Publication Guidelines
Last Updated: February 15, 2013
TCGA defines a global analysis publication as the first paper authored by The Cancer Genome Atlas Research Network which includes the data from at least 100 cases of a specific tumor type and includes analysis of much of the existing TCGA data on that tumor type at the time. Specifically, these manuscripts report on the comprehensive, integrated analysis of multiple TCGA datasets available including, but not limited to, copy number variation, gene and miRNA expression, promoter methylation and DNA sequence/mutation analysis. Prior to a global analysis publication (marker paper) on a specific tumor type, available data sets should be considered pre-publication data subject to the standard principles of scientific etiquette regarding publication of findings using data obtained from other sources.
The TCGA program has established the following policy to clarify freedom of TCGA and non-TCGA users to publish findings using TCGA data. There are no limitations on publications containing analyses using any TCGA data set if the data set meets one of the following three freedom-to-publish criteria:
- A marker paper has been published on that tumor type; or
- 18 months after 100 cases of a given tumor type have shipped from BCR to characterization and sequencing centers; or
- The author receives specific approval from the TCGA Publication Committee in consultation with appropriate disease-specific analysis group(s).
Specifically, the status of each tumor dataset is available below. If you have questions, do not hesitate to contact tcga@mail.nih.gov.
Tumor Type | Data Status |
Breast cancer (BRCA) | No restrictions; all data available without limitations |
Clear cell kidney cancer (KIRC) | No restrictions; all data available without limitations |
Colon and rectal adenocarcinoma (COAD, READ) | No restrictions; all data available without limitations |
Endometrial cancer (UCEC) | No restrictions; all data available without limitations |
GBM | No restrictions; all data available without limitations |
Lung squamous carcinoma (LUSC) | No restrictions; all data available without limitations |
Ovarian (OV) | No restrictions; all data available without limitations |
Projects with limitations until specific dates or until a marker paper is published, whichever comes first. Please contact tcga@mail.nih.gov before publishing. | |
Lung adenocarcinoma (LUAD) | Publication limitations in place until 5/30/2013 |
Head and neck squamous cell carcinoma (HNSC) | Publication limitations in place until 6/14/2013 |
Papillary thyroid cancer (THCA) | Publication limitations in place until 7/17/2013 |
Cutaneous melanoma (SKCM) | Publication limitations in place until 8/15/2013 |
Stomach adenocarcinoma (STAD) | Publication limitations in place until 9/14/2013 |
Bladder cancer (BLCA) | Publication limitations in place until 12/27/2013 |
Lower Grade Glioma (LGG) | Publication limitations in place until 3/11/2014 |
Projects that have not yet shipped 50% expected cases; Please check with TCGA prior to publication. | |
Acute Myeloid Leukemia (LAML), Cervical (CESC), Diffuse large B Cell Lymphoma (DLBC), Esophageal Carcinoma (ESCA), Papillary Kidney (KIRP), Liver (LIHC), Pancreatic adenocarcinoma (PAAD), Prostate adenocarcinoma (PRAD) | Projects have not reached 100 cases; Please check with TCGA prior to any publication |
Use of TCGA Data in Publications Prior to Initial TCGA Global Analysis Publication
Researchers are free, and indeed encouraged, to publish results based on TCGA data. These results may include, but would not be limited to, integrating TCGA data with data from other sources, particularly in efforts to study the role of specific genes and genomic changes in the biology of cancer. Researchers also are encouraged to use TCGA data to publish on the development of novel methods to analyze genomic data related to cancer and genotype-phenotype relationships in cancer. This may include the application of these methods to portions of the data, for example, specific cancer subtypes, the role of specific genes or gene sets, or particular aspects of tumor biology.
The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) do not consider the deposition of data from TCGA, like those from other large-scale genomic projects, into its own Data Portal or public databases as the equivalent of publication in a peer-reviewed journal. Therefore, although the data are available to others, the producers consider these data as unpublished and expect that the data will be used in accord with standard scientific etiquette and practices concerning unpublished data.
Specifically, both TCGA and non-TCGA investigators using TCGA data that have not met a freedom-to-publish criterion per TCGA policy are asked to provide the TCGA Publications Committee and appropriate tumor-specific analysis groups with an abstract summarizing the findings and use of TCGA data. Authors will receive feedback on whether the TCGA Research Network requests that the findings be submitted in coordination with our marker paper of a specific tumor type or whether the submission can occur independent of a TCGA publication. This assessment may also apply to submission of manuscripts to journal editors. This request can be made via email to tcga@mail.nih.gov.
Use of TCGA Data in Publications after Initial TCGA Global Analysis (Marker Paper) Publication
There are no restrictions on the use of TCGA data to publish work after the initial TCGA global analysis publication. Once the TCGA Research Network has published tumor-specific analyses, no specific permission is needed for other investigators to publish using these data or future data generated on the same tumor type. Specifically, all data on that tumor type are released from any limitations as soon as the marker paper is published.
Use of TCGA Data for Research Purposes other than Publication
There are no restrictions on the use of TCGA data for legitimate research purposes not involving publication or public presentation. For example, researchers may use TCGA data in research grant applications or proposals at anytime, regardless of whether the initial TCGA global analysis has been published.
TCGA Program Attribution in Publications and Presentations
TCGA requests that authors who use data from TCGA acknowledge the TCGA Research Network in their work by properly referencing the TCGA dataset. Authors are also encouraged to recognize the contribution of the appropriate specimen donors and research groups via the acknowledgements section in their publication. Similarly, the TCGA Program requests that journal editors and reviewers attempt to ascertain if TCGA is cited and if appropriate acknowledgements are made.
For questions, please contact the TCGA Publications Committee through the Program Office at tcga@mail.nih.gov.
