Web of Science: 18 citations, Scopus: 20 citations, Google Scholar: citations,
Jitterbug : somatic and germline transposon insertion detection at single-nucleotide resolution
Hénaff, Elizabeth (Centre de Recerca en Agrigenòmica)
Zapata, Luís (Centre de Regulació Genòmica (Barcelona))
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Ossowski, Stephan (Centre de Regulació Genòmica (Barcelona))

Date: 2015
Note: Background: Transposable elements are major players in genome evolution. Transposon insertion polymorphisms can translate into phenotypic differences in plants and animals and are linked to different diseases including human cancer, making their characterization highly relevant to the study of genome evolution and genetic diseases. - Results: Here we present Jitterbug, a novel tool that identifies transposable element insertion sites at single-nucleotide resolution based on the pairedend mapping and clipped-read signatures produced by NGS alignments. Jitterbug can be easily integrated into existing NGS analysis pipelines, using the standard BAM format produced by frequently applied alignment tools (e.g. bwa, bowtie2), with no need to realign reads to a set of consensus transposon sequences. Jitterbug is highly sensitive and able to recall transposon insertions with a very high specificity, as demonstrated by benchmarks in the human and Arabidopsis genomes, and validation using long PacBio reads. In addition, Jitterbug estimates the zygosity of transposon insertions with high accuracy and can also identify somatic insertions. - Conclusions: We demonstrate that Jitterbug can identify mosaic somatic transposon movement using sequenced tumor-normal sample pairs and allows for estimating the cancer cell fraction of clones containing a somatic TE insertion. We suggest that the independent methods we use to evaluate performance are a step towards creating a gold standard dataset for benchmarking structural variant prediction tools.
Note: Número d'acord de subvenció MICINN/BFU2009-11932
Note: Número d'acord de subvenció MINECO/AGL2013-43244-R
Note: Número d'acord de subvenció MINECO/SEV2012-0208
Rights: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès.
Document: article ; recerca ; publishedVersion
Subject: Transposons ; Mobile elements ; NGS ; Somatic mutation ; Cancer ; Structural variation ; Genomics Evolution
Published in: BMC genomics, Vol. 16 art. 768 (2015) , ISSN 1471-2164

DOI: 10.1186/s12864-015-1975-5
PMID: 26459856

16 p, 773.0 KB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (scientific output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles

 Record created 2017-06-15, last modified 2019-11-05

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