotyped using high-throughput technology with a very high reproducibility to the original DNA but with slightly lower call rates. DNA amplification methodologies provide a useful solution for current and future large-scale genetic analyses especially with limited quantities of samples and DNA.
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Liang X, Trentham-Dietz A, Titus-Ernstoff L, Newcomb PA, Welch RA, Hutchinson AA, Hampton JM, Sutcliffe CB, Haines JL, Egan KM. Whole-genome amplification of oral rinse self-collected DNA in a population-based case-control study of breast cancer. Cancer Epidemiol Biomarkers Prev 2007; 16:1610-4. [PMID: 17684135 DOI: 10.1158/1055-9965.epi-07-0110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The availability of large amounts of genomic DNA (gDNA) is the limiting factor for many of the molecular biology assays in genetic epidemiologic studies. Whole-genome amplification using multiple displacement amplification is used to amplify a representative sample of gDNA from small amounts of gDNA to optimize gDNA yield. We collected oral rinse DNA samples through the mail from 3,377 women enrolled in a population-based U.S. breast cancer case-control study and did whole-genome amplification by multiple displacement amplification. Genotyping was done for 66 single nucleotide polymorphisms (SNP) in 18 candidate susceptibility genes using amplified DNA with genomic replicates included for quality control. The concordance rates (percentages of agreement) in 95 quality control replicates of gDNA and amplified DNA for 66 SNPs ranged from 88% to 100% (median, 97%). The average allelic error rate was 0.9%. However, in further analyses based on the full control series (n = 1,492), >60% of the SNPs failed tests for Hardy-Weinberg equilibrium (P < 0.05), with evidence of heterozygote loss in the great majority. Even eliminating the 9% of samples with lower quality or input DNA, tests for Hardy-Weinberg equilibrium indicated persistent allele bias in nearly a third of the SNPs. Whole-genome amplification may introduce substantial allele amplification bias in gDNA collected using a common protocol in population-based epidemiologic studies.
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Affiliation(s)
- Xueying Liang
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Increasing amplification success of forensic DNA samples using multiple displacement amplification. Forensic Sci Med Pathol 2007; 3:182-7. [DOI: 10.1007/s12024-007-0017-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2007] [Indexed: 10/22/2022]
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Ribacke U, Mok BW, Wirta V, Normark J, Lundeberg J, Kironde F, Egwang TG, Nilsson P, Wahlgren M. Genome wide gene amplifications and deletions in Plasmodium falciparum. Mol Biochem Parasitol 2007; 155:33-44. [PMID: 17599553 DOI: 10.1016/j.molbiopara.2007.05.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 04/13/2007] [Accepted: 05/15/2007] [Indexed: 11/24/2022]
Abstract
The extent to which duplications and deletions occur in the Plasmodium falciparum genome, outside of the subtelomeres, and their contribution to the virulence of the malaria parasite is not known. Here we show the presence of multiple genome wide copy number polymorphisms (CNPs) covering 82 genes, the most extensive spanning a cumulative size of 110kilobases. CNPs were identified in both laboratory strains and fresh clinical isolates using a 70-mer oligonucleotide microarray in conjunction with fluorescent in situ hybridizations and real-time quantitative PCR. The CNPs were found on all chromosomes except on chromosomes 6 and 8 and involved a total of 50 genes with increased copy numbers and 32 genes with decreased copy numbers relative to the 3D7 parasite. The genes, amplified in up to six copies, encode molecules involved in cell cycle regulation, cell division, drug resistance, erythrocyte invasion, sexual differentiation and unknown functions. These together with previous findings, suggest that the malaria parasite employs gene duplications and deletions as general strategies to enhance its survival and spread. Further analysis of the impact of discovered genetic differences and the underlying mechanisms is likely to generate a better understanding of the biology and the virulence of the malaria parasite.
