Home - The Cancer Genome Atlas - Cancer Genome - TCGA
TCGA Data Consumption by the Scientific Community
Since the inception of The Cancer Genome Atlas (TCGA) in 2006, almost 6,000 cases (with a case defined as tumor and a source of germline) have been characterized, representing more than 25 different tumor types. Extensive DNA/RNA/miRNA sequencing, expression, methylation, SNP and copy number data have been provided to the public via the TCGA Data Portal and the Cancer Genomics Hub (CGHub). In addition to generating the core datasets, the TCGA Research Network has published comprehensive tumor-specific marker papers that describe global analyses of the data, novel discoveries and clinical insights. The generation of comprehensive, high-quality cancer genomics data and initial integrative analysis of the data are important goals of TCGA. However, the data and reports are intended to be only starting points, and the participation of the broader research community in analyzing the datasets is necessary to realize their full value.
Therefore we examined three metrics of TCGA data usage to determine whether the scientific community has been consuming and analyzing TCGA data: (1) usage of the TCGA Data Portal and Cancer Genomics Hub, (2) grant applications that cite TCGA data in the research objectives and (3) publications that incorporate TCGA data.
Usage of the TCGA Data Portal
Figure 1. Number of unique visitors to the TCGA Data Portal from 2011-2012. Courtesy of NCI CBIIT.
Figure 1 shows the number of unique visitors to the TCGA Data Portal from 2011 to 2012*. In just two years, the number of unique visitors more than doubled from 3,386 to 8,267 between January 2011 and December 2012. This shows that more and more users are seeking TCGA data.
*Earlier usage statistics were unavilable.
Usage of the Cancer Genomics Hub
The Cancer Genomics Hub (CGHub) was established in late 2011 as a repository for the secure storage, cataloging and dissemination of large-scale primary sequence data for TCGA and other projects. As of December 2012, over 150 users have downloaded almost 4,400 terabytes of data. The top users come from a variety of institutions (universities, research centers, pharmaceutical companies, etc.) and from many different countries.
Grant Applications
Figure 2. The number of grant applications that cite TCGA data submitted to the NIH each year from 2006-2012
Figure 2 shows the number of new grant applications submitted to the NIH that cite TCGA data in the research objectives. The sum of applications has increased from 46 applications submitted in 2006 (at the beginning of TCGA’s pilot project) to 215 applications submitted in 2012. This shows that more and more researchers are incorporating TCGA data in their projects and are seeking funding to analyze TCGA data. As of December 2012, almost 800 unique applications citing the use of TCGA data have been submitted.
Of the 800 grant applications submitted, 278 were awarded. This is an award rate of almost 35 percent. The award rate for all applications submitted to the National Cancer Institute is on average 15 percent.
Publications
Figure 3. The number of articles that analyzed TCGA data published each year from 2008-2012
Figure 3 shows the number of papers published that analyzed TCGA data has increased dramatically from three papers in 2008 to 157 papers in 2012. At the end of 2012, more than 265 papers were published in total. By May 2013, more than 350 papers have been published in total.
There has been wide speculation that almost all papers that analyze TCGA data are authored by members of the TCGA Research Network, however the opposite is true. Most of these papers (65 percent) were authored by non-TCGA consortium scientists, dispelling the misconception that TCGA data are only accessible to “insiders.”
TCGA’s first marker paper,
Conclusions
Together, these observations suggest that TCGA is on its way to meeting goals of creating an atlas that is broadly used by the cancer research community. However, we have a long way yet to go as TCGA works to complete this phase of the catalog by the end of 2014. We continue to challenge the community to utilize the data to develop new algorithms, form new hypotheses, initiate molecularly-informed clinical trials and make discoveries that will inform how we will better diagnose, treat and prevent cancer in the future.
Therefore we examined three metrics of TCGA data usage to determine whether the scientific community has been consuming and analyzing TCGA data: (1) usage of the TCGA Data Portal and Cancer Genomics Hub, (2) grant applications that cite TCGA data in the research objectives and (3) publications that incorporate TCGA data.
Usage of the TCGA Data Portal
Figure 1. Number of unique visitors to the TCGA Data Portal from 2011-2012. Courtesy of NCI CBIIT.
Figure 1 shows the number of unique visitors to the TCGA Data Portal from 2011 to 2012*. In just two years, the number of unique visitors more than doubled from 3,386 to 8,267 between January 2011 and December 2012. This shows that more and more users are seeking TCGA data.
*Earlier usage statistics were unavilable.
Usage of the Cancer Genomics Hub
The Cancer Genomics Hub (CGHub) was established in late 2011 as a repository for the secure storage, cataloging and dissemination of large-scale primary sequence data for TCGA and other projects. As of December 2012, over 150 users have downloaded almost 4,400 terabytes of data. The top users come from a variety of institutions (universities, research centers, pharmaceutical companies, etc.) and from many different countries.
Grant Applications
Figure 2. The number of grant applications that cite TCGA data submitted to the NIH each year from 2006-2012
Figure 2 shows the number of new grant applications submitted to the NIH that cite TCGA data in the research objectives. The sum of applications has increased from 46 applications submitted in 2006 (at the beginning of TCGA’s pilot project) to 215 applications submitted in 2012. This shows that more and more researchers are incorporating TCGA data in their projects and are seeking funding to analyze TCGA data. As of December 2012, almost 800 unique applications citing the use of TCGA data have been submitted.
Of the 800 grant applications submitted, 278 were awarded. This is an award rate of almost 35 percent. The award rate for all applications submitted to the National Cancer Institute is on average 15 percent.
