# Compilation of TCGA molecular subtypes

TCGAbiolinks retrieved molecular subtypes information from TCGA samples. The functions `PanCancerAtlas_subtypes` and `TCGAquery_subtype` can be used to get the information tables.

While the `PanCancerAtlas_subtypes` function gives access to a curated table retrieved from synapse (probably with the most updated molecular subtypes) the `TCGAquery_subtype` function has the complete table also with sample information retrieved from the TCGA marker papers.

# `PanCancerAtlas_subtypes`: Curated molecular subtypes.

Data and description retrieved from synapse (https://www.synapse.org/#!Synapse:syn8402849)

Synapse has published a single file with all available molecular subtypes that have been described by TCGA (all tumor types and all molecular platforms), which can be accessed using the `PanCancerAtlas_subtypes` function as below:

    subtypes <- PanCancerAtlas_subtypes()
    DT::datatable(
        data = subtypes,
        filter = 'top',
        options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
        rownames = FALSE
    )

The columns “Subtype_Selected” was selected as most prominent subtype classification (from the other columns)

| All available molecular data based-subtype | Selected subtype | Number of samples | Link to file | Reference | link to paper
--- | --- | --- | --- | --- | --- | ---
ACC | mRNA, DNAmeth, protein, miRNA, CNA, COC, C1A.C1B | DNAmeth | 91 | Link | Cancer Cell 2016 | Link
AML | mRNA and miRNA | mRNA | 187 | Link | NEJM 2013 | Link
BLCA | mRNA subtypes | mRNA | 129 | Link | Nature 2014 | Link
BRCA | PAM50 (mRNA) | PAM50 | 1218 | Link | Nature 2012 | Link
GBM/LGG* | mRNA, DNAmeth, protein, Supervised_DNAmeth | Supervised_DNAmeth | 1122 | Link | Cell 2016 | Link
Pan-GI (preliminary) ESCA/STAD/COAD/READ | Molecular_Subtype | Molecular_Subtype | 1011 | Link | Cancer Cell 2018 | Link
HNSC | mRNA, DNAmeth, RPPA, miRNA, CNA, Paradigm | mRNA | 279 | Link (TabS7.2) | Nature 2015 | Link
KICH | Eosinophilic | Eosinophilic | 66 | Link | Cancer Cell 2014 | Link
KIRC | mRNA, miRNA | mRNA | 442 | Link | Nature 2013 | Link
KIRP | mRNA, DNAmeth, protein, miRNA, CNA, COC | COC | 161 | Link | NEJM 2015 | Link
LIHC (preliminary) | mRNA, DNAmeth, protein, miRNA, CNA, Paradigma, iCluster | iCluster | 196 | Link (Table S1A) | not published |
LUAD | DNAmeth, iCluster | iCluster | 230 | Link (Table S7) | Nature 2014 | Link
LUSC | mRNA | mRNA | 178 | Link (Data file S7.5) | Nature 2012 | Link
OVCA | mRNA | mRNA | 489 | Link | Nature 2011 | Link
PCPG | mRNA, DNAmeth, protein, miRNA, CNA | mRNA | 178 | tableS2 | Cancer Cell 2017 | Link
PRAD | mRNA, DNAmeth, protein, miRNA, CNA, icluster, mutation/fusion | mutation/fusion | 333 | Link | Cell 2015 | Link
SKCM | mRNA, DNAmeth, protein, miRNA, mutation | mutation | 331 | Link (Table S1D) | Cell 2015 | Link
THCA | mRNA, DNAmeth, protein, miRNA, CNA, histology | mRNA | 496 | Link (Table S2 - Tab1) | Cell 2014 | Link
UCEC | iCluster, MSI, CNA, mRNA | iCluster - updated according to Pan-Gyne/Pathways groups | 538 | Link (datafile S1.1) | Nature 2013 | Link
|  |  |  | Link |  |
UCS (preliminary) | mRNA | mRNA | 57 | Link | not published |

# `TCGAquery_subtype`: Working with molecular subtypes data.

The Cancer Genome Atlas (TCGA) Research Network has reported integrated genome-wide studies of various diseases. We have added some of the subtypes defined by these report in our package:

