Molecular data available in GDC

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July 30, 2020

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    <h1><center><b>Genomic Data Commons (GDC)</b></center></h1>
    <p><a href="https://gdc.cancer.gov" target="_blank"> The NCI's Genomic Data Commons (GDC) </a> provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. </p>
   <p>The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET). </p>
    <p><a href="https://gdc.cancer.gov/support/gdc-workshops" target="_blank"> Navigating the GDC - A Case Study </a> is a workshop which helps users to learn GDC tools and data types available to support cancer genomic study. </p>
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Molecular data available in GDC.

Cancer Types	Primary Site	Program	# Cases	Genotyping Array	WXS	RNA-Seq	miRNA-Seq	Methylation array	Protein expression array	Gene expression array	miRNA expression array	Total RNA-Seq	Bisulfite-Seq
Acute Myeloid Leukemia[AML]	Blood	TARGET	923	0	19	179	265	0	0	0	0	0	0
Acute Myeloid Leukemia[LAML]	Bone Marrow	TCGA	200	143	149	151	103	140	0	140	0	0	0
Adrenocortical Carcinoma[ACC]	Adrenal Gland	TCGA	80	92	92	79	80	80	46	0	0	0	0
Bladder Urothelial Carcinoma[BLCA]	Bladder	TCGA	412	412	412	408	409	417	344	0	0	4	6
Brain Lower Grade Glioma[LGG]	Brain	TCGA	516	514	515	512	512	516	430	27	0	0	0
Breast Invasive Carcinoma[BRCA]	Breast	TCGA	1097	1096	1050	1092	1079	1095	885	527	0	11	5
Cervical Squamous Cell Carcinoma and endocervical adenocarcinoma[CESC]	Cervix	TCGA	307	302	305	304	307	307	173	0	0	0	0
Cholangiocarcinoma[CHOL]	Bile Duct	TCGA	36	36	51	36	36	36	30	0	0	0	0
Clear Cell Sarcoma of the Kidney[CCSK]	Kidney	TARGET	13	0	0	0	0	0	0	0	0	0	0
Colon Adenocarcinoma[COAD]	Colorectal	TCGA	461	458	443	456	444	459	362	162	0	13	2
Esophageal Carcinoma[ESCA]	Esophagus	TCGA	185	185	184	164	184	185	126	0	0	0	0
Glioblastoma Multiforme[GBM]	Brain	TCGA	528	593	401	166	5	599	238	587	576	0	6
Head and Neck Squamous Cell Carcinoma[HNSC]	Head and Neck	TCGA	528	521	527	501	524	528	357	0	0	0	0
High-Risk Wilms Tumor[WT]	Kidney	TARGET	663	0	41	122	127	0	0	0	0	0	0
Kidney Chromophobe[KICH]	Kidney	TCGA	66	66	66	66	66	66	63	0	0	0	0
Kidney Renal Clear Cell Carcinoma[KIRC]	Kidney	TCGA	536	532	345	530	516	533	476	72	0	4	0
Kidney Renal Papillary Cell Carcinoma[KIRP]	Kidney	TCGA	291	290	290	289	291	291	215	16	0	0	0
Liver Hepatocellular Carcinoma[LIHC]	Liver	TCGA	377	376	376	371	373	377	184	0	0	0	0
Lung Adenocarcinoma[LUAD]	Lung	TCGA	521	518	582	515	513	579	365	32	0	12	5
Lung Squamous Cell Carcinoma[LUSC]	Lung	TCGA	504	504	502	501	478	503	328	154	0	0	4
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma[DLBC]	Lymph Nodes	TCGA	48	48	48	48	47	48	33	0	0	0	0
Mesothelioma[MESO]	Pleura	TCGA	87	87	83	86	87	87	63	0	0	0	0
Neuroblastoma[NBL]	Nervous System	TARGET	1120	0	221	151	0	0	0	0	0	0	0
Osteosarcoma[OS]	Bone	TARGET	384	0	0	0	0	0	0	0	0	0	0
Ovarian Serous Cystadenocarcinoma[OV]	Ovary	TCGA	586	573	460	376	489	602	426	582	578	0	0
Pancreatic Adenocarcinoma[PAAD]	Pancreas	TCGA	185	185	185	177	178	184	123	0	0	0	0
Pheochromocytoma and Paraganglioma[PCPG]	Adrenal Gland	TCGA	179	179	179	179	179	179	80	0	0	0	0
Prostate Adenocarcinoma[PRAD]	Prostate	TCGA	498	498	498	496	494	498	352	0	0	4	0