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Affiliation(s)
- Ulf Ribacke
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
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Production of in vitro amplified DNA pseudolibraries and high-throughput cDNA target amplification. BMC Biotechnol 2007; 7:31. [PMID: 17565673 PMCID: PMC1894961 DOI: 10.1186/1472-6750-7-31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 06/12/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many structural biology- and high-throughput laboratories experience the acquisition of multiple cDNAs from different sources as a rather time- and resource-consuming procedure. The techniques presented here solve these problems. RESULTS An advanced target cDNA amplification procedure employing RNA- or cDNA-derived pseudolibraries circumvents the usual DNA transfection during library establishment. A small sample of reverse transcribed ss- or ds-cDNA or DNA from a pre-existing library is multiplied by in vitro rolling circle ramification amplification. The resulting cDNA pseudolibrary serves as a template for numerous highly efficient PCR amplifications and permits production and analysis of target cDNAs on an automated liquid handling workstation. CONCLUSION The overall efficiency of the simple protocol collection approaches 100% for targets from libraries with low complexity such as Drosophila and yields >80% of amplicons up to 3 kb size in the case of human cDNA.
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Ballantyne KN, van Oorschot RAH, Muharam I, van Daal A, John Mitchell R. Decreasing amplification bias associated with multiple displacement amplification and short tandem repeat genotyping. Anal Biochem 2007; 368:222-9. [PMID: 17583668 DOI: 10.1016/j.ab.2007.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 05/07/2007] [Accepted: 05/19/2007] [Indexed: 11/27/2022]
Abstract
Although multiple displacement amplification (MDA) is being used increasingly to amplify genomes, the amplification bias generated by the varphi29 polymerase can be a concern with genotyping applications. It has been noted that the bias is pronounced with small template amounts, particularly with single nucleotide polymorphism (SNP) and short tandem repeat (STR) genotyping. Bias may occur between loci, or between alleles within a locus, and may differ between sample donors at the same loci. Previous research has suggested that omitting denaturation of the template prior to amplification can reduce the observed bias significantly. Comparison of the two methods (with and without denaturation) has found that nondenaturation of template reverses the direction of bias observed between allelic pairs following MDA. By combining two MDA reactions, one denatured and one nondenatured, the bias was found to be reduced significantly, aiding copy number analysis and subsequent genotyping.
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Affiliation(s)
- Kaye N Ballantyne
- Biology Division, Victoria Police Forensic Services Department, Macleod, 3085 VIC, Australia.
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Sørensen KM, Jespersgaard C, Vuust J, Hougaard D, Nørgaard-Pedersen B, Andersen PS. Whole Genome Amplification on DNA from Filter Paper Blood Spot Samples: An Evaluation of Selected Systems. ACTA ACUST UNITED AC 2007; 11:65-71. [PMID: 17394394 DOI: 10.1089/gte.2006.0503] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
As the number of single-nucleotide polymorphism (SNP) screening and other mutation scanning studies have increased explosively, following the development of high-throughput instrumentation, it becomes even more important to have sufficient template DNA. The source of DNA is often limited, especially in epidemiological studies, which require many samples as well as enough DNA to perform numerous SNP screenings or mutation scannings. Therefore, the aim is to solve the problem of stock DNA limitation. This need has been an important reason for the development of whole genome amplification (WGA) methods. Several systems are based on Phi29 polymerase multiple displacement amplification (MDA) or on DNA fragmentation (OmniPlex). Using TaqMan SNP genotyping assays, we have tested four WGA systems -- AmpliQ Genomic Amplifier Kit, GenomiPhi, Repli-g, and GenomePlex -- on DNA extracted from Guthrie cards to evaluate the amplification bias, concordance- and call rates, cost efficiency, and flexibility. All systems successfully amplified picograms of DNA from Guthrie cards to micrograms of product without loss of heterozygosity and with minimal allelic bias. A modified AmpliQ set up was chosen for further evaluation. In all, 2,000 SNP genotyping results from amplified and nonamplified samples were compared and the concordance rates between the samples were 99.7%. The call rate using the TaqMan system was 99.8%. DNA extracted from Guthrie cards and amplified with one of the four evaluated WGA systems is applicable in epidemiological genetic screenings. System choice should be based on requirements for system flexibility, product yield, and use in subsequent analysis.
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Peng W, Takabayashi H, Ikawa K. Whole genome amplification from single cells in preimplantation genetic diagnosis and prenatal diagnosis. Eur J Obstet Gynecol Reprod Biol 2007; 131:13-20. [PMID: 17157976 DOI: 10.1016/j.ejogrb.2006.07.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Revised: 06/12/2006] [Accepted: 07/16/2006] [Indexed: 10/23/2022]
Abstract
The literature on whole genome amplification (WGA) techniques and their application to preimplantation genetic diagnosis (PGD) and prenatal diagnosis is reviewed. General polymerase chain reaction (PCR) fails to provide adequate information from limited cells in PGD and non-invasive prenatal diagnosis. Therefore several WGA techniques, such as primer extension preamplification (PEP) and degenerate oligonucleotide primed PCR (DOP-PCR), have been developed and successfully applied to clinical work during the past decade, especially in PGD and prenatal diagnosis. These techniques can provide ample amplification of genetic sequences from single cells for a series of subsequent PCR analyses such as restriction fragment length polymorphisms (RFLP) and comparative genomic hybridization (CGH), thus opening up a new area for prenatal diagnosis. However, several problems have been reported in the application of these techniques. The ideal WGA technique should have high yield, faithful representation of the original template, complete coverage of the genome, and simply performed procedure. In order to make good use of these techniques in future research and clinical work, it is undoubtedly necessary for an extensive understanding of the merits and pitfalls of these recently developed techniques.
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Affiliation(s)
- Wen Peng
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Jinan 250021, China; Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, Kanazawa, Ishikawa 920-0293, Japan.
| | - Haruo Takabayashi
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, Kanazawa, Ishikawa 920-0293, Japan
| | - Kazumi Ikawa
- Cytogenetic Laboratory, Ishikawa Health Service Association, Kanazawa, Ishikawa 920-0365, Japan
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Ballantyne KN, van Oorschot RAH, Mitchell RJ. Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples. Forensic Sci Int 2007; 166:35-41. [PMID: 16687226 DOI: 10.1016/j.forsciint.2006.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/27/2006] [Accepted: 03/29/2006] [Indexed: 10/24/2022]
Abstract
The analysis of LCN or highly degraded DNA samples presents a challenge for forensic science. Improving the quantity and/or quality of samples would greatly increase the profiling success rate from LCN and degraded samples. Whole genome amplification (WGA) is one method that has such potential. Two commercially available WGA kits, GenomePlex and GenomiPhi, were investigated for use on LCN and degraded DNA samples. Both kits amplified genomic DNA, producing microgram quantities from sub-nanogram templates. Profiling success of LCN DNA samples was increased, with improvements of over 700% from 10pg template DNA compared to non-WGA-amplified control samples. The amplification success with degraded DNA was also improved by WGA. Degraded DNA was simulated using restriction enzymes to demonstrate that the application of WGA can result in the typing of STR loci that could not previously be amplified. An increase in artefacts, such as stutter alleles and amplification biases, were observed in many samples. Results show that WGA is capable of increasing both the quality and quantity of DNA, and has the potential to improve profiling success from difficult samples in forensic casework.
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Affiliation(s)
- Kaye N Ballantyne
- Victoria Police Forensic Services Department, Macleod, VIC, Australia.
