PeSV-fisher : identification of somatic and non-somatic structural variants using next generation sequencing data

Autor: Mario Cáceres, Stephan Ossowski, Geòrgia Escaramís, Alexander Martínez-Fundichely, Laia Bassaganyas, Cristian Tornador, Xavier Estivill, Raquel Rabionet, Marta Gut, Jose M. C. Tubio
Rok vydání: 2021
Předmět:
lcsh:Medicine
Human genomics
Genome
Chromosomal Disorders
0302 clinical medicine
Sequence alignment
Databases
Genetic
Cancer genomics
Genomic library
Genome Sequencing
lcsh:Science
Genètica -- Bases de dades
Cancers and neoplasms
Genetics
0303 health sciences
Multidisciplinary
Chromosomal Deletions and Duplications
ADN -- Anàlisi
Genomics
Genome Scans
Identification (information)
Translocations
Sequence Analysis
Algorithms
Research Article
Genome evolution
Sequence analysis
Computational biology
Biology
Genome Complexity
DNA sequencing
03 medical and health sciences
Genome Analysis Tools
Cancer Genetics
Humans
030304 developmental biology
Comparative genomics
Genome
Human
lcsh:R
Breakpoint
Computational Biology
Human Genetics
Sequence Analysis
DNA
Genome analysis
Leukemia
Lymphocytic
Chronic
B-Cell
Genòmica
Genomic Structural Variation
Computer Science
Genetics of Disease
lcsh:Q
Structural Genomics
Transposable elements
030217 neurology & neurosurgery
Zdroj: Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
PLoS ONE
Recercat. Dipósit de la Recerca de Catalunya
instname
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
PLoS ONE; Vol 8
PLoS ONE, Vol 8, Iss 5, p e63377 (2013)
Popis: Next-generation sequencing technologies expedited research to develop efficient computational tools for the identification of structural variants (SVs) and their use to study human diseases. As deeper data is obtained, the existence of higher complexity SVs in some genomes becomes more evident, but the detection and definition of most of these complex rearrangements is still in its infancy. The full characterization of SVs is a key aspect for discovering their biological implications. Here we present a pipeline (PeSV-Fisher) for the detection of deletions, gains, intra- and inter-chromosomal translocations, and inversions, at very reasonable computational costs. We further provide comprehensive information on co-localization of SVs in the genome, a crucial aspect for studying their biological consequences. The algorithm uses a combination of methods based on paired-reads and read-depth strategies. PeSV-Fisher has been designed with the aim to facilitate identification of somatic variation, and, as such, it is capable of analysing two or more samples simultaneously, producing a list of non-shared variants between samples. We tested PeSV-Fisher on available sequencing data, and compared its behaviour to that of frequently deployed tools (BreakDancer and VariationHunter). We have also tested this algorithm on our own sequencing data, obtained from a tumour and a normal blood sample of a patient with chronic lymphocytic leukaemia, on which we have also validated the results by targeted re-sequencing of different kinds of predictions. This allowed us to determine confidence parameters that influence the reliability of breakpoint predictions. This work was supported by AGAUR (Generalitat de Catalunya, 2009 SGR 1502) (X.E.); CIBERESP (Instituto de Salud Carlos III) (G.E.); ESGI (European Commission, 262055_ESGI) (R.R., X.E.), ENGAGE (European Commission, ENGAGE_201413), TECHGENE (European Commission, TECHGENE_223143), and GEUVADIS (European Commission, 261123_GEUVADIS) (X.E.); NOVADIS (Ministerio de Ciencia y Technologia, SAF2008-00357) (X.E.); Galicia Government Xunta de Galicia (Spain) through the project number 10PXIB918057 (J.M.C.T.); MAEC-AEC1 Predoctoral Fellowship (Ministerio de Asuntos Exteriores y Cooperación, Spain) (A.M.F.); and Ramón y Cajal position and grant BFU2007-60930 (Ministerio de Educación y Ciencia) (M.C.).
Databáze: OpenAIRE
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