Rectum Adenocarcinoma[READ]	Colorectal	TCGA	171	166	168	167	161	165	131	69	0	0	2
Rhabdoid Tumor[RT]	Kidney	TARGET	75	0	0	5	44	0	0	0	0	0	72
Sarcoma[SARC]	Soft Tissue	TCGA	261	261	255	259	259	261	223	0	0	0	0
Skin Cutaneous Melanoma[SKCM]	Skin	TCGA	470	470	470	468	448	470	353	0	0	0	0
Stomach Adenocarcinoma[STAD]	Stomach	TCGA	443	443	443	380	436	478	392	0	0	0	4
Testicular Germ Cell Tumors[TGCT]	Testis	TCGA	150	134	150	150	50	140	118	0	0	0	0
Thymoma[THYM]	Thymus	TCGA	127	124	123	119	124	124	90	0	0	0	0
Thyroid Carcinoma[THCA]	Thyroid	TCGA	507	505	502	502	506	507	372	0	0	0	0
Uterine Carcinosarcoma[UCS]	Uterus	TCGA	54	57	57	56	57	57	47	0	0	0	0
Uterine Corpus Endometrial Carcinoma[UCEC]	Uterus	TCGA	548	547	553	555	550	559	440	69	0	4	5
Uveal Melanoma[UVM]	Eye	TCGA	80	80	80	80	80	80	12	0	0	0	0

--- title: Molecular data available in GDC author: '' date: '2020-07-30' slug: molecular-data-available-in-gdc categories: - how_to tags: [] --- <div class="jumbotron"> <div class="container"> <br> <br> <h1><center><b>Genomic Data Commons (GDC)</b></center></h1> <p><a href="https://gdc.cancer.gov" target="_blank"> The NCI's Genomic Data Commons (GDC) </a> provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. </p> <p>The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET). </p> <p><a href="https://gdc.cancer.gov/support/gdc-workshops" target="_blank"> Navigating the GDC - A Case Study </a> is a workshop which helps users to learn GDC tools and data types available to support cancer genomic study. </p> </div> </div> <div> <h1><center><b>Molecular data available in GDC.  </b></center></h1> <p> </p> </div> <table class="tableizer-table"> <thead><tr class="tableizer-firstrow"><th>Cancer Types</th><th>Primary Site</th><th>Program</th><th># Cases</th><th>Genotyping Array</th><th>WXS</th><th>RNA-Seq</th><th>miRNA-Seq</th><th>Methylation array</th><th>Protein expression array</th><th>Gene expression array</th><th>miRNA expression array</th><th>Total RNA-Seq</th><th>Bisulfite-Seq</th></tr></thead><tbody> <tr><td>Acute Myeloid Leukemia[AML]</td><td>Blood</td><td>TARGET</td><td>923</td><td>0</td><td>19</td><td>179</td><td>265</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Acute Myeloid Leukemia[LAML]</td><td>Bone Marrow</td><td>TCGA</td><td>200</td><td>143</td><td>149</td><td>151</td><td>103</td><td>140</td><td>0</td><td>140</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Adrenocortical Carcinoma[ACC]</td><td>Adrenal Gland</td><td>TCGA</td><td>80</td><td>92</td><td>92</td><td>79</td><td>80</td><td>80</td><td>46</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Bladder Urothelial Carcinoma[BLCA]</td><td>Bladder</td><td>TCGA</td><td>412</td><td>412</td><td>412</td><td>408</td><td>409</td><td>417</td><td>344</td><td>0</td><td>0</td><td>4</td><td>6</td></tr> <tr><td>Brain Lower Grade Glioma[LGG]</td><td>Brain</td><td>TCGA</td><td>516</td><td>514</td><td>515</td><td>512</td><td>512</td><td>516</td><td>430</td><td>27</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Breast Invasive Carcinoma[BRCA]</td><td>Breast</td><td>TCGA</td><td>1097</td><td>1096</td><td>1050</td><td>1092</td><td>1079</td><td>1095</td><td>885</td><td>527</td><td>0</td><td>11</td><td>5</td></tr> <tr><td>Cervical