Publications
Figure 3. The number of articles that analyzed TCGA data published each year from 2008-2012
Figure 3 shows the number of papers published that analyzed TCGA data has increased dramatically from three papers in 2008 to 157 papers in 2012. At the end of 2012, more than 265 papers were published in total. By May 2013, more than 350 papers have been published in total.
There has been wide speculation that almost all papers that analyze TCGA data are authored by members of the TCGA Research Network, however the opposite is true. Most of these papers (65 percent) were authored by non-TCGA consortium scientists, dispelling the misconception that TCGA data are only accessible to “insiders.”
TCGA’s first marker paper,
The Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 455 (7216):1061-1068.
remains in the top 10 of the most cited cancer research papers since 2008 (based on an analysis from the Scopus database).Conclusions
Together, these observations suggest that TCGA is on its way to meeting goals of creating an atlas that is broadly used by the cancer research community. However, we have a long way yet to go as TCGA works to complete this phase of the catalog by the end of 2014. We continue to challenge the community to utilize the data to develop new algorithms, form new hypotheses, initiate molecularly-informed clinical trials and make discoveries that will inform how we will better diagnose, treat and prevent cancer in the future.
Cancers Selected for Study
Following the success of The Cancer Genome Atlas (TCGA) Pilot Project, NIH announced in September 2009 that it is investing $275 million in TCGA over the next two years of this five-year program to chart the genomic changes involved in more than 20 types of cancer. To date, TCGA has achieved comprehensive sequencing, characterization, and analysis of the genomic changes in the brain cancer, glioblastoma multiforme, and ovarian cancer.Cancers selected for study were chosen based on specific criteria that include:
- Poor prognosis and overall public health impact
- Availability of human tumor and matched-normal tissue samples that meet TCGA standards for patient consent, quality and quantity
Please note that the list of cancers below is not a comprehensive list and TCGA is actively seeking samples for additional cancer types. This list is subject to change based on the flow of tissues to the project pipeline.
TCGA leadership will continue to keep the cancer community apprised of changes to this list.
CANCER TISSUES BEING COLLECTED FOR POTENTIAL STUDY
Last Updated: June 04, 2013
Program Overview
Multimedia
 | Interactive: How It Works |
There are at least 200 forms of cancer, and many more subtypes. Each of these is caused by errors in DNA that cause cells to grow uncontrolled. Identifying the changes in each cancer’s complete set of DNA – its genome – and understanding how such changes interact to drive the disease will lay the foundation for improving cancer prevention, early detection and treatment.
The Cancer Genome Atlas (TCGA) began as a three-year pilot in 2006 with an investment of $50 million each from the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI). The TCGA pilot project confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Importantly, it proved that making the data freely available would enable researchers anywhere around the world to make and validate important discoveries. The success of the pilot led the National Institutes of Health to commit major resources to TCGA to collect and characterize more than 20 additional tumor types.
Learn more about the important role of tissue samples to TCGA.
Each cancer will undergo comprehensive genomic characterization and analysis. The comprehensive data that have been generated by TCGA’s network approach are freely available and widely used by to the cancer community through the TCGA Data Portal and the Cancer Genomics Hub (CGHub).
Learn more about the components of the TCGA Research Network by selecting a link below:
Biospecimen Core Resource (BCR) – Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient.
Genome Characterization Centers (GCCs) – Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers.
Genome Sequencing Centers (GSCs) – High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer.
Proteome Characterization Centers (PCCs) – The centers, a component of NCI’s Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples.
Data Coordinating Center (DCC) – The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal.
Cancer Genomics Hub (CGHub) – Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments.
Genome Data Analysis Centers (GDACs) – Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data.
Learn more about TCGA by selecting a link below:
Mission and GoalHow It WorksHistory and TimelineBackgrounder
Learn more about the cancer genomics field and TCGA's place in it by selecting a link below:
Chin, L., Hahn, W.C., Getz, G., Meyerson, M. (2011) Making sense of cancer genomic data. Genes and Development. 25(6): 534-555.
Chin, L., Andersen, J.N., Futreal, P.A. (2011) Cancer genomics: from discovery science to personalized medicine. Nature Medicine. 17(3): 297-303.
The Cancer Genome Atlas (TCGA) began as a three-year pilot in 2006 with an investment of $50 million each from the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI). The TCGA pilot project confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Importantly, it proved that making the data freely available would enable researchers anywhere around the world to make and validate important discoveries. The success of the pilot led the National Institutes of Health to commit major resources to TCGA to collect and characterize more than 20 additional tumor types.
Learn more about the important role of tissue samples to TCGA.
Each cancer will undergo comprehensive genomic characterization and analysis. The comprehensive data that have been generated by TCGA’s network approach are freely available and widely used by to the cancer community through the TCGA Data Portal and the Cancer Genomics Hub (CGHub).
Learn more about the components of the TCGA Research Network by selecting a link below:
Biospecimen Core Resource (BCR) – Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient.
Genome Characterization Centers (GCCs) – Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers.
Genome Sequencing Centers (GSCs) – High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer.
Proteome Characterization Centers (PCCs) – The centers, a component of NCI’s Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples.
Data Coordinating Center (DCC) – The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal.
Cancer Genomics Hub (CGHub) – Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments.
Genome Data Analysis Centers (GDACs) – Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data.
Learn more about TCGA by selecting a link below:
Mission and GoalHow It WorksHistory and TimelineBackgrounder
Learn more about the cancer genomics field and TCGA's place in it by selecting a link below:
Chin, L., Hahn, W.C., Getz, G., Meyerson, M. (2011) Making sense of cancer genomic data. Genes and Development. 25(6): 534-555.
Chin, L., Andersen, J.N., Futreal, P.A. (2011) Cancer genomics: from discovery science to personalized medicine. Nature Medicine. 17(3): 297-303.
No hay comentarios:
Publicar un comentario