MIDAS/IMS-MDA/ddMDA
Microwell displacement amplification system/Immunomagnetic Separation for Targeted Bacterial Enrichment for MDA/Digital Droplet MDA
Several variations on the original MDA methodã (Dean et al., 2001) such 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).
Microwell and droplet displacement amplification systems are protocol variations of MDA in which single cells are randomly distributed into hundreds to thousands of nanoliter wells or droplets, and their genetic material is simultaneously amplified (Gole et al., 2013). Sequencing individual cells simplifies the genomic diversity and reduces inherent amplification biases among cells. It results in improved representation and sensitivity in heterogeneous cell populations. In an alternative approach to simplify genomic diversity, IMS-MDA uses immunomagnetic separation for targeted bacterial enrichment (Seth-Smith et al., 2013).
Advantages:
- Templates used for this method 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:
- PCR biases can underrepresent GC-rich templates
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X., et al. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312
Grun D. and van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015;163:799-810
Saadatpour A., Lai S., Guo G. and Yuan G. C. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015;31:576-586
Sun H. J., Chen J., Ni B., Yang X. and Wu Y. Z. Recent advances and current issues in single-cell sequencing of tumors. Cancer Lett. 2015;365:1-10
References:
Rhee M., Light Y. K., Meagher R. J. and Singh A. K. Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. PLoS One. 2016;11:e0153699
Sidore A. M., Lan F., Lim S. W. and Abate A. R. Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res. 2016;44:e66
Lan F., Haliburton J. R., Yuan A. and Abate A. R. Droplet barcoding for massively parallel single-molecule deep sequencing. Nat Commun. 2016;7:11784
Nishikawa Y., Hosokawa M., Maruyama T., Yamagishi K., Mori T. and Takeyama H. Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification. PLoS One. 2015;10:e0138733
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
Eastburn D. J., Huang Y., Pellegrino M., Sciambi A., Ptacek L. J. and Abate A. R. Microfluidic droplet enrichment for targeted sequencing. Nucleic Acids Res. 2015;43:e86
Fu Y., Li C., Lu S., et al. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proc Natl Acad Sci U S A. 2015;112:11923-11928
Related
History: MIDAS/IMS-MDA/ddMDA
Revision by sbrumpton on 2017-06-21 09:06:26 - Show/Hide
Microwell displacement amplification system/Immunomagnetic Separation for Targeted Bacterial Enrichment for MDA/Digital Droplet MDA
Several variations on the original MDA methodã (Dean et al., 2001) such 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).
Microwell and droplet displacement amplification systems are protocol variations of MDA in which single cells are randomly distributed into hundreds to thousands of nanoliter wells or droplets, and their genetic material is simultaneously amplified (Gole et al., 2013). Sequencing individual cells simplifies the genomic diversity and reduces inherent amplification biases among cells. It results in improved representation and sensitivity in heterogeneous cell populations. In an alternative approach to simplify genomic diversity, IMS-MDA uses immunomagnetic separation for targeted bacterial enrichment (Seth-Smith et al., 2013).
Advantages:- Templates used for this method 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:- PCR biases can underrepresent GC-rich templates
Reagents:Illumina Library prep and Array Kit SelectorReviews:Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X., et al. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312Grun D. and van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015;163:799-810Saadatpour A., Lai S., Guo G. and Yuan G. C. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015;31:576-586Sun H. J., Chen J., Ni B., Yang X. and Wu Y. Z. Recent advances and current issues in single-cell sequencing of tumors. Cancer Lett. 2015;365:1-10References:Rhee M., Light Y. K., Meagher R. J. and Singh A. K. Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. PLoS One. 2016;11:e0153699Sidore A. M., Lan F., Lim S. W. and Abate A. R. Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res. 2016;44:e66Lan F., Haliburton J. R., Yuan A. and Abate A. R. Droplet barcoding for massively parallel single-molecule deep sequencing. Nat Commun. 2016;7:11784Nishikawa Y., Hosokawa M., Maruyama T., Yamagishi K., Mori T. and Takeyama H. Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification. PLoS One. 2015;10:e0138733Bigdeli 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:e0117738Eastburn D. J., Huang Y., Pellegrino M., Sciambi A., Ptacek L. J. and Abate A. R. Microfluidic droplet enrichment for targeted sequencing. Nucleic Acids Res. 2015;43:e86Fu Y., Li C., Lu S., et al. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proc Natl Acad Sci U S A. 2015;112:11923-11928