Cell. Volume 159: 676-690, 23 October 2014 10.1016/j.cell.2014.09.050
We describe the genomic landscape of papillary thyroid carcinoma (PTC), the most common type of thyroid cancer. We identify novel PTC driver mutations and perform integrated analyses of genomic variants, gene expression and DNA methylation. Our results have strong clinical implications and the potential to improve the classification of thyroid cancer and the management of patients.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (28 Files)
- Controlled-Access Data - Download Manifest (6 Files)
Supplemental Data
These data represent a data freeze from July 14, 2013.
The data are supported by different organizations. All data marked by [Supplementary] were created by the manuscript authors and you should contact the corresponding author for support.
- THCA Batch Effects Supplement
- Integrated Analysis and Interactive Exploration using Regulome Explorer
- Figure SEPI
- Table SEPI
- SRNA Clusters Figure
- CALEYDO Stratomex Analysis
- Full THCA Sample List:
- BAM File list:
- IlluminaGA: Wig, VCF and MAF files:
- Open Access Mutation Data - THCA.Broad.Public_Mutations.tar.gz [1.3G]
- Controlled Access Mutation Data
- THCA.Broad.Protected_Mutations.tar.gz [1.8G]
- THCA.Baylor.Protected_Mutations.tar.gz [5.8M]
- THCA.UCSC.Protected_Mutations.tar.gz [3.0G]
- Reverse Phase Protein Array (RPPA) Expression
- Level 3 Data Archives - THCA.RPPA.Level_3.tar.gz
- Level 2 Data Archives - THCA.RPPA.Level_2.tar.gz
- Level 1 Data Archives - THCA.RPPA.Level_1.tar.gz (984M)
- Mage-tab Data Archives - THCA.RPPA.mage-tab.tar.gz
- RNA Expression from IlluminaHiseq RNASeq and RNASeqV2
- Level 3 Data Archives - THCA.RNASeq.Level_3.tar.gz [4.6G]
- mage-tab Data Archives - THCA.RNASeq.mage-tab.tar.gz
- SNP and Copy Number variation from Affymetrix SNP6 and IlluminaHiSeq Low Pass Whole Genome sequencing
- Level 3 Data Archives
- Level 2 Data Archives
- THCA.Genome_Wide_SNP_6.Level_2.tar.gz [45.2G]
- THCA.LowPass.Level_2.tar.gz
- Level 1 Data Archives - THCA.Genome_Wide_SNP_6.Level_1.tar.gz [28.1G]
- mage-tab Data Archives
- miRNA from Illumina HiSeq 2000
- Level 3 Data Archives - THCA.miRNASeq.Level_3.tar.gz
- mage-tab Data Archives - THCA.miRNASeq.mage-tab.tar.gz
- Methylation from Illumina Infinium Human Methylation450
- Level 3 Data Archives - THCA.Methylation450.Level_3.tar.gz [5.3G]
- Level 2 Data Archives - THCA.Methylation450.Level_2.tar.gz [5.1G]
- Level 1 Data Archives - THCA.Methylation450.Level_1.tar.gz [4.3G]
- Mage-tab Data Archives : - THCA.Methylation450.mage-tab.tar.gz
- Clinical
- THCA.Clinical.tar.gz XML files containing biospecimen processing and clinical data
Supplemental Clinical Data
Additional Resources
- GDC Encyclopedia
- Descriptions of TCGA data are provided in the TCGA Barcode Encyclopedia Page
- Genomic Data Commons Portal
Instructions for Data Download
Open Access Data
- Download the appropriate manifest file from the publication page
- Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
- GDC DTT (Download, User's Guide)
- GDC API (User’s Guide)
Controlled Access Data
- Download the appropriate manifest file from the publication page
- Download a token from the GDC Data Portal
- GDC Data Portal (Launch, User’s Guide)
- Use the manifest file and token to download data using the GDC DTT or the GDC API
- GDC DTT (Download, User’s Guide)
- GDC API (User’s Guide)
For assistance, please contact the GDC Help Desk: support@nci-gdc. datacommons.io.