PeSV-Fisher: Identification of Somatic and Non-Somatic Structural Variants Using Next Generation Sequencing Data
作者： Geòrgia Escaramís , Cristian Tornador , Laia Bassaganyas , Raquel Rabionet , Jose M. C. Tubio
DOI: 10.1371/JOURNAL.PONE.0063377
关键词: Genome 、 Biology 、 Sequence analysis 、 Genome evolution 、 Identification (information) 、 Genetics 、 DNA sequencing 、 Comparative genomics 、 Breakpoint 、 Genomic library 、 Computational biology
摘要: Next-generation sequencing technologies expedited research to develop efficient computational tools for the identification of structural variants (SVs) and their use study human diseases. As deeper data is obtained, existence higher complexity SVs in some genomes becomes more evident, but detection definition most these complex rearrangements still its infancy. The full characterization a key aspect discovering biological implications. Here we present pipeline (PeSV-Fisher) deletions, gains, intra- inter-chromosomal translocations, inversions, at very reasonable costs. We further provide comprehensive information on co-localization genome, crucial studying consequences. algorithm uses combination methods based paired-reads read-depth strategies. PeSV-Fisher has been designed with aim facilitate somatic variation, and, as such, it capable analysing two or samples simultaneously, producing list non-shared between samples. tested available data, compared behaviour that frequently deployed (BreakDancer VariationHunter). have also this our own obtained from tumour normal blood sample patient chronic lymphocytic leukaemia, which validated results by targeted re-sequencing different kinds predictions. This allowed us determine confidence parameters influence reliability breakpoint
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