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Systematic Characteristic Exploration of the Chimeras Generated in Multiple Displacement Amplification through Next Generation Sequencing Data Reanalysis.

Tu J, Guo J, Li J, Gao S, Yao B, Lu Z - PLoS ONE (2015)

Bottom Line: The chimeric distance between the locations of adjacent parts on the chromosome followed an approximate bimodal distribution ranging from 0 to over 5,000 nt, whose peak was at about 250 to 300 nt.The overlap length of adjacent parts followed an approximate Poisson distribution and revealed a peak at 6 nt.Our work also illustrated the importance of NGS data reanalysis, not only for the improvement of data utilization efficiency, but also for more potential genomic information.

View Article: PubMed Central - PubMed

Affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.

ABSTRACT

Background: The chimeric sequences produced by phi29 DNA polymerase, which are named as chimeras, influence the performance of the multiple displacement amplification (MDA) and also increase the difficulty of sequence data process. Despite several articles have reported the existence of chimeric sequence, there was only one research focusing on the structure and generation mechanism of chimeras, and it was merely based on hundreds of chimeras found in the sequence data of E. coli genome.

Method: We finished data mining towards a series of Next Generation Sequencing (NGS) reads which were used for whole genome haplotype assembling in a primary study. We established a bioinformatics pipeline based on subsection alignment strategy to discover all the chimeras inside and achieve their structural visualization. Then, we artificially defined two statistical indexes (the chimeric distance and the overlap length), and their regular abundance distribution helped illustrate of the structural characteristics of the chimeras. Finally we analyzed the relationship between the chimera type and the average insertion size, so that illustrate a method to decrease the proportion of wasted data in the procedure of DNA library construction.

Results/conclusion: 131.4 Gb pair-end (PE) sequence data was reanalyzed for the chimeras. Totally, 40,259,438 read pairs (6.19%) with chimerism were discovered among 650,430,811 read pairs. The chimeric sequences are consisted of two or more parts which locate inconsecutively but adjacently on the chromosome. The chimeric distance between the locations of adjacent parts on the chromosome followed an approximate bimodal distribution ranging from 0 to over 5,000 nt, whose peak was at about 250 to 300 nt. The overlap length of adjacent parts followed an approximate Poisson distribution and revealed a peak at 6 nt. Moreover, unmapped chimeras, which were classified as the wasted data, could be reduced by properly increasing the length of the insertion segment size through a linear correlation analysis.

Significance: This study exhibited the profile of the phi29MDA chimeras by tens of millions of chimeric sequences, and helped understand the amplification mechanism of the phi29 DNA polymerase. Our work also illustrated the importance of NGS data reanalysis, not only for the improvement of data utilization efficiency, but also for more potential genomic information.

No MeSH data available.


Related in: MedlinePlus

The visualization of the chimeras with the read parts located on the reverse strands (1) or on the same strands (2).
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pone.0139857.g001: The visualization of the chimeras with the read parts located on the reverse strands (1) or on the same strands (2).

Mentions: The chimeras are consisted of two or more parts which locate inconsecutively but adjacently on the chromosome. Differing from the MDA primer polymer which are consisted of two or more sequence primers with the concordant length of 20–25 bp, the phi29MDA chimeras had at least one chimeric part whose length was definitely no shorter than 30 bp based on our bioinformatics pipeline (Materials and Methods), which meant the primer polymers would not mistakenly classified as the chimeras in our bioinformatics pipeline. On the aspect of the internal structure among the chimeric parts, there were overlap segments between the tail of the former part and the head of the following part. As for the chimeric strand specificity, this phenomena not only happened between two reverse strands, but also was observed on the same strand. Following the nomenclature of the previous research [11], fundamental chimerism could be divided into two types: inverted chimeras and direct chimeras. Two subsections of inverted chimeras are aligned to two reverse strands, while two subsections of direct chimera could be aligned concordantly to one strand. (Fig 1).


