TCGA cancer datasets summaries

Datasets availability as for December 13th, 2011

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Cancer,Code,Methylation,Expression,miRNA,Sequence
Acute Myeloid Leukemia,AML,193/0/0,0/0/0,0/0/0,200/200/0
Bladder Urothenial Carcinoma,BLCA,38/11/0,0/0/0,0/0/0,38/40/0
Brain Lower Grade Glioma,LGG,24/2/0,27/0/0/,0/0/0,80/80/0
Breast Invasive Carcinoma, BRCA,816/117/8,536/62/2,0/0/0,807/834/28
Cervical squamous cell carcinoma,CESC,0/0/0,0/0/0,0/0/0,37/37/2
Colon adenocarcinoma,COAD,166/37/3,154/12/9,0/0/0,421/474/19
Glioblastoma multiforme,GBM,541/0/1,572/0/11,492/0/,580/515/28
Head and neck squamous cell carcinoma,HNSC,0/0/0,0/0/0,0/0/0,170/191/6
Kidney renal cell carcinoma,KIRC,391/346/6,72/0/1,0/0/0,494/504/11
Kidney renal papillary cell carcinoma,KIRP,16/5/1,16/0/0/,0/0/0,43/46/0
Liver hepatocellular carcinoma,LIHC,0/0/0,0/0/0,0/0/0,55/69/1
Lung adenocarcinoma,LUAD,127/24/1,32/0/1,0/0/0,205/234/2
Lung squamous cell carcinoma,LUSC,228/67/3,154/0/1,0/0/0, 229/246/23
Lymphoid neoplasm diffuse large B-cell Lymphoma,DLBC,0/0/0,0/0/0,0/0/0,0/0/0
Lymphoid neoplasm Non-Hodkins Lymphoma,LNNH, 0/0/0,0/0/0,0/0/0,0/0/0
Ovarian serous adenocarcinoma,OV,573/4/9,589/0/9,586/0/8,590/574/30
Pancreatic adenocarcinoma,PAAD,0/0/0,0/0/0,0/0/0,14/14/14
Prostate adenocarcinoma,PRAD,0/0/0,0/0/0,0/0/0,83/96/1
Rectum adenocarcinoma,READ,69/5/3,69/3/2,0/0/0,165/170/4
Skin cutateneous melanoma,SKCM,0/0/0,0/0/0,0/0/0,0/0/0
Stomach adenocarcinoma,STAD,118/45/1/,0/0/0,0/0/0,135/148/2
Thyroid carcinoma,THCA,0/0/0,0/0/0,0/0/0,86/96/1
Uterine corpus endometrioid carcinoma,UCEC,373/16/12,54/0/0,0/0/0,371/376/14

DNA methylation data availability for 27k and 450k arrays for the selected cancer types:

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Cancer Type,Code,Methylation/# patients,27k,450 k Level 1 type,450 k Level 1 # tumors,450 k Level 2 # tumors,Number of batches,Barcode # batches
Acute Myeloid Leukemia,LAML,193/0/0,188,txt (GenomeStudio export),190,didn't download,2,3
Breast Invasive Carcinoma,BRCA,816/117/8,26,idat (bead level),didn't download,91,,24
COLON (COAD+READ),butt,166/37/3,237,not available,not available,not available,,9
Glioblastoma Multiforme,GBM,541/0/1,294,txt (GenomeStudio export),74,didn't download,19,19
Kidney Renal Cell Carcinoma,KIRC,391/346/6,219,idat (bead level),didn't download,173,12,16
Lung Adenocarcinoma,LUAD,127/24/1,32,not available,not available,not available,11,8
Lung Squamous Cell Carcinoma,LUSC,228/67/3,134,idat (bead level),didn't download,95,11,12
Stomach Adenocarcinoma,STAD,118/45/1,66,idat (bead level),didn't download,52,6,6
Uterine Corpus Endometrioid Carcinoma,UCEC,373/16/12,117,idat (bead level),didn't download,256,19,6

COAD

#Exact correspondence between the number in the derived data matrix (single number before
#lvl_x in the file name) and TCGA Archive Name after Level_X.
#derb1 = number in the derived data matrix
#newFiles[,4] = TCGA Archive Name
> table(newFiles$derb1,newFiles[,4])

    1.1.0 2.2.0 3.0.0 4.0.0 5.2.0 6.0.0 7.0.0 8.0.0
  1    49     0     0     0     0     0     0     0
  2     0    13     0     0     0     0     0     0
  3     0     0    16     0     0     0     0     0
  4     0     0     0    18     0     0     0     0
  5     0     0     0     0    32     0     0     0
  6     0     0     0     0     0    53     0     0
  7     0     0     0     0     0     0     7     0
  8     0     0     0     0     0     0     0    25

