LuminalA Breast cancer subtype samples from GEO GSE62944
Entering edit mode
Last seen 8.1 years ago

Hi All,

is there a way to pull out samples of Luminal A subtype of breast cancer from TCGA data or GEO GSE62944?

I did 

    eh = AnnotationHub()
    query(eh , "GSE62944")
    tcga_data <- eh[["AH28855"]]

    brca_data_lumA <- brca_data[, which(phenoData(brca_data)$er_status_by_ihc=="Positive")]
    brca_data_lumA <- brca_data[, which(phenoData(brca_data)$her2_status_by_ihc=="Negative")]


Considering Luminal A subtype = ER Positive, Her2 Negative and low ki67 !

I do not know how to determine samples with low ki67 ?

Is there a better way to do it? Is there a predefined attribute dedicated to molecular subtype of Breast Cancer?

tcga cancer BreastCancer gse62944 luminalA • 1.3k views
Entering edit mode
phil.chapman ▴ 150
Last seen 7.7 years ago
United Kingdom

Not sure how to do it in Bioconductor but the cgdsr package (from CRAN) that accompanies the cBio Portal has some useful pre-defined sets of cases that relate to different breast cancer subtypes.  I think that these have been manually curated from the original publication.  Anyway, take a look at the cBio Portal itself and the cgdsr package documentation, and perhaps you can incorporate this information into your analysis to do what you want.  An example is below:

> library(cgdsr)
> mycgds <- CGDS("")
> getCancerStudies(mycgds)[1:10,1]
 [1] "paac_jhu_2014"                 "laml_tcga_pub"                 "laml_tcga"                    
 [4] "acyc_mskcc"                    "acc_tcga"                      "blca_mskcc_solit_2014"        
 [7] "blca_mskcc_solit_2012"         "blca_mskcc_signet_ring_impact" "blca_plasmacytoid_mskcc_2016"
[10] "blca_bgi" 
> brca_case_lists <- getCaseLists(mycgds,'brca_tcga_pub2015')
> brca_case_lists[1:5,1:2]
                     case_list_id              case_list_name
1 brca_tcga_pub2015_3way_complete         All Complete Tumors
2           brca_tcga_pub2015_all                  All Tumors
3         brca_tcga_pub2015_erpos           ER+ breast tumors
4         brca_tcga_pub2015_erneg           ER- breast tumors
5       brca_tcga_pub2015_her2pos Her2-positive breast tumors

> substr(brca_case_lists[brca_case_lists$case_list_id == 'brca_tcga_pub2015_idc_luma', 'case_ids'], 1, 80)
[1] "TCGA-BH-A1ES-01 TCGA-BH-A1ET-01 TCGA-BH-A1EW-01 TCGA-C8-A1HI-01 TCGA-A2-A1G0-01 "



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