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Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification

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 recombi...

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Autores principales: Tu, Jing, Lu, Na, Duan, Mengqin, Huang, Mengting, Chen, Liang, Li, Junji, Guo, Jing, Lu, Zuhong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372508/
https://www.ncbi.nlm.nih.gov/pubmed/28245591
http://dx.doi.org/10.3390/ijms18030492
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author Tu, Jing
Lu, Na
Duan, Mengqin
Huang, Mengting
Chen, Liang
Li, Junji
Guo, Jing
Lu, Zuhong
author_facet Tu, Jing
Lu, Na
Duan, Mengqin
Huang, Mengting
Chen, Liang
Li, Junji
Guo, Jing
Lu, Zuhong
author_sort Tu, Jing
collection PubMed
description 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.
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spelling pubmed-53725082017-04-10 Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification Tu, Jing Lu, Na Duan, Mengqin Huang, Mengting Chen, Liang Li, Junji Guo, Jing Lu, Zuhong Int J Mol Sci Article 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. MDPI 2017-02-24 /pmc/articles/PMC5372508/ /pubmed/28245591 http://dx.doi.org/10.3390/ijms18030492 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tu, Jing
Lu, Na
Duan, Mengqin
Huang, Mengting
Chen, Liang
Li, Junji
Guo, Jing
Lu, Zuhong
Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
title Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
title_full Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
title_fullStr Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
title_full_unstemmed Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
title_short Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification
title_sort hotspot selective preference of the chimeric sequences formed in multiple displacement amplification
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372508/
https://www.ncbi.nlm.nih.gov/pubmed/28245591
http://dx.doi.org/10.3390/ijms18030492
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