Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
AbstractMultiple displacement amplification (MDA) is considered to be a conventional approach to comprehensive amplification from low input DNA. The chimeric reads generated in MDA lead to severe disruption in some studies, including those focusing on heterogeneity, structural variation, and genetic recombination. Meanwhile, the generation of by-products gives a new approach to gain insights into the reaction process of φ29 polymerase. Here, we analyzed 36.7 million chimeras and screened 196 billion chimeric hotspots in the human genome, as well as evaluating the hotspot selective preference of chimeras. No significant preference was captured in the distributions of chimeras and hotspots among chromosomes. Hotspots with overlaps for 12–13 nucleotides (nt) were most likely to be selected as templates in chimera generation. Meanwhile, a regularly selective preference was noticed in overlap GC content. The preferences in overlap length and GC content was shown to be pertinent to the sequence denaturation temperature, which pointed out the optimization direction for reducing chimeras. Distance preference between two segments of chimeras was 80–280 nt. The analysis is beneficial for reducing the chimeras in MDA, and the characterization of MDA chimeras is helpful in distinguishing MDA chimeras from chimeric sequences caused by disease. View Full-Text
- Supplementary File 1:
PDF-Document (PDF, 545 KB)
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Tu, J.; Lu, N.; Duan, M.; Huang, M.; Chen, L.; Li, J.; Guo, J.; Lu, Z. Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification. Int. J. Mol. Sci. 2017, 18, 492.
Tu J, Lu N, Duan M, Huang M, Chen L, Li J, Guo J, Lu Z. Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification. International Journal of Molecular Sciences. 2017; 18(3):492.Chicago/Turabian Style
Tu, Jing; Lu, Na; Duan, Mengqin; Huang, Mengting; Chen, Liang; Li, Junji; Guo, Jing; Lu, Zuhong. 2017. "Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification." Int. J. Mol. Sci. 18, no. 3: 492.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.