MALBAC
Multiple Annealing and Looping_Based Amplification Cycles
MALBAC is intended to address some of the shortcomings of MDA (Zong et al., 2012). In this method, MALBAC primers randomly anneal to a DNA template. A polymerase with displacement activity at elevated temperatures amplifies the template, generating –semiamplicons.” As the amplification and annealing process is repeated, the semiamplicons are amplified into full amplicons that have a 3ê end complementary to the 5ê end. As a result, full-amplicon ends hybridize to form a looped structure, inhibiting further amplification of the looped amplicon, while only the semiamplicons and gDNA undergo amplification. Deep sequencing of the full-amplicon sequences allows for accurate representation of reads, while sequencing depth provides improved alignment for consensus sequences . This method can also be applied to cDNA for transcriptome analysis (Briese et al., 2016).
Advantages:
- Can sequence large templates
- Can perform single-cell sequencing or sequencing for samples with limited amounts of starting material
- Full-amplicon looping inhibits overrepresentation of templates, reducing PCR bias
- Can amplify GC-rich regions
- Provides uniform genome coverage
- Lower allele dropout rate compared to MDA
Disadvantages:
- Polymerase is relatively error prone, compared to Phi 29 (Gole et al., 2013)
- Temperature-sensitive protocol
- Provides genome coverage up to ~90% (Lovett et al., 2013), but some regions of the genome are underrepresented consistently (Lasken et al., 2013)
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Leung M. L., Wang Y., Kim C., et al. Highly multiplexed targeted DNA sequencing from single nuclei. Nat Protoc. 2016;11:214-235
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
Bowers R. M., Clum A., Tice H., et al. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics. 2015;16:856
Grun D. and van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015;163:799-810
Hou Y., Wu K., Shi X., Li F., Song L., et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. Gigascience. 2015;4:37
Li N., Wang L., Wang H., Ma M., Wang X., 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
Saadatpour A., Lai S., Guo G. and Yuan G. C. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015;31:576-586
Snyder M. W., Adey A., Kitzman J. O. and Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet. 2015;16:344-358
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
Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609
References:
Gui B., Yang P., Yao Z., et al. A New Next-Generation Sequencing-Based Assay for Concurrent Preimplantation Genetic Diagnosis of Charcot-Marie-Tooth Disease Type 1A and Aneuploidy Screening. J Genet Genomics. 2016;43:155-159
Mehetre G. T., Paranjpe A. S., Dastager S. G. and Dharne M. S. Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India. Genom Data. 2016;7:140-143
Briese M., Saal L., Appenzeller S., Moradi M., Baluapuri A. and Sendtner M. Whole transcriptome profiling reveals the RNA content of motor axons. Nucleic Acids Res. 2016;44:e33
Huang J., Yan L., Lu S., Zhao N., Xie X. S. and Qiao J. Validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of blastocysts. Fertil Steril. 2016;105:1532-1536
Yan L., Huang L., Xu L., et al. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci U S A. 2015;112:15964-15969
Chapman A. R., He Z., Lu S., et al. Single cell transcriptome amplification with MALBAC. PLoS One. 2015;10:e0120889
Dey S. S., Kester L., Spanjaard B., Bienko M. and van Oudenaarden A. Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol. 2015;33:285-289
Ning L., Li Z., Wang G., Hu W., Hou Q., et al. Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons. Sci Rep. 2015;5:11415
Yan L., Huang L., Xu L., Huang J., Ma F., et al. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci U S A. 2015;112:15964-15969
Zhang C. Z., Adalsteinsson V. A., Francis J., et al. Calibrating genomic and allelic coverage bias in single-cell sequencing. Nat Commun. 2015;6:6822