title: Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification.
abstract: Multiple 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.
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. jtu@seu.edu.cn.
authors.forename: Jing
authors.initials: J
authors.lastname: Tu
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. nlu@seu.edu.cn.
authors.forename: Na
authors.initials: N
authors.lastname: Lu
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. 220163884@seu.edu.cn.
authors.forename: Mengqin
authors.initials: M
authors.lastname: Duan
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. 213133851@seu.edu.cn.
authors.forename: Mengting
authors.initials: M
authors.lastname: Huang
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. tongust@163.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. 230139150@seu.edu.cn.
authors.forename: Junji
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. lebrowngj@126.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. zhlu@seu.edu.cn.
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D001482:Base Composition; D002678:Chimera / Q000235:genetics*; D002874:Chromosome Mapping; D002877:Chromosomes, Human; D015894:Genome, Human; D023281:Genomics / Q000379:methods / Q000592:standards; D006801:Humans; D021141:Nucleic Acid Amplification Techniques
keywords: chimeras; chimeric hotspots; multiple displacement amplification (MDA); φ29 polymerase