The Cancer Genome Atlas

The Cancer Genome Atlas (TCGA) is a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing and bioinformatics.^[1][2] TCGA represents an effort in the War on Cancer that is applying high-throughput genome analysis techniques to improve our ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of this disease.

TCGA is supervised by the National Cancer Institute and the National Human Genome Research Institute funded by the US government. A three-year pilot project, begun in 2006, focused on characterization of three types of human cancers: glioblastoma multiforme, lung, and ovarian cancer.^[3] In 2009, it expanded into phase II, which plans to complete the genomic characterization and sequence analysis of 20-25 different tumor types by 2014. Funding is split between genome characterization centers (GCCs), which perform the sequencing, and genome data analysis centers (GDACs), which perform the bioinformatic analyses.

The project scheduled 500 patient samples, more than most genomics studies, and used different techniques to analyze the patient samples. Techniques gene expression profiling, copy number variation profiling, SNP genotyping, genome wide DNA methylation profiling, microRNA profiling, and exon sequencing of at least 1,200 genes. The TCGA is sequencing the entire genomes of some tumors, including at least 6,000 candidate genes and microRNA sequences. This targeted sequencing is being performed by all three sequencing centers using hybrid-capture technology. In phase II, TCGA is performing whole exon sequencing on 80% of the cases and whole genome sequencing on 80% of the cases used in the project.

Goals

The goal of the pilot project was to demonstrate that advanced genomic technologies could be utilized by a team of scientists from various institutions to generate statistically and biologically significant conclusions from the genomic data set generated.^[4] Two tumor types were explored during the pilot phase, Glioblastoma Multiforma (GBM) and Cystadenocarcinoma of the Ovary. The goal of TCGA Phase II is to expand the success experienced in the pilot project to more cancer types, providing a large, statistically significant data set for further discovery. More information about TCGA is available at the TCGA home page (http://cancergenome.nih.gov/) and TCGA data can be accessed through the TCGA Data Portal (http://tcga-data.nci.nih.gov/tcga/).

Management

TCGA is co-managed by scientists and managers from the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). With the expansion of TCGA from the pilot phase to Phase II in October, 2009, the NCI created a TCGA Program Office. This office is responsible for the operation of six Genome Characterization Centers, seven Genome Analysis Centers, the Biospecimen Core Resource, the Data Coordination Center, and approximately one third of the sequencing done for the project by the three Genome Sequencing Centers. In addition, the TCGA Project Office is responsible for coordinating the accrual of tissues for TCGA. NHGRI directs two thirds of the sequencing at the Genome Sequencing Centers.

Tissue accrual

Tissue requirements vary from tissue type to tissue type and from cancer type to cancer type. Disease experts from the project’s Disease Working Groups help to define the characteristics of the typical tissue samples accrued as “standard of care” in the United States and how TCGA can best utilize the tissue. For example, the Brain Disease Working Group determined that samples containing more than 50% necrosis would not be suitable for TCGA and that 80% tumor nuclei were required in the viable portion of the tumor. TCGA has some general guidelines that it follows as a starting point for collecting samples from any types of tumors. These include a minimum of 200 mg in size, no less than 80% tumor nuclei and a matched source of germline DNA (such as blood or purified DNA). In addition, institutions submitting tissues to TCGA must have a minimal clinical data set as defined by the Disease Working Group, signed consents which have been approved by their institution’s IRB as well as a material transfer agreement with TCGA.

In 2009, the NCI removed approximately $130 million of ARRA from the NCI’s “Prime Contract” with Science Applications International Corporation (SAIC) to fund tissue accrual and a variety of other activities through the NCI Office of Acquisition. $42 million is available for tissue accrual through the NCI using “Requests for Quotations” (RFQs) and “Requests for Proposals” (RFPs) to generate purchase orders and contracts, respectively. RFQs are primarily used for the collection of retrospective samples from established banks while RFPs are used for the prospective collection of samples.

Institutions that contribute samples to TCGA are paid, and have access to molecular data generated on their samples, while maintaining a link between the TCGA unique identifier and their own unique identifier. This permits contributing institutions to link back to the clinical data for their samples and to enter into collaborations with other institutions that have similar data on TCGA samples, thus increasing the power of outcome analysis.

Funding

The NCI and NHGRI equally co-funded the Pilot Project with $50M for the first three years. The NCI has committed $25M/year of appropriated funds for five years for TCGA Phase II. The NHGRI has committed $25M/year of appropriated funds for two years. The beginning of the second phase of the project coincided with the American Recovery and Reinvestment Act of 2009 (ARRA), providing $153.5M of additional funding to the NCI beyond their appropriated funds. The Office of the Director of the NIH has provided another $25M of ARRA funds dedicated to sequence analysis and another $25M of ARRA funds in the second year of Phase II if substantial progress is made during year 1. In all, $150M will be spent on sequencing. Another $70M will be spent on tissue accrual, sample QC and biomolecule (DNA and RNA) isolation.