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21
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Leanza SM, Burk RD, Rohan TE. Whole genome amplification of DNA extracted from hair samples: Potential for use in molecular epidemiologic studies. ACTA ACUST UNITED AC 2007; 31:480-8. [DOI: 10.1016/j.cdp.2007.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2007] [Indexed: 10/22/2022]
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Ballantyne KN, van Oorschot RAH, Mitchell RJ, Koukoulas I. Molecular crowding increases the amplification success of multiple displacement amplification and short tandem repeat genotyping. Anal Biochem 2006; 355:298-303. [PMID: 16737679 DOI: 10.1016/j.ab.2006.04.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 04/19/2006] [Accepted: 04/19/2006] [Indexed: 11/20/2022]
Abstract
Multiple displacement amplification (MDA) can generate large quantities of genomic DNA product from small amounts of template. We investigated the ability of MDA to amplify samples containing very small amounts of target DNA (5 pg to 1 ng) in the presence of a second, larger DNA sample for downstream short tandem repeat (STR) multiplex genotyping. We observed that STR amplification success of the minor fraction was increased in these mixed samples when compared with standard PCR only or MDA containing only the single trace DNA sample. Increased numbers of alleles were detected, with less amplification bias between loci than in single source samples undergoing the same protocol. To improve the STR genotyping accuracy, animal DNA was substituted for the additional human DNA, maintaining the increase in the number and quality of human-specific STR loci amplified. Polyethylene glycol 400, a commonly used crowding agent, was used as a replacement for the added genomic DNA in the MDA reaction and produced very similar results. Therefore, we suggest that additional DNA is acting as a molecular crowding agent during MDA. Performing MDA on trace amounts of DNA under crowded conditions results in greater numbers of alleles being amplified and more balanced amplification occurring between alleles.
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Affiliation(s)
- Kaye N Ballantyne
- Biology Division, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia.
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23
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Lovmar L, Syvänen AC. Multiple displacement amplification to create a long-lasting source of DNA for genetic studies. Hum Mutat 2006; 27:603-14. [PMID: 16786504 DOI: 10.1002/humu.20341] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In many situations there may not be sufficient DNA collected from patient or population cohorts to meet the requirements of genome-wide analysis of SNPs, genomic copy number polymorphisms, or acquired copy number alternations. When the amount of available DNA for genotype analysis is limited, high performance whole-genome amplification (WGA) represents a new development in genetic analysis. It is especially useful for analysis of DNA extracted from stored histology slides, tissue samples, buccal swabs, or blood stains collected on filter paper. The multiple displacement amplification (MDA) method, which relies on isothermal amplification using the DNA polymerase of the bacteriophage phi29, is a recently developed technique for high performance WGA. This review addresses new trends in the technical performance of MDA and its applications to genetic analyses. The main challenge of WGA methods is to obtain balanced and faithful replication of all chromosomal regions without the loss of or preferential amplification of any genomic loci or allele. In multiple comparisons to other WGA methods, MDA appears to be most reliable for genotyping, with the most favorable call rates, best genomic coverage, and lowest amplification bias.
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Affiliation(s)
- Lovisa Lovmar
- Molecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
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24
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Riddle EL, Rana BK, Murthy KK, Rao F, Eskin E, O'Connor DT, Insel PA. Polymorphisms and Haplotypes of the Regulator of G Protein Signaling-2 Gene in Normotensives and Hypertensives. Hypertension 2006; 47:415-20. [PMID: 16432041 DOI: 10.1161/01.hyp.0000200714.81990.61] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Regulator of G protein signaling (RGS) proteins stimulate the GTPase activity of Galpha subunits of heterotrimeric G proteins, thereby negatively regulating G protein-coupled receptor signaling. RGS2, which preferentially alters Galphaq-mediated signaling, may be important for cardiovascular health, because knockout of RGS2 in mice is associated with altered smooth muscle relaxation and hypertension. In this study, we determined genetic variation in the human RGS2 gene by sequencing DNA in normotensive and hypertensive populations of whites (n=128) and blacks (n=122). We identified 14 single nucleotide polymorphisms and 2 two-base insertion/deletions (in/del; 1891 to 1892 TC and 2138 to 2139 AA). Although most of the genetic variants were found at low allelic frequency, in particular in coding regions, the 1891 to 1892 TC and 2138 to 2139 AA intronic in/del were in linkage disequilibrium and were associated with hypertension in blacks (P<0.05). We defined several haplotypes for the RGS2 gene, certain of which showed striking differences between whites and blacks. Additionally, 2 haplotypes had significantly different frequencies between hypertensive and normotensive black groups (P<0.05). We conclude that RGS2 is genetically conserved within coding regions but that the intronic in/del define ethnicity-specific haplotypes. Moreover, certain RGS2 variants that occur at greater frequency in hypertensive blacks may serve as ethnicity-specific genetic variants for this disease.
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Affiliation(s)
- Evan L Riddle
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
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