What Is The Cancer Genome Atlas? Its History and Major Milestones

One of the most important milestones for humanity and science is undoubtedly the Human Genome Project! Beginning in 1990 and completed in 2003, it is also one of humanity's greatest investments. When the Human Genome Project was completed, our knowledge of many diseases, including cancer, increased many times over, but it also revealed how little we knew about cancer biology and genetics. The Cancer Genome Atlas Project was therefore launched in 2005. This genetic project is the starting point for innovative treatments (most targeted cancer drugs) used today and to be used in the future.

Before beginning TCGA's detailed history, below is a brief history of genetic research in cancer for reference:

What Is The Cancer Genome Atlas?

The Cancer Genome Atlas (The Cancer Genome Atlas = TCGA) is a genomic project that molecularly characterized more than 20 thousand tumors from 33 cancer types and compared them with normal tissue samples.

The project was effectively launched in 2006, bringing together researchers from multiple disciplines through the US National Cancer Institute (US-NCI) and the US National Human Genome Research Institute (NHGRI).

In the following years, the TCGA project generated more than 2.5 petabytes of genomic, epigenomic, transcriptomic and proteomic data. These data, which enable advances in what we can do to diagnose, treat and prevent cancer, remain openly accessible to anyone wishing to conduct research.

TCGA Timeline and Milestones

2005

February

The US National Cancer Advisory Board's working group on biomedical technology recommended launching a “Human Cancer Genome Project” to provide a comprehensive understanding of the genomic alterations underlying all major cancers.

What Is a Genome?

A genome is the complete set of instructions in  DNA. The nucleus of each of our cells contains 2 copies of DNA, one from the mother and one from the father. Our DNA is folded/packaged in a special way to form chromosomes. Our cells contain chromosomes holding 46 packaged DNA helices (23 from the mother and 23 from the father).

July

NCI and NHGRI held a workshop called “Toward a Comprehensive Genomic Analysis of Cancer” on implementing the pilot phase of the Human Cancer Genome Project.

December

NIH provided a pilot budget of 100 million dollars to launch the 3-year “Cancer Genome Atlas” project.

2006

May

TCGA held a workshop to discuss data-release policies that would give researchers easy access to data while protecting patient privacy.

September

NIH announced that lung, brain and ovarian cancers would be the first cancers to be mapped genomically by TCGA.

October

NIH announced TCGA's Cancer Genome Characterization Centers and Data Coordinating Center components.

November

NHGRI announced funding for 3 large-scale genome sequencing centers. 

2007

June

TCGA announced funding awards to support the development of genomic characterization technologies.

The first data flowed from the Cancer Genome Characterization Centers to the Data Coordinating Center.

2008

January

The project team met to discuss the first iteration of TCGA's Data Portal and data-analysis tools.

April

TCGA updated its informed-consent policies.

September

It published an interim analysis of glioblastoma identifying 3 critical signaling pathways.  

2009

February

Ovarian cancer data were uploaded to the Data Coordinating Center.

March

The Genome Sequencing Center moved from sequencing 601 genes to hybrid-capture techniques targeting more than 6000 genes and miRNA sequences.

June

The Genome Sequencing Center began using second-generation sequencing to generate whole-exome and whole-genome data.

September

NIH funded 7 Genome Data Analysis Centers to integrate and analyze the large quantities of different data types produced by the characterization centers.

2010

September

Supported by the 2009 American Recovery and Reinvestment Act, NIH expanded TCGA to map 20 types of cancer.

December

TCGA's open-access data were made available for the first time through the International Cancer Genome Consortium Data Portal.

2011

July

TCGA published a paper on ovarian cancer.

October

TCGA communicated its 5000th milestone to the Genome Characterization Centers.

November

The Genome Sequencing Center supported TCGA's sequencing effort with renewed funding.

TCGA held its First Annual Scientific Symposium.

2012

January

TCGA established the Cancer Genomics Hub (CGHub) as a new TCGA data resource.

July

It published a paper on colorectal carcinoma showing colon and rectal tumors as forming a single cancer subtype.

September

TCGA published a paper on squamous cell lung cancer presenting complex genomic alterations and recurrent mutations in genes including TP53.

October

TCGA published a paper on breast cancer presenting molecular similarities to ovarian cancer.

November

TCGA held its Second Annual Symposium.

December

NCI signed a contract to develop the TCGA Protected Data Cloud so researchers could analyze large amounts of genomic data in a secure cloud environment.

2013

May

TCGA published papers on acute myeloid leukemia and endometrial carcinoma.