Organization

TCGA has a number of different types of centers that are funded to generate and analyze data. TCGA is the first large-scale genomics project funded by the NIH to include significant resources to bioinformatic discovery. The NCI has devoted 50% of TCGA appropriated funds, approximately $12M/year, to fund bioinformatic discovery. Genome Characterization Centers and Genome Sequencing Centers generate data. Two types of Genome Data Analysis Centers utilize the data for bioinformatic discovery. Two centers are funded to isolated biomolecules from patient samples and one center is funded to store the data. For more information on TCGA project organization, see http://cancergenome.nih.gov/newsevents/multimedialibrary/interactives/howitworks.

Biospecimen core resource

The Biospecimen Core Resource (BCR) is responsible for verifying the quality and quantity of tissue shipped by tissue source sites, the isolation of DNA and RNA from the samples, quality control of these biomolecules and the shipment of samples to the GSCs and GCCs. The International Genomics Consortium was awarded the contract to initiate the BCR for the pilot project. There were two BCRs funded by the NCI at the start of the full project: Nationwide Children's Hospital and the International Genomics Consortium. The BCRs were recompeted with due date for proposals June 4, 2010 and Nationwide Children's Hospital was awarded the contract.^[5]

Genome sequencing centers

Three Genome Sequencing Centers were co-funded by the NCI and NHGRI: the Broad Institute, The Genome Center at Washington University and Baylor College of Medicine. All three of these sequencing centers have shifted from Sanger sequencing to next-generation sequencing (NGS), although a variety of NGS technologies are being implemented simultaneously.

Genome characterization centers

The NCI funded six Genome characterization centers: the Broad Institute, Harvard, University of North Carolina, University of Southern California, Baylor College of Medicine and the British Columbia Cancer Center.

Data coordinating center

The data coordinating center is the central repository for TCGA data. It is also responsible for the quality control of data entering the TCGA database. The DCC also maintains the TCGA Data Portal which is where users access TCGA data. This work is performed under contract by bioinformatics scientists and developers from SRA International, Inc. The DCC does not host lower levels of sequence data. NCI's Cancer Genomics Hub (CGHub) is the secure repository for storing, cataloging, and accessing sequence-related data. This work is performed under contract by scientists and staff at the University of California, Santa Cruz.

Genome data analysis centers

Seven Genome data analysis centers funded by the NCI/NHGRI are responsible for the integration of data across all characterization and sequencing centers as well as biological interpretation of TCGA data. The GDACs include The Broad Institute, University of North Carolina, the Lawrence Berkeley National Laboratory, University of California at Santa Cruz, MD Anderson Cancer Center, Memorial Sloan Kettering Cancer Center, and The Institute for Systems Biology. All seven GDACs work together to develop an analysis pipeline for automated data analysis.

Tumors

A preliminary list of tumors for TCGA to study was generated by compiling incidence and survival statistics from the SEER Cancer Statistic website (http://seer.cancer.gov/). In addition, U.S. current “Standard of Care” was considered when choosing the top 25 tumor types, as TCGA is targeting tumor types where resection prior to adjunct therapy is the standard of care. Availability of samples also plays a critical role in determining which tumor types to study and the order in which tumor projects are started. The more common the tumor is, the more likely that samples will be accrued quickly, resulting in common tumor types, such as colon, lung and breast cancer becoming the first tumor types entered into the project, before rare tumor types.

TCGA Targeted Tumors: lung squamous cell carcinoma, kidney papillary carcinoma, clear cell kidney carcinoma, breast ductal carcinoma, diffuse large B-cell lymphoma, renal cell carcinoma, cervical cancer (squamous), colon adenocarcinoma, stomach adenocarcinoma, rectal carcinoma, hepatocellular carcinoma, astrocytoma, Head and neck (oral) squamous cell carcinoma, thyroid carcinoma, bladder urothelial carcinoma - nonpapillary, uterine corpus (endometrial carcinoma), invasive urothelial bladder cancer, pancreatic ductal adenocarcinoma, acute myeloid leukemia, prostate adenocarcinoma, lung adenocarcinoma, cutaneous melanoma, breast lobular carcinoma and multiple myeloma.

TCGA is accruing samples for all of these tumor types simultaneously. As samples become available, the tumor types with the most samples accrued will be entered into production. For more rare tumor types, tumor types where samples are difficult to accrue and for tumor types where TCGA cannot identify a source of high quality samples, these types of cancer will enter the “TCGA production pipeline” in the second year of the project. This will give the TCGA Program Office additional time to accrue sufficient samples for the project. If TCGA plans to characterized 20 tumor types in five years and there are 25 potential tumor types on the list, obviously, five types of cancer will not be studied unless additional funds are made available.