Systematic Characteristic Exploration of the Chimeras Generated in Multiple Displacement Amplification through Next Generation Sequencing Data Reanalysis.

Tu J, Guo J, Li J, Gao S, Yao B, Lu Z - PLoS ONE (2015)

The visualization of the chimeras with the read parts located on the reverse strands (1) or on the same strands (2).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595205&req=5

pone.0139857.g001: The visualization of the chimeras with the read parts located on the reverse strands (1) or on the same strands (2).
Mentions: The chimeras are consisted of two or more parts which locate inconsecutively but adjacently on the chromosome. Differing from the MDA primer polymer which are consisted of two or more sequence primers with the concordant length of 20–25 bp, the phi29MDA chimeras had at least one chimeric part whose length was definitely no shorter than 30 bp based on our bioinformatics pipeline (Materials and Methods), which meant the primer polymers would not mistakenly classified as the chimeras in our bioinformatics pipeline. On the aspect of the internal structure among the chimeric parts, there were overlap segments between the tail of the former part and the head of the following part. As for the chimeric strand specificity, this phenomena not only happened between two reverse strands, but also was observed on the same strand. Following the nomenclature of the previous research [11], fundamental chimerism could be divided into two types: inverted chimeras and direct chimeras. Two subsections of inverted chimeras are aligned to two reverse strands, while two subsections of direct chimera could be aligned concordantly to one strand. (Fig 1).

Bottom Line: The chimeric distance between the locations of adjacent parts on the chromosome followed an approximate bimodal distribution ranging from 0 to over 5,000 nt, whose peak was at about 250 to 300 nt.The overlap length of adjacent parts followed an approximate Poisson distribution and revealed a peak at 6 nt.Our work also illustrated the importance of NGS data reanalysis, not only for the improvement of data utilization efficiency, but also for more potential genomic information.

View Article: PubMed Central - PubMed

Affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.

ABSTRACT

Background: The chimeric sequences produced by phi29 DNA polymerase, which are named as chimeras, influence the performance of the multiple displacement amplification (MDA) and also increase the difficulty of sequence data process. Despite several articles have reported the existence of chimeric sequence, there was only one research focusing on the structure and generation mechanism of chimeras, and it was merely based on hundreds of chimeras found in the sequence data of E. coli genome.

Method: We finished data mining towards a series of Next Generation Sequencing (NGS) reads which were used for whole genome haplotype assembling in a primary study. We established a bioinformatics pipeline based on subsection alignment strategy to discover all the chimeras inside and achieve their structural visualization. Then, we artificially defined two statistical indexes (the chimeric distance and the overlap length), and their regular abundance distribution helped illustrate of the structural characteristics of the chimeras. Finally we analyzed the relationship between the chimera type and the average insertion size, so that illustrate a method to decrease the proportion of wasted data in the procedure of DNA library construction.

Results/conclusion: 131.4 Gb pair-end (PE) sequence data was reanalyzed for the chimeras. Totally, 40,259,438 read pairs (6.19%) with chimerism were discovered among 650,430,811 read pairs. The chimeric sequences are consisted of two or more parts which locate inconsecutively but adjacently on the chromosome. The chimeric distance between the locations of adjacent parts on the chromosome followed an approximate bimodal distribution ranging from 0 to over 5,000 nt, whose peak was at about 250 to 300 nt. The overlap length of adjacent parts followed an approximate Poisson distribution and revealed a peak at 6 nt. Moreover, unmapped chimeras, which were classified as the wasted data, could be reduced by properly increasing the length of the insertion segment size through a linear correlation analysis.

Significance: This study exhibited the profile of the phi29MDA chimeras by tens of millions of chimeric sequences, and helped understand the amplification mechanism of the phi29 DNA polymerase. Our work also illustrated the importance of NGS data reanalysis, not only for the improvement of data utilization efficiency, but also for more potential genomic information.

No MeSH data available.


Related in: MedlinePlus