Squamous Cell Carcinoma and endocervical adenocarcinoma[CESC]</td><td>Cervix</td><td>TCGA</td><td>307</td><td>302</td><td>305</td><td>304</td><td>307</td><td>307</td><td>173</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Cholangiocarcinoma[CHOL]</td><td>Bile Duct</td><td>TCGA</td><td>36</td><td>36</td><td>51</td><td>36</td><td>36</td><td>36</td><td>30</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Clear Cell Sarcoma of the Kidney[CCSK]</td><td>Kidney</td><td>TARGET</td><td>13</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Colon Adenocarcinoma[COAD]</td><td>Colorectal</td><td>TCGA</td><td>461</td><td>458</td><td>443</td><td>456</td><td>444</td><td>459</td><td>362</td><td>162</td><td>0</td><td>13</td><td>2</td></tr> <tr><td>Esophageal Carcinoma[ESCA]</td><td>Esophagus</td><td>TCGA</td><td>185</td><td>185</td><td>184</td><td>164</td><td>184</td><td>185</td><td>126</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Glioblastoma Multiforme[GBM]</td><td>Brain</td><td>TCGA</td><td>528</td><td>593</td><td>401</td><td>166</td><td>5</td><td>599</td><td>238</td><td>587</td><td>576</td><td>0</td><td>6</td></tr> <tr><td>Head and Neck Squamous Cell Carcinoma[HNSC]</td><td>Head and Neck</td><td>TCGA</td><td>528</td><td>521</td><td>527</td><td>501</td><td>524</td><td>528</td><td>357</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>High-Risk Wilms Tumor[WT]</td><td>Kidney</td><td>TARGET</td><td>663</td><td>0</td><td>41</td><td>122</td><td>127</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Kidney Chromophobe[KICH]</td><td>Kidney</td><td>TCGA</td><td>66</td><td>66</td><td>66</td><td>66</td><td>66</td><td>66</td><td>63</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Kidney Renal Clear Cell Carcinoma[KIRC]</td><td>Kidney</td><td>TCGA</td><td>536</td><td>532</td><td>345</td><td>530</td><td>516</td><td>533</td><td>476</td><td>72</td><td>0</td><td>4</td><td>0</td></tr> <tr><td>Kidney Renal Papillary Cell Carcinoma[KIRP]</td><td>Kidney</td><td>TCGA</td><td>291</td><td>290</td><td>290</td><td>289</td><td>291</td><td>291</td><td>215</td><td>16</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Liver Hepatocellular Carcinoma[LIHC]</td><td>Liver</td><td>TCGA</td><td>377</td><td>376</td><td>376</td><td>371</td><td>373</td><td>377</td><td>184</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Lung Adenocarcinoma[LUAD]</td><td>Lung</td><td>TCGA</td><td>521</td><td>518</td><td>582</td><td>515</td><td>513</td><td>579</td><td>365</td><td>32</td><td>0</td><td>12</td><td>5</td></tr> <tr><td>Lung Squamous Cell Carcinoma[LUSC]</td><td>Lung</td><td>TCGA</td><td>504</td><td>504</td><td>502</td><td>501</td><td>478</td><td>503</td><td>328</td><td>154</td><td>0</td><td>0</td><td>4</td></tr> <tr><td>Lymphoid Neoplasm Diffuse Large B-cell Lymphoma[DLBC]</td><td>Lymph Nodes</td><td>TCGA</td><td>48</td><td>48</td><td>48</td><td>48</td><td>47</td><td>48</td><td>33</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Mesothelioma[MESO]</td><td>Pleura</td><td>TCGA</td><td>87</td><td>87</td><td>83</td><td>86</td><td>87</td><td>87</td><td>63</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Neuroblastoma[NBL]</td><td>Nervous