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---
title: "Compilation of TCGA molecular subtypes"
bibliography: bibliography.bib
vignette: >
%\VignetteIndexEntry{6. Compilation of TCGA molecular subtypes}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(dpi = 300)
knitr::opts_chunk$set(cache=FALSE)
```
```{r message=FALSE, warning=FALSE, include=FALSE}
library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)
```
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:
```{r message=FALSE, warning=FALSE}
subtypes <- PanCancerAtlas_subtypes()
DT::datatable(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](http://www.cell.com/cms/attachment/2062093088/2063584534/mmc3.xlsx) | Cancer Cell 2016 | [Link](http://www.cell.com/cancer-cell/fulltext/S1535-6108(16)30160-X) |
| AML | mRNA and miRNA | mRNA | 187 | [Link](https://tcga-data.nci.nih.gov/docs/publications/laml_2012/TCGA.LAML.cNMF-clustering.20140820.xlsx) | NEJM 2013 | [Link](http://www.nejm.org/doi/full/10.1056/NEJMoa1301689) |
| BLCA | mRNA subtypes | mRNA | 129 | [Link](https://tcga-data.nci.nih.gov/docs/publications/blca_2013/BLCA_cluster-assign-k4.tsv) | Nature 2014 | [Link](http://www.nature.com/nature/journal/v507/n7492/full/nature12965.html) |
| BRCA | PAM50 (mRNA) | PAM50 | 1218 | [Link](https://www.synapse.org/#!Synapse:syn3853594) | Nature 2012 | [Link](http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html#close) |
| GBM/LGG* | mRNA, DNAmeth, protein, Supervised_DNAmeth | Supervised_DNAmeth | 1122 | [Link](http://www.cell.com/cms/attachment/2045372863/2056783242/mmc2.xlsx) | Cell 2016 | [Link](http://www.cell.com/cell/abstract/S0092-8674(15)01692-X) |
| Pan-GI (preliminary) ESCA/STAD/COAD/READ | Molecular_Subtype | Molecular_Subtype | 1011 | [Link](https://www.cell.com/cms/10.1016/j.ccell.2018.03.010/attachment/f1963baa-114d-4bb6-9595-0854aec15dbf/mmc2.xlsx) | Cancer Cell 2018 | [Link](https://doi.org/10.1016/j.ccell.2018.03.010) |
| HNSC | mRNA, DNAmeth, RPPA, miRNA, CNA, Paradigm | mRNA | 279 | [Link](http://www.nature.com/nature/journal/v517/n7536/extref/nature14129-s2.zip) (TabS7.2) | Nature 2015 | [Link](http://www.nature.com/nature/journal/v517/n7536/full/nature14129.html) |
| KICH | Eosinophilic | Eosinophilic | 66 | [Link](https://www.synapse.org/#!Synapse:syn4463858) | Cancer Cell 2014 | [Link](http://www.cell.com/cancer-cell/abstract/S1535-6108(14)00304-3) |
| KIRC | mRNA, miRNA | mRNA | 442 | [Link](http://www.nature.com/nature/journal/v499/n7456/extref/nature12222-s2.zip) | Nature 2013 | [Link](http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html) |
| KIRP | mRNA, DNAmeth, protein, miRNA, CNA, COC | COC | 161 | [Link](http://www.nejm.org/doi/suppl/10.1056/NEJMoa1505917/suppl_file/nejmoa1505917_appendix_3.xlsx) | NEJM 2015 | [Link](http://www.nejm.org/doi/full/10.1056/NEJMoa1505917#t=article) |
| LIHC (preliminary) | mRNA, DNAmeth, protein, miRNA, CNA, Paradigma, iCluster | iCluster | 196 | [Link](https://wiki.nci.nih.gov/download/attachments/139067884/Supplementary%20Tables-1-2016.xlsx?version=1&modificationDate=1452270515000&api=v2) (Table S1A) | not published | |
| LUAD | DNAmeth, iCluster | iCluster | 230 | [Link](http://www.nature.com/nature/journal/v511/n7511/extref/nature13385-s2.xlsx) (Table S7) | Nature 2014 | [Link](http://www.nature.com/nature/journal/v511/n7511/full/nature13385.html) |
| LUSC | mRNA | mRNA | 178 | [Link](http://www.nature.com/nature/journal/v489/n7417/extref/nature11404-s2.zip) (Data file S7.5) | Nature 2012 | [Link](http://www.nature.com/nature/journal/v489/n7417/full/nature11404.html) |
| OVCA | mRNA | mRNA | 489 | [Link](https://www.synapse.org/#!Synapse:syn4213428) | Nature 2011 | [Link](http://www.nature.com/nature/journal/v474/n7353/full/nature10166.html) |
| PCPG | mRNA, DNAmeth, protein, miRNA, CNA | mRNA | 178 | tableS2 | Cancer Cell 2017 | [Link](http://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30001-6) |
| PRAD | mRNA, DNAmeth, protein, miRNA, CNA, icluster, mutation/fusion | mutation/fusion | 333 | [Link](http://www.cell.com/cms/attachment/2062406705/2064289081/mmc2.xls) | Cell 2015 | [Link](http://www.cell.com/cell/abstract/S0092-8674(15)01339-2) |
| SKCM | mRNA, DNAmeth, protein, miRNA, mutation | mutation | 331 | [Link](http://www.cell.com/cms/attachment/2048142118/2058244319/mmc2.xlsx) (Table S1D) | Cell 2015 | [Link](http://www.cell.com/cell/abstract/S0092-8674(15)00634-0) |
| THCA | mRNA, DNAmeth, protein, miRNA, CNA, histology | mRNA | 496 | [Link](http://www.cell.com/cms/attachment/2019646612/2039684990/mmc3.xlsx) (Table S2 - Tab1) | Cell 2014 | [Link](http://www.cell.com/cell/fulltext/S0092-8674(14)01238-0#) |
| UCEC | iCluster, MSI, CNA, mRNA | iCluster - updated according to Pan-Gyne/Pathways groups | 538 | [Link](http://www.nature.com/nature/journal/v497/n7447/extref/nature12113-s2.zip) (datafile S1.1) | Nature 2013 | [Link](http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html) |
| | | | | [Link](https://docs.google.com/spreadsheets/d/1Z1H3mXdO_sk9nc0v8df7VNS_XzXiu6vKGJRbK1qYoh4/edit#gid=2047911448) | | |
| UCS (preliminary) | mRNA | mRNA | 57 | [Link](https://www.synapse.org/#!Synapse:syn4214438) | 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.
```{r, eval = FALSE}
lgg.gbm.subtype <- TCGAquery_subtype(tumor = "lgg")
```
A subset of the LGG subytpe is shown below:
```{r, eval = TRUE, echo = FALSE}
datatable(
lgg.gbm.subtype[1:10,],
caption = "Table with LGG molecular subtypes from TCGAquery_subtype",
filter = 'top',
options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
rownames = FALSE
)
```
# Session Information
******
```{r sessionInfo}
sessionInfo()
```
|