TCGA dataset | Link | Paper | Journal
--- | --- | --- | ---
ACC | doi:10.1016/j.ccell.2016.04.002 | Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. | Cancer cell 2016
BRCA | https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30119-3 | A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers | Cancer cell 2018
BLCA | http://www.cell.com/cell/fulltext/S0092-8674(17)31056-5 | Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer Cell 2017 |
CHOL | http://www.sciencedirect.com/science/article/pii/S2211124717302140?via%3Dihub | Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles | Cell Reports 2017
COAD | http://www.nature.com/nature/journal/v487/n7407/abs/nature11252.html | Comprehensive molecular characterization of human colon and rectal cancer | Nature 2012
ESCA | https://www.nature.com/articles/nature20805 | Integrated genomic characterization of oesophageal carcinoma | Nature 2017
GBM | http://dx.doi.org/10.1016/j.cell.2015.12.028 | Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma | Cell 2016
HNSC | http://www.nature.com/nature/journal/v517/n7536/abs/nature14129.html | Comprehensive genomic characterization of head and neck squamous cell carcinomas | Nature 2015
KICH | http://www.sciencedirect.com/science/article/pii/S1535610814003043 | The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma | Cancer cell 2014
KIRC | http://www.nature.com/nature/journal/v499/n7456/abs/nature12222.html | Comprehensive molecular characterization of clear cell renal cell carcinoma | Nature 2013
KIRP | http://www.nejm.org/doi/full/10.1056/NEJMoa1505917 | Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma | NEJM 2016
LIHC | http://linkinghub.elsevier.com/retrieve/pii/S0092-8674(17)30639-6 | Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma | Cell 2017
LGG | http://dx.doi.org/10.1016/j.cell.2015.12.028 | Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma | Cell 2016
LUAD | http://www.nature.com/nature/journal/v511/n7511/abs/nature13385.html | Comprehensive molecular profiling of lung adenocarcinoma | Nature 2014
LUSC | http://www.nature.com/nature/journal/v489/n7417/abs/nature11404.html | Comprehensive genomic characterization of squamous cell lung cancers | Nature 2012
PAAD | http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30299-4 | Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma | Cancer Cell 2017
PCPG | http://dx.doi.org/10.1016/j.ccell.2017.01.001 | Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma | Cancer cell 2017
PRAD | http://www.sciencedirect.com/science/article/pii/S0092867415013392 | The Molecular Taxonomy of Primary Prostate Cancer | Cell 2015
READ | http://www.nature.com/nature/journal/v487/n7407/abs/nature11252.html | Comprehensive molecular characterization of human colon and rectal cancer | Nature 2012
SARC | http://www.cell.com/cell/fulltext/S0092-8674(17)31203-5 | Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas | Cell 2017
SKCM | http://www.sciencedirect.com/science/article/pii/S0092867415006340 | Genomic Classification of Cutaneous Melanoma | Cell 2015
STAD | http://www.nature.com/nature/journal/v511/n7511/abs/nature13385.html | Comprehensive molecular characterization of gastric adenocarcinoma | Nature 2013
THCA | http://www.sciencedirect.com/science/article/pii/S0092867414012380 | Integrated Genomic Characterization of Papillary Thyroid Carcinoma | Cell 2014
UCEC | http://www.nature.com/nature/journal/v497/n7447/abs/nature12113.html | Integrated genomic characterization of endometrial carcinoma | Nature 2013
UCS | http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30053-3 | Integrated Molecular Characterization of Uterine Carcinosarcoma Cancer | Cell 2017
UVM | http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30295-7 | Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma | Cancer Cell 2017

These subtypes will be automatically added in the summarizedExperiment object through GDCprepare. But you can also use the `TCGAquery_subtype` function to retrieve this information.

    lgg.gbm.subtype <- TCGAquery_subtype(tumor = "lgg")

    ## lgg subtype information from:doi:10.1016/j.cell.2015.12.028

A subset of the LGG subytpe is shown below:

# Session Information

    sessionInfo()