Publications

Progress as of January 16, 2011

Cancer Type Studied	Sample collection Complete	Data Publicly Available	Some Identified Mutation
Glioblastoma Multiforme	X	X	EGFR, NF1, TP53, PlK3R1, PIK3CA, IDH1, PTEN, RB1, LZTR1
Lower Grade Glioma		X	IDH1, IDH2, TP53, FUBP1, CIC, 1p/19q deletion
Breast Lobular Carcinoma		X
Breast Ductal Carcinoma	X	X	ESR1, GATA3, FOXA1, XBP1, and cMYB
Colorectal Adenocarcinoma	X	X	New Potential drivers: ARlD1A, SOX9, FAM123B/WTX; Overexpression of: ERBB2, IGF2; mutations i WNT pathway
Stomach Adenocarcinoma		X
Ovarian Serous Cystadenocarcinoma	X	X	mutations in TP53 occurred in 96% of the cases studied; mutations in BRCA1 and BRCA2 occurred in 21% of the cases
Uterine Corpus Endometrial Carcinoma	X	X
Cervical Squamous Cell Carcinoma and Adenocarcinoma		X
Head and Neck Squamous Cell Carcinoma		X
Thyroid Carcinoma		X
Acute Myeloid Leukemia		X
Cutaneous Melanoma
Lung Adenocarcinoma		X
Lung Squamous Cell Carcinoma		X
Clear Cell Carcinoma	X	X
Kidney Papillary Carcinoma		X
Invasive Urothelial Bladder Cancer
Prostate Adenocarcinoma
Chromophobe Renal Cell Carcinoma	X	X

Glioblastoma multiforme

In 2008, the TCGA published its first results on Glioblastoma multiforme (GBM) in Nature.^[6] These first results published on 91 tumor-normal matched pairs. While 587 biospecimens were collected for the study, most were rejected during quality control: the tumor samples needed to contain at least 80% tumor nuclei and no more than 50% necrosis, and a secondary pathology assessment had to agree that the original diagnosis of GBM was accurate. A last batch of samples were excluded because the DNA or RNA collected was not of sufficient quality or quantity to be analyzed by all of the different platforms used in this study.

All of the data from the paper, as well as data that has been collected since the publication are publicly available at the Data Coordinating Center (DCC) for public access.^[7] Most of the TCGA data is completely open access, except for data that could potentially identify specific patients. This Clinically Controlled-Access data can be accessed through application to the Data Access Committee (DAC), which evaluates whether the end user is a bona fide researcher and is asking a legitimate scientific question that merits access to individual-level data.^[8] This process is similar to that of other NIH-funded programs, including dbGAP.

Since the publication of the first marker paper, several analysis groups within the TCGA Network have presented more detailed analysis of the glioblastoma data. An analysis group led by Roel Verhaak, PhD, Katie Hoadley, PhD, and Neil Hayes, MD, successfully correlated glioma gene expression subtypes with genomic abnormalities.^[9] The DNA methylation data analysis team, led by Houtan Noushmehr, PhD and Peter Laird, PhD, identified a distinct subset of glioma samples which displays concerted hypermethylation at a large number of loci, indicating the existence of a glioma-CpG island methylator phenotype (G-CIMP). G-CIMP tumors belong to the proneural subgroup and were tightly associated with IDH1 somatic mutations.^[10][11]

Serous ovarian

Starting a new era in cancer genome sequencing, TCGA reported on the exome sequencing of 316 tumor samples of high grade serous ovarian cancer in Nature in June 2011.^[12]

Colorectal carcinoma

TCGA reported on the exome sequencing and gene expression analysis of 276 tumor samples of colon and rectal cancers, including whole genome sequencing of 97 samples, in Nature in July 2012.^[13]

Status as of 2013: mutational landscape of 12 common cancer subtypes

In 2013, TCGA published a description of the "mutational landscape" defined as frequently recurring mutations identified from whole-genome sequencing of 3,281 cancer genomes from 12 commonly occurring cancer subtypes. The twelve subtypes studied were breast adenocarcinoma, lung adenocarcinoma, lung squamous cell carcinoma, endometrial carcinoma, glioblastoma multiforme, squamous cell carcinoma of the head and neck, colon cancer, rectal cancer, bladder cancer, kidney clear cell carcinoma, ovarian carcinoma and acute myeloid leukaemia.^[14]

See also

• Cancer Genome Project at the Wellcome Trust Sanger Institute
• International Cancer Genome Consortium

References

External links

• The Cancer Genome Atlas
• NCI Office of Cancer Genomics
• Cancer Genomics Hub at UC Santa Cruz
• CGAP Genetic Annotation Initiative
• NCI Wiki