MDA
Multiple Displacement Amplification
MDA is a method commonly used for sequencing microbial genomes due to its ability to amplify templates larger than 0.5 Mbp, but it can also be used to study genomes of other sizes (Dean et al., 2001). In this method, 3ê-blocked random hexamer primers are hybridized to the template, followed by strand-displacement DNA synthesis with Phi 29 polymerase. The method allows for efficient and rapid DNA amplification. Deep sequencing of the amplified DNA provides accurate representation of reads, while sequencing depth provides better alignment and consensus for sequences. Several variations on the original MDA methodãsuch as MIDAS (Gole et al., 2013), ddMDA (Rhee et al., 2016), SNES (Leung et al., 2015), and IMS-MDA (Seth-Smith et al., 2013) ãhave been developed to improve the amplification bias and throughput (Seth-Smith et al., 2013).
Advantages:
- Templates can be circular DNA (eg, plasmids, bacterial DNA)
- Can sequence large templates
- Can perform single-cell sequencing or sequencing for samples with limited amounts of starting material
Disadvantages:
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Sauvage V. and Eloit M. Viral metagenomics and blood safety. Transfus Clin Biol. 2016;23:28-38
Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X. and Wu S. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312
Hou Y., Wu K., Shi X., et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. Gigascience. 2015;4:37
Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609
References:
Newton I. L., Clark M. E., Kent B. N., et al. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. Genome Biol Evol. 2016;8:1526-1542
Salman V., Berben T., Bowers R. M., Woyke T., Teske A. and Angert E. R. Insights into the single cell draft genome of “Candidatus Achromatium palustre”. Stand Genomic Sci. 2016;11:28
Troell K., Hallstrom B., Divne A. M., et al. Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics. 2016;17:471
Ning L., Li Z., Wang G., et al. Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons. Sci Rep. 2015;5:11415
Brito I. L., Yilmaz S., Huang K., et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature. 2016;535:435-439
Eloe-Fadrosh E. A., Paez-Espino D., Jarett J., et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 2016;7:10476
Hatzenpichler R., Connon S. A., Goudeau D., Malmstrom R. R., Woyke T. and Orphan V. J. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A. 2016;113:E4069-4078
Moutailler S., Popovici I., Devillers E., Vayssier-Taussat M. and Eloit M. Diversity of viruses in Ixodes ricinus, and characterization of a neurotropic strain of Eyach virus. New Microbes New Infect. 2016;11:71-81
Ottolini C. S., Capalbo A., Newnham L., et al. Generation of meiomaps of genome-wide recombination and chromosome segregation in human oocytes. Nat Protoc. 2016;11:1229-1243
Peterson S. W., Knox N. C., Golding G. R., et al. A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker. PLoS One. 2016;11:e0152493
Thoendel M., Jeraldo P. R., Greenwood-Quaintance K. E., et al. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J Microbiol Methods. 2016;127:141-145
Bigdeli S., Dettloff R. O., Frank C. W., Davis R. W. and Crosby L. D. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. PLoS One. 2015;10:e0117738
Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55
Li N., Wang L., Wang H., et al. The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities. J Genet Genomics. 2015;42:151-159
Macaulay I. C., Haerty W., Kumar P., et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods. 2015;
Ottolini C. S., Newnham L. J., Capalbo A., et al. Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates. Nat Genet. 2015;
Zhang C. Z., Spektor A., Cornils H., et al. Chromothripsis from DNA damage in micronuclei. Nature. 2015;522:179-184
Related
History: MDA
Revision by on 2017-06-21 09:15:21 - Show/Hide
Multiple Displacement Amplification
MDA is a method commonly used for sequencing microbial genomes due to its ability to amplify templates larger than 0.5 Mbp, but it can also be used to study genomes of other sizes (Dean et al., 2001). In this method, 3ê-blocked random hexamer primers are hybridized to the template, followed by strand-displacement DNA synthesis with Phi 29 polymerase. The method allows for efficient and rapid DNA amplification. Deep sequencing of the amplified DNA provides accurate representation of reads, while sequencing depth provides better alignment and consensus for sequences. Several variations on the original MDA methodãsuch as MIDAS (Gole et al., 2013), ddMDA (Rhee et al., 2016), SNES (Leung et al., 2015), and IMS-MDA (Seth-Smith et al., 2013) ãhave been developed to improve the amplification bias and throughput (Seth-Smith et al., 2013).
Advantages:- Templates can be circular DNA (eg, plasmids, bacterial DNA)
- Can sequence large templates
- Can perform single-cell sequencing or sequencing for samples with limited amounts of starting material
Disadvantages:Reagents:Illumina Library prep and Array Kit SelectorReviews:Sauvage V. and Eloit M. Viral metagenomics and blood safety. Transfus Clin Biol. 2016;23:28-38Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X. and Wu S. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312Hou Y., Wu K., Shi X., et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. Gigascience. 2015;4:37Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609References:Newton I. L., Clark M. E., Kent B. N., et al. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. Genome Biol Evol. 2016;8:1526-1542Salman V., Berben T., Bowers R. M., Woyke T., Teske A. and Angert E. R. Insights into the single cell draft genome of "Candidatus Achromatium palustre". Stand Genomic Sci. 2016;11:28Troell K., Hallstrom B., Divne A. M., et al. Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics. 2016;17:471Ning L., Li Z., Wang G., et al. Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons. Sci Rep. 2015;5:11415Brito I. L., Yilmaz S., Huang K., et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature. 2016;535:435-439Eloe-Fadrosh E. A., Paez-Espino D., Jarett J., et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 2016;7:10476Hatzenpichler R., Connon S. A., Goudeau D., Malmstrom R. R., Woyke T. and Orphan V. J. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A. 2016;113:E4069-4078Moutailler S., Popovici I., Devillers E., Vayssier-Taussat M. and Eloit M. Diversity of viruses in Ixodes ricinus, and characterization of a neurotropic strain of Eyach virus. New Microbes New Infect. 2016;11:71-81Ottolini C. S., Capalbo A., Newnham L., et al. Generation of meiomaps of genome-wide recombination and chromosome segregation in human oocytes. Nat Protoc. 2016;11:1229-1243Peterson S. W., Knox N. C., Golding G. R., et al. A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker. PLoS One. 2016;11:e0152493Thoendel M., Jeraldo P. R., Greenwood-Quaintance K. E., et al. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J Microbiol Methods. 2016;127:141-145Bigdeli S., Dettloff R. O., Frank C. W., Davis R. W. and Crosby L. D. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. PLoS One. 2015;10:e0117738Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55Li N., Wang L., Wang H., et al. The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities. J Genet Genomics. 2015;42:151-159Macaulay I. C., Haerty W., Kumar P., et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods. 2015;Ottolini C. S., Newnham L. J., Capalbo A., et al. Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates. Nat Genet. 2015;Zhang C. Z., Spektor A., Cornils H., et al. Chromothripsis from DNA damage in micronuclei. Nature. 2015;522:179-184Revision by sbrumpton on 2017-06-21 09:06:26 - Show/Hide
Multiple Displacement Amplification
MDA is a method commonly used for sequencing microbial genomes due to its ability to amplify templates larger than 0.5 Mbp, but it can also be used to study genomes of other sizes (Dean et al., 2001). In this method, 3ê-blocked random hexamer primers are hybridized to the template, followed by strand-displacement DNA synthesis with Phi 29 polymerase. The method allows for efficient and rapid DNA amplification. Deep sequencing of the amplified DNA provides accurate representation of reads, while sequencing depth provides better alignment and consensus for sequences. Several variations on the original MDA methodãsuch as MIDAS (Gole et al., 2013), ddMDA (Rhee et al., 2016), SNES (Leung et al., 2015), and IMS-MDA (Seth-Smith et al., 2013) ãhave been developed to improve the amplification bias and throughput (Seth-Smith et al., 2013).
Advantages:- Templates can be circular DNA (eg, plasmids, bacterial DNA)
- Can sequence large templates
- Can perform single-cell sequencing or sequencing for samples with limited amounts of starting material
Disadvantages:Reagents:Illumina Library prep and Array Kit SelectorReviews:Sauvage V. and Eloit M. Viral metagenomics and blood safety. Transfus Clin Biol. 2016;23:28-38Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X. and Wu S. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312Hou Y., Wu K., Shi X., et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. Gigascience. 2015;4:37Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609References:Newton I. L., Clark M. E., Kent B. N., et al. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. Genome Biol Evol. 2016;8:1526-1542Salman V., Berben T., Bowers R. M., Woyke T., Teske A. and Angert E. R. Insights into the single cell draft genome of "Candidatus Achromatium palustre". Stand Genomic Sci. 2016;11:28Troell K., Hallstrom B., Divne A. M., et al. Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics. 2016;17:471Ning L., Li Z., Wang G., et al. Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons. Sci Rep. 2015;5:11415Brito I. L., Yilmaz S., Huang K., et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature. 2016;535:435-439Eloe-Fadrosh E. A., Paez-Espino D., Jarett J., et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 2016;7:10476Hatzenpichler R., Connon S. A., Goudeau D., Malmstrom R. R., Woyke T. and Orphan V. J. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A. 2016;113:E4069-4078Moutailler S., Popovici I., Devillers E., Vayssier-Taussat M. and Eloit M. Diversity of viruses in Ixodes ricinus, and characterization of a neurotropic strain of Eyach virus. New Microbes New Infect. 2016;11:71-81Ottolini C. S., Capalbo A., Newnham L., et al. Generation of meiomaps of genome-wide recombination and chromosome segregation in human oocytes. Nat Protoc. 2016;11:1229-1243Peterson S. W., Knox N. C., Golding G. R., et al. A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker. PLoS One. 2016;11:e0152493Thoendel M., Jeraldo P. R., Greenwood-Quaintance K. E., et al. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J Microbiol Methods. 2016;127:141-145Bigdeli S., Dettloff R. O., Frank C. W., Davis R. W. and Crosby L. D. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. PLoS One. 2015;10:e0117738Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55Li N., Wang L., Wang H., et al. The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities. J Genet Genomics. 2015;42:151-159Macaulay I. C., Haerty W., Kumar P., et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods. 2015;Ottolini C. S., Newnham L. J., Capalbo A., et al. Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates. Nat Genet. 2015;Zhang C. Z., Spektor A., Cornils H., et al. Chromothripsis from DNA damage in micronuclei. Nature. 2015;522:179-184