    ## R version 4.6.0 (2026-04-24)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] grid      stats4    stats     graphics  grDevices utils     datasets
    ## [8] methods   base
    ##
    ## other attached packages:
    ##  [1] maftools_2.29.0             jpeg_0.1-11
    ##  [3] png_0.1-9                   DT_0.34.0
    ##  [5] dplyr_1.2.1                 SummarizedExperiment_1.43.0
    ##  [7] Biobase_2.73.1              GenomicRanges_1.65.0
    ##  [9] Seqinfo_1.3.0               IRanges_2.47.0
    ## [11] S4Vectors_0.51.1            BiocGenerics_0.59.0
    ## [13] generics_0.1.4              MatrixGenerics_1.25.0
    ## [15] matrixStats_1.5.0           TCGAbiolinks_2.41.0
    ## [17] testthat_3.3.2
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] RColorBrewer_1.1-3          sys_3.4.3
    ##   [3] rstudioapi_0.18.0           jsonlite_2.0.0
    ##   [5] magrittr_2.0.5              GenomicFeatures_1.65.0
    ##   [7] farver_2.1.2                rmarkdown_2.31
    ##   [9] fs_2.1.0                    BiocIO_1.23.3
    ##  [11] vctrs_0.7.3                 memoise_2.0.1
    ##  [13] Rsamtools_2.29.0            RCurl_1.98-1.18
    ##  [15] htmltools_0.5.9             S4Arrays_1.13.0
    ##  [17] BiocBaseUtils_1.15.1        usethis_3.2.1
    ##  [19] progress_1.2.3              curl_7.1.0
    ##  [21] SparseArray_1.13.2          sass_0.4.10
    ##  [23] bslib_0.10.0                htmlwidgets_1.6.4
    ##  [25] desc_1.4.3                  plyr_1.8.9
    ##  [27] httr2_1.2.2                 cachem_1.1.0
    ##  [29] GenomicAlignments_1.49.0    buildtools_1.0.0
    ##  [31] lifecycle_1.0.5             pkgconfig_2.0.3
    ##  [33] Matrix_1.7-5                R6_2.6.1
    ##  [35] fastmap_1.2.0               digest_0.6.39
    ##  [37] ShortRead_1.71.0            AnnotationDbi_1.75.0
    ##  [39] rprojroot_2.1.1             pkgload_1.5.2
    ##  [41] crosstalk_1.2.2             RSQLite_3.52.0
    ##  [43] hwriter_1.3.2.1             filelock_1.0.3
    ##  [45] httr_1.4.8                  abind_1.4-8
    ##  [47] compiler_4.6.0              bit64_4.8.0
    ##  [49] withr_3.0.2                 downloader_0.4.1
    ##  [51] S7_0.2.2                    BiocParallel_1.47.0
    ##  [53] DBI_1.3.0                   pkgbuild_1.4.8
    ##  [55] R.utils_2.13.0              biomaRt_2.69.0
    ##  [57] rappdirs_0.3.4              DelayedArray_0.39.1
    ##  [59] sessioninfo_1.2.3           rjson_0.2.23
    ##  [61] DNAcopy_1.87.0              tools_4.6.0
    ##  [63] otel_0.2.0                  R.oo_1.27.1
    ##  [65] glue_1.8.1                  restfulr_0.0.16
    ##  [67] gtable_0.3.6                tzdb_0.5.0
    ##  [69] R.methodsS3_1.8.2           tidyr_1.3.2
    ##  [71] data.table_1.18.4           hms_1.1.4
    ##  [73] xml2_1.5.2                  XVector_0.53.0
    ##  [75] pillar_1.11.1               stringr_1.6.0
    ##  [77] vroom_1.7.1                 splines_4.6.0
    ##  [79] BiocFileCache_3.3.0         lattice_0.22-9
    ##  [81] deldir_2.0-4                aroma.light_3.43.0
    ##  [83] survival_3.8-6              rtracklayer_1.73.0
    ##  [85] bit_4.6.0                   tidyselect_1.2.1
    ##  [87] maketools_1.3.2             Biostrings_2.81.1
    ##  [89] knitr_1.51                  xfun_0.57
    ##  [91] devtools_2.5.2              brio_1.1.5
    ##  [93] stringi_1.8.7               yaml_2.3.12
    ##  [95] cigarillo_1.3.0             TCGAbiolinksGUI.data_1.33.0
    ##  [97] evaluate_1.0.5              codetools_0.2-20
    ##  [99] interp_1.1-6                tibble_3.3.1
    ## [101] EDASeq_2.47.0               BiocManager_1.30.27
    ## [103] cli_3.6.6                   jquerylib_0.1.4
    ## [105] Rcpp_1.1.1-1.1              dbplyr_2.5.2
    ## [107] XML_3.99-0.23               parallel_4.6.0
    ## [109] ellipsis_0.3.3              ggplot2_4.0.3
    ## [111] readr_2.2.0                 blob_1.3.0
    ## [113] prettyunits_1.2.0           latticeExtra_0.6-31
    ## [115] bitops_1.0-9                pwalign_1.9.0
    ## [117] scales_1.4.0                purrr_1.2.2
    ## [119] crayon_1.5.3                BiocStyle_2.41.0
    ## [121] rlang_1.2.0                 KEGGREST_1.53.0
    ## [123] rvest_1.0.5