The cBio Cancer Genomics Portal providesvisualization,analysisanddownloadof large-scalecancer genomicsdata sets.

The portal is developed and maintained by theComputational Biology CenteratMemorial Sloan-Kettering Cancer Center.
目前來能夠從TCGA數據庫中提取數據的處理工具有cBioPortal（http://www.cbioportal.org/public-portal/cgds_r.jsp），ICGC（http://dcc.icgc.org/download/current）和GenePattern（http://www.broadinstitute.org/cancer/software/genepattern/download/index）。這些工具使用起來還是有其局限性，都不能夠輕易獲取每個癌癥類型的二維數據矩陣（例如基因為rows，樣本為columns）。

TCGA中每個樣本都是相互獨立的，兩個樣本的barcode中sample type為06或01，而其他都相同，但是這兩個樣本都有可能來自同個病人的不同組織。例如：兩個乳腺癌樣本TCGA-BH-A1FE-01，TCGA-BH-A1FE-06，01意味著原始癌癥樣本來自乳腺，06意味著轉移樣本，經過查證來自卵巢。具體查找方法，見以下郵件內容：

Each sample in TCGA is a separate sample.I think the best place to look for site information of each sample is the pathology report.You can find the pathology report file name (they are pdf files) in the biospecimen_sample file in the pathology_report_file_name column.Once you have the file name, you can search for it using the Bulk Download toolathttps://tcga-data.nci.nih.gov/tcga/findArchives.htm.You will want to copy and paste the pathology report file name in the File Name field and click the Find button.This will give you the directory that contains the pdf file.You can then click the View Files link and it will display all the pathology files in that directory.You will need to search for the pdf file you are interested in and you can open it for viewing there.

Let me give you an example.Sample TCGA-D3-A1Q6-06A has pathology report TCGA-D3-A1Q6.5BA4EDD7-8462-4028-8CB9-8FE2DDC51D3E.pdf, and sample TCGA-D3-A1Q6-07A has pathology report TCGA-D3-A1Q6.7E74D698-CA50-40D9-8A06-6CECFD8580DA.pdf. Using the Bulk Download tool, you will find that both of these files are in directory nationwidechildrens.org_SKCM.pathology_reports.Level_1.180.9.0.You can View Files directly in the Bulk Download tool, or you can go to the Open-Access HTTP Directory athttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/and drill down to the pathology reports for the disease you are interested in and find the pdf files in there.To drill down you would select the disease you are interested in (e.g., skcm) and then select bcr, nationwidechildrens.org, pathology_reports, reports, and then select the directory that you found using the Builk Download tool.In that directory you will find both pdf files of interest.

If you look at the pdf file for sample TCGA-D3-A1Q6-06A, you will see in the hand-written notes at the top right, “Site: subcutaneous tissue.”This matches diagnosis A, found at right upper arm.If you look at the pdf file for sample TCGA-D3-A1Q6-07A, you will see the hand-written notes “Site: lymph nodes, axillary.”This matches diagnosis D, lymph nodes.

This is probably the best place to find any details about the location of the sample in question.Note however, that normal samples (such as the BRCA normal sample TCGA-BH-A18V-11, do not have pathology reports. Normal solid tissue samples are typically normal tissue collected adjacent to the tumor sample.