June

It published a paper on clear cell renal cell carcinoma.

October

TCGA published an expanded study on glioblastoma using newer next-generation sequencing (NGS) data.

It established a Pan-Cancer analysis working group to collect and study data from multiple cancer types.

December

TCGA created a sample collection containing more than 20,000 pooled biospecimens.

2014

January

TCGA published a paper on bladder cancer.

May

TCGA held its Third Annual Scientific Symposium.

June

The final samples for genome characterization were delivered.

July

TCGA published papers on lung adenocarcinoma and gastric adenocarcinoma.

August

TCGA published a paper on chromophobe renal cell carcinoma, a rare form of kidney cancer.

October

TCGA published a paper on papillary thyroid carcinoma.

2015

January

TCGA published papers on head and neck squamous cell carcinomas.

May

TCGA published its Fourth Annual Scientific Symposium.

June

TCGA published papers on low-grade glioma and cutaneous melanoma.

October

TCGA published a paper on invasive lobular carcinoma, the most common subtype of invasive breast cancer.

TCGA directors Jean C. Zenklusen and Carolyn Hutter won the People's Choice Award at the 2015 Samuel J. Heyman Service to America Medals (Sammies).

November

TCGA published a paper on prostate cancer.

2016

January

TCGA published a paper on papillary renal cell carcinoma.

May

TCGA published a paper on adrenocortical carcinoma, a rare cancer, and on a comparison of lung carcinoma and squamous cell carcinoma.

June

NCI established the Genomic Data Commons (GDC), a unified data system that would contain genomic data from TCGA and other programs and studies.

July

The TCGA Data Portal and CGHub closed.

2017

January

TCGA published a paper on esophageal and cervical cancers.

February

TCGA published a paper on pheochromocytomas and paragangliomas, rare neuroendocrine tumors.

March

TCGA published papers on uterine carcinosarcoma and cholangiocarcinoma.

June

TCGA published a paper on hepatocellular (liver) carcinoma.

August

TCGA published papers on pancreatic ductal adenocarcinoma and uveal (eye) melanoma.

October

TCGA published an expanded bladder cancer study.

November

TCGA published a paper on soft tissue sarcoma.

2018

February

TCGA published a paper on thymic epithelial tumors.

April

TCGA published a collection of cross-cancer analyses examining overarching cancer themes in detail using the entire TCGA dataset, entitled "Pan-Cancer Atlas".

June

TCGA published a paper on testicular germ cell tumors.

TCGA published a paper on mesothelioma.

September

A Cell Symposium on TCGA Legacy: Multi-Omic Studies in Cancer (TCGA Legacy: Multli-Omic Studies in Cancer) was held. The TCGA Analysis Network continues to mine the data for new insights.

2020

February

The pan-cancer analysis of whole genomes (Pan-Cancer Analysis of Whole Genomes, PCAWG), a collaboration among more than 1300 scientists and doctors from 37 countries, resulted in Nature and its affiliated journals simultaneously publishing 23 scientific papers.

This analysis found that:

• Approximately five driver mutations were identified in each cancer genome (5% had no driver mutations).
• Most driver mutations were found in the genome's coding region.
• A “molecular clock” can identify which mutations occurred early in cancer evolution.
• Patterns of genetic mutations can help identify the cancer type (which may help doctors identify a cancer with an unknown primary site/origin).

Outcomes and Impact of The Cancer Genome Atlas

With the final samples collected, sequenced and uploaded, the Genomic Data Commons (GDC) opened for access and TCGA officially ended in 2018, while the Pan-Cancer Analysis of Whole Genomes (PCAWG), a product of TCGA, was published in 2020. This large-scale program has profoundly influenced cancer research. Its impact continues as the data are used in different ways. TCGA helped establish the importance of cancer genomics, changed our understanding of cancer and began changing its clinical treatment. The project's influence extends to health and science technologies, computational biology and research in many other fields. The enormous dataset generated with contributions from more than 20 thousand patients is also openly accessible. Both researchers in the program and independent researchers using these data have consequently produced many scientific studies.

The Cancer Genome Atlas has:

• Deepened our understanding of cancer by classifying and characterizing it at the molecular level
• Created rich genomic data resources for broad research communities
• Supported the field of computational biology
• Helped advance health and science technologies
• Changed clinical treatment pathways for cancer patients

The Genomic Data Commons (GDC) hosts TCGA and other datasets that scientists can access from anywhere. It also has many enhanced capabilities that allow researchers to answer more clinically relevant questions more easily.