Dataset Information

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

ABSTRACT: Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.

SUBMITTER: Yao F

PROVIDER: S-EPMC3461012 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

Yao Fei F Ariyaratne Pramila N PN Hillmer Axel M AM Lee Wah Heng WH Li Guoliang G Teo Audrey S M AS Woo Xing Yi XY Zhang Zhenshui Z Chen Jieqi P JP Poh Wan Ting WT Zawack Kelson F B KF Chan Chee Seng CS Leong See Ting ST Neo Say Chuan SC Choi Poh Sum D PS Gao Song S Nagarajan Niranjan N Thoreau Hervé H Shahab Atif A Ruan Xiaoan X Cacheux-Rataboul Valère V Wei Chia-Lin CL Bourque Guillaume G Sung Wing-Kin WK Liu Edison T ET Ruan Yijun Y

PloS one 20120928 9

Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequ ...[more]

PMID: 23029419

Similar Datasets

Project description:BackgroundTaxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to capture the entire amplicon sequence when the read ends overlap. However, the exclusion of unmerged reads from further analysis can result in underestimating the diversity in the sequenced microbial community and is influenced by bioinformatic processes such as read trimming and the choice of reference database. A potential solution to overcome this is to concatenate (join) reads that do not overlap and keep them for taxonomic classification. The use of concatenated reads can outperform taxonomic recovery from single-end reads, but it remains unclear how their performance compares to merged reads. Using various sequenced mock communities with different amplicons, read length, read depth, taxonomic composition, and sequence quality, we tested how merging and concatenating reads performed for genus recall and precision in bioinformatic pipelines combining different parameters for read trimming and taxonomic classification using different reference databases.ResultsThe addition of concatenated reads to merged reads always increased pipeline performance. The top two performing pipelines both included read concatenation, with variable strengths depending on the mock community. The pipeline that combined merged and concatenated reads that were quality-trimmed performed best for mock communities with larger amplicons and higher average quality sequences. The pipeline that used length-trimmed concatenated reads outperformed quality trimming in mock communities with lower quality sequences but lost a significant amount of input sequences for taxonomic classification during processing. Genus level classification was more accurate using the SILVA reference database compared to Greengenes.ConclusionsMerged sequences with the addition of concatenated sequences that were unable to be merged increased performance of taxonomic classifications. This was especially beneficial in mock communities with larger amplicons. We have shown for the first time, using an in-depth comparison of pipelines containing merged vs concatenated reads combined with different trimming parameters and reference databases, the potential advantages of concatenating sequences in improving resolution in microbiome investigations.

Dataset Information

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

Publications

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets