Data Sources V180819

 

Tissue Type

Database	Normal	Adjacent	Primary	Recurrent	Metastatic	Sample Size
St Jude’s	0	0	66	0	0	66
GTEx	7412	0	0	0	0	7412
MET500	0	0	0	0	387	387
TARGET	0	11	602	120	1	734
TCGA	0	726	9366	44	393	10529
TOTAL	7412	737	10034	164	781	19128

 

 

GTEx (Genotype-Tissue Expression) n= 7412 (2741 F, 4671 M)

• For info, visit   https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v7.p2
• For stats, visit  https://www.gtexportal.org/home/tissueSummaryPage
• GTEx is a biobank funded by NIH to study how genetic variation affect RNA expression levels in normal tissue samples.
• The GTEx samples are named as GTEX-XXXXX-YYYY-SM-ZZZZZ. XXXXX is the patient ID, YYYY is the code for the tissue, and ZZZZZ is the sample aliquot used for sequencing.
• Enrollment concluded in 2015 and sample collection is still ongoing. The goal to have ~960 donors at the end of project
• Data downloaded from UCSC Xenabrowser (which included GTEx, TARGET, and TCGA data) https://xenabrowser.net/datapages/?hub=https://toil.xenahubs.net:443
• We filtered for data with complete phenotype metadata e.g. tissue origin and filtered out for cell lines in the GTEx.

TARGET (Therapeutically Applicable Research to Generate Effective Treatments) n= 734 (359 F, 375 M)

• For info, visit  https://ocg.cancer.gov/programs/target
• For stats, visit  https://portal.gdc.cancer.gov/exploration
• TARGET is the data source for childhood cancers, including Neuroblastoma, Acute Myeloid Leukemia, Wilms Tumor, Rhabdoid kidney tumor, and Clear Cell Sarcoma of the kidney
• Sample ID are headed by “TARGET”
• Data downloaded from UCSC Xenabrowser (which included GTEx, TARGET, and TCGA data) https://xenabrowser.net/datapages/?hub=https://toil.xenahubs.net:443
• We filtered for data with complete phenotype metadata e.g. tissue origin or cancer type.

TCGA (The Cancer Genome Atlas) n= 10529 (5282 F, 5247 M)

• For info, visit  https://cancergenome.nih.gov/
• For stats, visit  https://portal.gdc.cancer.gov/exploration
• TCGA is a collaboration between National Cancer Institute(NCI) and National Human genome research Institute (NHGRI) involving 20 institutions from the US and Canada to collect adjacent and cancerous tissues.
• Sample IDs are headed with “TCGA”
• Sample collection ended in 2013 after obtaining 20,000 tissues of 33 types of cancer from over 11,000 patients.  
• We filtered for data with complete phenotype metadata e.g. tissue origin or cancer type.

MET 500 n= 387 (187 F, 200 M)

• For info, visit  https://www.nature.com/articles/nature23306.pdf
• Dan R. Robinson et al. Integrative Clinical Genomics of Metastatic Cancer.  Nature. 2017. 548:297-303.
• Sample IDs headed by “SRR”
• Metastatic cancer samples from 500 adult patients
• This data contains 101 unique cancers. The top 2 metastatic cancer were prostate adenocarcinoma and breast invasive carcinoma.
• Counts were computed using UC Santa Cruz TOIL.
• The data had both polyA and Hybrid RNASeq runs. In order to ensure consistent comparison we only retained the polyA counts.

St. Jude’s Hospital n= 66 (29 F, 37 M)

• This set of data of data are High Grade Glioma samples containing 22 samples of Diffuse Intrinsic Pontine Glioma and 44 samples of Non-Brainstem High Grade Glioma
• Sample IDs are headed by “SJHGG”
• Counts were computed using UC Santa Cruz TOIL.