System</td><td>TARGET</td><td>1120</td><td>0</td><td>221</td><td>151</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Osteosarcoma[OS]</td><td>Bone</td><td>TARGET</td><td>384</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Ovarian Serous Cystadenocarcinoma[OV]</td><td>Ovary</td><td>TCGA</td><td>586</td><td>573</td><td>460</td><td>376</td><td>489</td><td>602</td><td>426</td><td>582</td><td>578</td><td>0</td><td>0</td></tr> <tr><td>Pancreatic Adenocarcinoma[PAAD]</td><td>Pancreas</td><td>TCGA</td><td>185</td><td>185</td><td>185</td><td>177</td><td>178</td><td>184</td><td>123</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Pheochromocytoma and Paraganglioma[PCPG]</td><td>Adrenal Gland</td><td>TCGA</td><td>179</td><td>179</td><td>179</td><td>179</td><td>179</td><td>179</td><td>80</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Prostate Adenocarcinoma[PRAD]</td><td>Prostate</td><td>TCGA</td><td>498</td><td>498</td><td>498</td><td>496</td><td>494</td><td>498</td><td>352</td><td>0</td><td>0</td><td>4</td><td>0</td></tr> <tr><td>Rectum Adenocarcinoma[READ]</td><td>Colorectal</td><td>TCGA</td><td>171</td><td>166</td><td>168</td><td>167</td><td>161</td><td>165</td><td>131</td><td>69</td><td>0</td><td>0</td><td>2</td></tr> <tr><td>Rhabdoid Tumor[RT]</td><td>Kidney</td><td>TARGET</td><td>75</td><td>0</td><td>0</td><td>5</td><td>44</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>72</td></tr> <tr><td>Sarcoma[SARC]</td><td>Soft Tissue</td><td>TCGA</td><td>261</td><td>261</td><td>255</td><td>259</td><td>259</td><td>261</td><td>223</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Skin Cutaneous Melanoma[SKCM]</td><td>Skin</td><td>TCGA</td><td>470</td><td>470</td><td>470</td><td>468</td><td>448</td><td>470</td><td>353</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Stomach Adenocarcinoma[STAD]</td><td>Stomach</td><td>TCGA</td><td>443</td><td>443</td><td>443</td><td>380</td><td>436</td><td>478</td><td>392</td><td>0</td><td>0</td><td>0</td><td>4</td></tr> <tr><td>Testicular Germ Cell Tumors[TGCT]</td><td>Testis</td><td>TCGA</td><td>150</td><td>134</td><td>150</td><td>150</td><td>50</td><td>140</td><td>118</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Thymoma[THYM]</td><td>Thymus</td><td>TCGA</td><td>127</td><td>124</td><td>123</td><td>119</td><td>124</td><td>124</td><td>90</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Thyroid Carcinoma[THCA]</td><td>Thyroid</td><td>TCGA</td><td>507</td><td>505</td><td>502</td><td>502</td><td>506</td><td>507</td><td>372</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Uterine Carcinosarcoma[UCS]</td><td>Uterus</td><td>TCGA</td><td>54</td><td>57</td><td>57</td><td>56</td><td>57</td><td>57</td><td>47</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> <tr><td>Uterine Corpus Endometrial Carcinoma[UCEC]</td><td>Uterus</td><td>TCGA</td><td>548</td><td>547</td><td>553</td><td>555</td><td>550</td><td>559</td><td>440</td><td>69</td><td>0</td><td>4</td><td>5</td></tr> <tr><td>Uveal Melanoma[UVM]</td><td>Eye</td><td>TCGA</td><td>80</td><td>80</td><td>80</td><td>80</td><td>80</td><td>80</td><td>12</td><td>0</td><td>0</td><td>0</td><td>0</td></tr> </tbody></table>