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TCGA to Complete its Final Analysis: the PanCanAtlas

, by Amy E. Blum, M.A.

Cancer types, each in a different color, mapped according to their mRNA expression.

Credit: UCSC Interactive Tumor Map

As its concluding project, The Cancer Genome Atlas (TCGA) Research Network will complete the most comprehensive cross-cancer analysis to date: The Pan-Cancer Atlas (PanCanAtlas). This project aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset.

Utilizing the Complete TCGA Dataset

In October 2013, TCGA published the first round of “pan-cancer” analyses, which identified underlying genomic and cellular patterns in 12 tumor types.

Building on the success of the pan-cancer 12, TCGA is now poised to generate an even more comprehensive resource. The PanCanAtlas will study the complete set of TCGA data, which catalogues the alterations in DNA, epigenetics, and gene expression in more than 11,000 patient cases across 33 tumor types. Some cases also include whole genome sequencing and protein expression analysis.

Incorporating New Mutation Calls 

The PanCanAtlas project will also include new information from a genomic analysis initiative by the TCGA network called Multi-Center Mutation Calling Multi-tumor Completion effort, or MC3. MC3 identified cancer-related mutations in the whole TCGA dataset by analyzing the differences between tumor DNA sequences and the sequences of matched normal samples. Because MC3 did this analysis in a standard fashion across the entire dataset, this effort will enable the PanCanAtlas to study uniformly called DNA mutations in all 11,000 cases at once.

Pan-Cancer Themes

With the completed TCGA dataset and MC3 effort, the PanCanAtlas will be able to identify patterns that unite the tumors studied by TCGA, and characteristics that distinguish tumor types and subtypes from each other. The PanCanAtlas effort will focus on three overarching themes in cancer: cell-of-origin, oncogenic processes, and pathways.

The Cancer Genome Atlas project will be complete when the PanCanAtlas is published, having accomplished its mission of mapping the key genomic changes in an array of cancer types, and met its goal of providing a community resource that accelerates our understanding of the molecular basis of cancer.

Though TCGA will come to a close, the PanCanAtlas, pan-can 12, TCGA tissue-specific publications, and the rich TCGA dataset will continue to facilitate new discoveries about cancer for years to come.

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