000144575 001__ 144575
000144575 005__ 20240229112629.0
000144575 0247_ $$2doi$$a10.1186/s12859-019-3014-z
000144575 0247_ $$2pmid$$apmid:31419933
000144575 0247_ $$2pmc$$apmc:PMC6697926
000144575 0247_ $$2altmetric$$aaltmetric:65102660
000144575 037__ $$aDKFZ-2019-02018
000144575 041__ $$aeng
000144575 082__ $$a610
000144575 1001_ $$0P:(DE-He78)3fdc3623477264cb5d0e14f256dbfbb8$$aJohann, Pascal$$b0$$eFirst author$$udkfz
000144575 245__ $$aRF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression.
000144575 260__ $$aHeidelberg$$bSpringer$$c2019
000144575 3367_ $$2DRIVER$$aarticle
000144575 3367_ $$2DataCite$$aOutput Types/Journal article
000144575 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1577106984_15304
000144575 3367_ $$2BibTeX$$aARTICLE
000144575 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000144575 3367_ $$00$$2EndNote$$aJournal Article
000144575 520__ $$aWith the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of these approaches are not based on measuring individual cell methylation but rather the bulk tumor sample DNA, which contains a mixture of tumor cells, infiltrating immune cells and other stromal components. This raises questions about the purity of a certain tumor sample, given the varying degrees of stromal infiltration in different entities. Previous methods to infer tumor purity require or are based on the use of matching control samples which are rarely available. Here we present a novel, reference free method to quantify tumor purity, based on two Random Forest classifiers, which were trained on ABSOLUTE as well as ESTIMATE purity values from TCGA tumor samples. We subsequently apply this method to a previously published, large dataset of brain tumors, proving that these models perform well in datasets that have not been characterized with respect to tumor purity .Using two gold standard methods to infer purity - the ABSOLUTE score based on whole genome sequencing data and the ESTIMATE score based on gene expression data- we have optimized Random Forest classifiers to predict tumor purity in entities that were contained in the TCGA project. We validated these classifiers using an independent test data set and cross-compared it to other methods which have been applied to the TCGA datasets (such as ESTIMATE and LUMP). Using Illumina methylation array data of brain tumor entities (as published in Capper et al. (Nature 555:469-474,2018)) we applied this model to estimate tumor purity and find that subgroups of brain tumors display substantial differences in tumor purity.Random forest- based tumor purity prediction is a well suited tool to extrapolate gold standard measures of purity to novel methylation array datasets. In contrast to other available methylation based tumor purity estimation methods, our classifiers do not need a priori knowledge about the tumor entity or matching control tissue to predict tumor purity.
000144575 536__ $$0G:(DE-HGF)POF3-312$$a312 - Functional and structural genomics (POF3-312)$$cPOF3-312$$fPOF III$$x0
000144575 588__ $$aDataset connected to CrossRef, PubMed,
000144575 7001_ $$0P:(DE-He78)bff9e3e3d86865d2b0836bb8f3ce98f3$$aJäger, Natalie$$b1$$udkfz
000144575 7001_ $$0P:(DE-He78)f746aa965c4e1af518b016de3aaff5d9$$aPfister, Stefan M$$b2$$udkfz
000144575 7001_ $$0P:(DE-He78)45440b44791309bd4b7dbb4f73333f9b$$aSill, Martin$$b3$$eLast author$$udkfz
000144575 773__ $$0PERI:(DE-600)2041484-5$$a10.1186/s12859-019-3014-z$$gVol. 20, no. 1, p. 428$$n1$$p428$$tBMC bioinformatics$$v20$$x1471-2105$$y2019
000144575 909CO $$ooai:inrepo02.dkfz.de:144575$$pVDB
000144575 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)3fdc3623477264cb5d0e14f256dbfbb8$$aDeutsches Krebsforschungszentrum$$b0$$kDKFZ
000144575 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)bff9e3e3d86865d2b0836bb8f3ce98f3$$aDeutsches Krebsforschungszentrum$$b1$$kDKFZ
000144575 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)f746aa965c4e1af518b016de3aaff5d9$$aDeutsches Krebsforschungszentrum$$b2$$kDKFZ
000144575 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)45440b44791309bd4b7dbb4f73333f9b$$aDeutsches Krebsforschungszentrum$$b3$$kDKFZ
000144575 9131_ $$0G:(DE-HGF)POF3-312$$1G:(DE-HGF)POF3-310$$2G:(DE-HGF)POF3-300$$3G:(DE-HGF)POF3$$4G:(DE-HGF)POF$$aDE-HGF$$bGesundheit$$lKrebsforschung$$vFunctional and structural genomics$$x0
000144575 9141_ $$y2019
000144575 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR$$bBMC BIOINFORMATICS : 2017
000144575 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS
000144575 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline
000144575 915__ $$0StatID:(DE-HGF)0310$$2StatID$$aDBCoverage$$bNCBI Molecular Biology Database
000144575 915__ $$0StatID:(DE-HGF)0320$$2StatID$$aDBCoverage$$bPubMed Central
000144575 915__ $$0StatID:(DE-HGF)0501$$2StatID$$aDBCoverage$$bDOAJ Seal
000144575 915__ $$0StatID:(DE-HGF)0500$$2StatID$$aDBCoverage$$bDOAJ
000144575 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bDOAJ : Blind peer review
000144575 915__ $$0LIC:(DE-HGF)CCBYNV$$2V:(DE-HGF)$$aCreative Commons Attribution CC BY (No Version)$$bDOAJ
000144575 915__ $$0StatID:(DE-HGF)0600$$2StatID$$aDBCoverage$$bEbsco Academic Search
000144575 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bASC
000144575 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bClarivate Analytics Master Journal List
000144575 915__ $$0StatID:(DE-HGF)0111$$2StatID$$aWoS$$bScience Citation Index Expanded
000144575 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection
000144575 915__ $$0StatID:(DE-HGF)1050$$2StatID$$aDBCoverage$$bBIOSIS Previews
000144575 915__ $$0StatID:(DE-HGF)9900$$2StatID$$aIF < 5
000144575 9201_ $$0I:(DE-He78)B062-20160331$$kB062$$lPädiatrische Neuroonkologie$$x0
000144575 9201_ $$0I:(DE-He78)L101-20160331$$kL101$$lDKTK Heidelberg$$x1
000144575 980__ $$ajournal
000144575 980__ $$aVDB
000144575 980__ $$aI:(DE-He78)B062-20160331
000144575 980__ $$aI:(DE-He78)L101-20160331
000144575 980__ $$aUNRESTRICTED