TNBCtype

[…] e majority of TNBC subtypes other than MSL and LAR were classified as BLBC. Recently, Lehmann et al revised their previous subclassification to a more concise system consisting of only four subtypes (TNBCtype-4): BL1, BL2, M and LAR. A noticeable remark from this study was that the IM phenotype was not an isolated molecular subtype, but can exist within all molecular subtypes to varying degrees. B […]

[…] -derived TNBC gene expression (RNAseq) data for primary tumors were obtained from The Cancer Genome Atlas (TCGA) [] via extraction from the UCSC Cancer Genome Browser []. For each patient sample, the TNBCtype webtool [] was used to classify that sample into the subtype according to Lehmann et al []. Differential gene expression analysis (DGEA) was performed in R [] where one TNBC patient subtype g […]

[…] the most correlation was seen in only the BL1/2 subtypes, and we couldn’t identify the 6 molecular subtypes using functional proteomics analysis.Lehmann et al refined TNBC molecular subtypes from 6 (TNBCtype) into 4 (TNBCtype-4) tumor-specific subtypes (BL1, BL2, M, and LAR) because they found significant evidence that the IM and MSL TNBC subtypes represent tumors with substantial numbers of infi […]

[…] To predict the TNBC subtypes of the PDX models, we used the TNBCtype web tool (http://cbc.mc.vanderbilt.edu/tnbc) (). RNA-seq data for these models were uploaded to the TNBCtype web tool. Based on the gene expression profiles, the TNBCtype was assigned to the […]

[…] l correlations; comparisons with immunofluorescence staining results; comparisons of immune marker expression; and application of self-normalizing tools such as Gene Set Variation Analysis (GSVA) and TNBCtype. […]

[…] e extended to FFPE samples profiled by RNA-seq, we performed subtyping on gene expression data derived from RNA prepared from 21 matched FF and FFPE pairs and sequenced on a HiSeq or MiSeq. Using the TNBCtype algorithm on samples sequenced on the HiSeq, we obtained subtype calls for 10 FF and 9 FFPE samples (with 9 sample pairs having calls for both FF and FFPE).The concordance rate was 67% (6 of […]