However I think that TCGA Archive name might be a better surrogate for the processing group. See the table for COAD below. TODO: verify it

#Correlation between processing groups (TCGA Archive Name) and BCR batches:
> table(newFiles$bcr,newFiles[,4])

       1.1.0 2.2.0 3.0.0 4.0.0 5.2.0 6.0.0 7.0.0 8.0.0
  0820    32     0     0     0     0     0     0     0
  0825     0     8     0     0     0     0     0     0
  0904     0     0     0     0    32     0     0     0
  1020     0     0     0     0     0    53     0     0
  1110     0     0     0     0     0     0     7     0
  1551    12     5     0     0     0     0     0     0
  1552     5     0     0     0     0     0     0     0
  A004     0     0    16     0     0     0     0     0
  A00B     0     0     0    18     0     0     0     0
  A081     0     0     0     0     0     0     0    25

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Batch on the download page,TCGA Archive code Level 1 from sdrf file,Comment for TCGA Arcive code from sdrf file,"# after ""HumanMethylation27k"" in the file name, Level 1",Batch as the sixth field in the patient barcode,Comments
Batch 28,1.1.0,,1,"0820, 1552, 1551",
Batch 29,2.2.0,,2,"0825, 1551",
Batch 30,3.0.0,,3,A004,
Batch 33,4.0.0,,4,A00B,
Batch 36,5.2.0,1110 is not there probably because sdrf file I have is for the tumor samples only,"5, 7","1110, 0904","all 0904 have 5, 1110 (one sample) is 7"
Batch 41,6.0.0,1110 is not there probably because sdrf file I have is for the tumor samples only,"6,7","1020, 1110","all 1020 have 6, 1110 (one sample) is 7"
Batch 45,7.0.0,,7,1110,
Batch 66,8.0.0,,8,A081,
Batch 76,,,no data,,
Batch 89,,,no data,,
Batch 116,,,no data,,
Batch 123,,,no data,,
Batch 132,,,no data,,
Batch 138,,,no data,,
Batch 154,,,no data,,
Batch 157,,,no data,,
Batch 172 ,,,no data,,

* Processing group/data/BCR batch distribution as of January 19th, 2011

Did TCGA shoot themselves in the foot? Compare sample by batch distribution for 27 and 450k arrays

Data downloaded on January 19th, 2012. DNA methylation Level 1 data 27k: 424 patients. DNA methylation 450k Level 1 data: . Even 27k arrays are .idat files which makes them impossible to process at this moment because minfi (Bioconductor package) handles only 450 k arrays.

BCR batch/processing batch distributions for 27 k arrays:

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Batch on the download page,"# after ""HumanMethylation27k"" in the file name, Level 2 data",Batch as the sixth field in the patient barcode,Comments
Batch 32,1,0859,"Level 1 data is uploaded again as .idat files split into green and red probes, I can't figure out how to get batch from the file names. Now, however, they provide slide number and the array letter!"
Batch 50,2,1186,
Batch 63,no data,,
Batch 64,3,"1287, 1284",
Batch 65,4,1303,
Batch 68,no data,,
Batch 69,5,1332,
Batch 70,no data,,
Batch 82,no data,,
Batch 90,no data,,
Batch 105,no data,,

Correlation between BCR batch and the Archive Name based on sdrf file that was downloaded together with the data:

table(KIRC27k$TCGAARchiveNameL1, KIRC27k$BCRbatch)

        0859 1186 1284 1287 1303 1332
  1.2.0   71    0    0    0    0    0
  2.2.0    0   61    0    0    0    0
  3.2.0    0    0   96    6    0    0
  4.2.0    0    0    0    0   95    0
  5.2.0    0    0    0    0    0   95

It shows the same correlation as for the table above that was composed based on the comparison of the files available per batch. In this case there is also the perfect correlattion between Derived Array Data Matrix (number before "lvl") and the TCGA Archive:

> table(KIRC27k$TCGAARchiveNameL1, KIRC27k$ArrayMatNumber)

          1   2   3   4   5
  1.2.0  71   0   0   0   0
  2.2.0   0  61   0   0   0
  3.2.0   0   0 102   0   0
  4.2.0   0   0   0  95   0
  5.2.0   0   0   0   0  95

#Also the same correlation with BCR batch:
> table(KIRC27k$ArrayMatNumber, KIRC27k$BCRbatch)

    0859 1186 1284 1287 1303 1332
  1   71    0    0    0    0    0
  2    0   61    0    0    0    0
  3    0    0   96    6    0    0
  4    0    0    0    0   95    0
  5    0    0    0    0    0   95