TumorBoost protocols

View TumorBoost computational protocol

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TumorBoost specifications

Information


Unique identifier OMICS_08929
Name TumorBoost
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Affymetrix, Agilent Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Henrik Bengtsson <>

Publication for TumorBoost

TumorBoost in pipelines

 (3)
2014
PMCID: 4535873
PMID: 26484062
DOI: 10.1016/j.gdata.2014.02.004

[…] used to assess genome wide copy number frequencies for the 15 patients. furthermore, aroma.affymetrix – another cbs implementation as part of the bioconductor's dnacopy library and the associated tumorboost algorithm (which normalize allele specific copy numbers for tumor samples with paired normal) – was also used to identify genomic events. we obtained conforming results […]

2013
PMCID: 3813709
PMID: 24204606
DOI: 10.1371/journal.pone.0076251

[…] usa) was used to assess genome wide copy number frequencies for the 15 patients. further, aroma.affymetrix – another cbs implementation as part of bioconductor's dnacopy library and the associated tumorboost algorithm (which normalize allele specific copy numbers for tumor samples with paired normals) were also used to identify genomic events. we obtained conforming results […]

2012
PMCID: 3468603
PMID: 23071531
DOI: 10.1371/journal.pone.0045950

[…] of all the blood samples processed using the same illumina platform. the b-allele frequencies from patients with two samples processed using the same illumina array type were corrected using the tumorboost algorithm ., segmentation, segment categorization and tumor purity estimation were performed using a slightly modified version of genocn . in the original algorithm, constraints […]


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TumorBoost in publications

 (8)
PMCID: 4824836
PMID: 26205786
DOI: 10.1007/s10120-015-0514-z

[…] probe-sequence effects, and (3) the effects of the various sizes of fragments generated by restriction enzyme digestion before hybridization. we then processed each tumor and nonmalignant pair with tumorboost [] to increase the signal-to-noise ratio of allele-specific signals. this improved the ability of subsequent analysis to detect copy-number loss, loh, and allelic imbalance. matched […]

PMCID: 4443545
PMID: 26015868
DOI: 10.1186/s40364-015-0033-4

[…] snp6 data from paired tumor-normal samples were normalized and preprocessed using the aroma affymetrix crmav2 algorithm [], and the b-allele fraction (baf) was adjusted using the calmate and tumorboost algorithms [,]. tumor copy number aberrations, ploidy and normal cell contamination was determined using ascat []. tumors with aberrant cell fraction (acf) below 0.36 was excluded […]

PMCID: 4220069
PMID: 25270265
DOI: 10.1186/s13059-014-0470-7

[…] of matched normal samples where available, or otherwise position-specific median total snp array signals across the normal samples, giving tcns for all tumors. bafs were obtained and processed using tumorboost. allele-specific cn segments were identified from tcns and bafs with the paired or non-paired pscbs method [] for samples with or without a matched normal sample. after this step […]

PMCID: 4249650
PMID: 25240281
DOI: 10.1038/ng.3095

[…] sample was hybridized to the affymetrix snp 6.0 arrays using protocols at the genomic core laboratory at mskcc. allele-specific copy number for each tumor-normal pair of arrays was calculated using tumorboost in the aroma package., tissue processing, embedding, sectioning, and h&e staining was performed by the mskcc pathology department. photographs were taken using an olympus dp21 camera. […]

PMCID: 4535873
PMID: 26484062
DOI: 10.1016/j.gdata.2014.02.004

[…] used to assess genome wide copy number frequencies for the 15 patients. furthermore, aroma.affymetrix – another cbs implementation as part of the bioconductor's dnacopy library and the associated tumorboost algorithm (which normalize allele specific copy numbers for tumor samples with paired normal) – was also used to identify genomic events. we obtained conforming results […]


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TumorBoost institution(s)
Department of Statistics, University of California, Berkeley, USA; Bioinformatics Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Australia

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