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Unique identifier OMICS_01408
Name PRADA
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Gad Getz <>
  • person_outline Roel Verhaak <>

Publication for PRADA

PRADA citations

 (10)
library_books

Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

2018
PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] in a sample., to reduce false positives (), we applied an integrative analysis of multiple fusion detection methods. we first applied four tools—tophat-fusion (), mapsplice (), fusionmap (), and prada ()—to detect putative fusions in our nine pairs of frozen wd/dd samples. then, fusions with at least one junction read and at least two supporting mate pair reads that mapped to candidate gene […]

library_books

Novel therapeutic strategy for cervical cancer harboring FGFR3 TACC3 fusions

2018
PMCID: 5833787
PMID: 29358619
DOI: 10.1038/s41389-017-0018-2

[…] was about 300 bp. the adapter-ligated cdna was amplified with 12 cycles of pcr. the samples were sequenced on the illumina hiseq 2500 platform with the 2 × 100-bp paired-end read module., we applied prada analysis to data from the above rna sequencing experiments and obtained a list of fusion transcripts and gene expression data for each sample., we used gene expression data to perform gsea […]

library_books

Characterization of fusion genes in common and rare epithelial ovarian cancer histologic subtypes

2017
PMCID: 5564530
PMID: 28423358
DOI: 10.18632/oncotarget.16781

[…] gene partners on the same chromosome. read-through fusions involve gene partners less than 1 mb away on the same strand., 2gene a is 5′ gene; gene b is 3′ gene., 3as predicted by the fusion caller prada based on fusion junction sites (in grch37/hg19, see for positions)., 4“yes” if predicted protein reading frame is in-frame, “no” if reading frame is out-of-frame, “unknown” […]

library_books

MRI Guided Stereotactic Biopsy of Murine GBM for Spatiotemporal Molecular Genomic Assessment

2017
PMCID: 5444878
PMID: 28553660
DOI: 10.18383/j.tom.2017.00112

[…] of rna-seq data were mapped to the mouse transcriptome (grcm38.p4/mm10) using bwa, duplicate reads were marked by picard, and base quality scores were recalibrated using gatk, by referring to the prada pipeline (), followed by proceeding with the mapped reads to calculate the read counts and rpkm (reads per kilobase of transcript per million mapped reads) values for 39,017 expressed genes […]

call_split

Integrated genetic and pharmacologic interrogation of rare cancers

2016
PMCID: 4917959
PMID: 27329820
DOI: 10.1038/ncomms11987
call_split See protocol

[…] illumina truseq platform. library construction protocols for the clf-ped-015-t were performed as previously reported. read alignment to reference genomes and fusion discovery was performed using the prada, chimerascan and star algorithms., cells were grown and collected at log-phase growth. rna was extracted using rneasy mini kit (qiagen, germantown, md, usa). rna was normalized using nanodrop […]

library_books

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

2016
PMCID: 4884143
PMID: 27158780
DOI: 10.1038/ng.3564

[…] exon skipping of met exon 14 was identified with juncbase as previously described. lists of fusions were obtained from previous studies,3061. fusions for additional tumors were identified with the prada pipeline. for plotting of exonic expression of fusion transcripts, exon expression levels were counted and normalized to reads per kilobase per million (rpkm) as previously described. […]


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PRADA institution(s)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Eli and Edythe L Broad Institute of Harvard University and MIT, Cambridge, MA, USA; Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
PRADA funding source(s)
Supported in part by NCI grant number CA143883/Chapman Foundation/Dell Foundation.

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