CGCI Publication Guidelines
Like other National Cancer Institute large-scale genomics initiatives, the Cancer Genome Characterization Initiative (CGCI) is a community resource project. After validation, data are rapidly made available for use by other researchers. To act in accord with the Fort Lauderdale principles and support the continued prompt public release of large-scale genomic data prior to publication, researchers preparing manuscripts that (1) contain descriptions of CGCI data and/or (2) are of comparable scope to an initial CGCI disease-specific comprehensive global analysis publication, are required to coordinate their independent reports with CGCI's publication schedule. Journal editors who receive such manuscripts are strongly encouraged to contact the Office of Cancer Genomic (OCG; firstname.lastname@example.org) to ensure that their publication timeline is in line with CGCI.
Comparable scope is defined as global genome-wide analysis of CGCI disease-specific data or data across diseases from one or more platforms (for disease types that encompass CGCI subprojects, see table below). As described below, publications of comparable scope are restricted prior to the release of first disease-specific manuscript.
As a general reminder, all use and publications based on CGCI data are required to follow the Data Use Limitations outlined in the CGCI Data Use Certification at the database of Genotypes and Phenotypes (dbGaP).
Use of CGCI Data in Manuscripts Prior to Publication of Initial CGCI Disease-Specific Integrated Analysis
Similar to standard practices of other large-scale genomic projects, the National Cancer Institute does not consider the deposition of CGCI data 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 Therefore, although the data are available to others, the data producers consider these data as unpublished and expect that the data will be used in accord with standard scientific etiquette and practices concerning unpublished data.
The first paper authored by each CGCI subproject team (https://ocg.cancer.gov/programs/cgci/projects) includes the data and analysis from a majority (~90%) of qualified CGCI cases. Specifically, these manuscripts report on the comprehensive, integrated analysis of multiple CGCI subproject datasets, including, but not limited to:
- Copy number variation, gene and miRNA expression, structural variants and DNA sequence/mutation analysis or a combination thereof; or
- An analysis of data from a single platform across more than one tumor type, where not all the subproject teams have published their first comprehensive analyses papers for the tumor types being analyzed
Investigators may only publish a manuscript before the CGCI subproject team has published the global analysis on that tumor type IF the publication uses a very limited dataset (less than 5 genes). Investigators should submit their abstract and request to OCG by emailing email@example.com.
Prior to the publication of comprehensive analysis on a specific tumor type, available datasets are subject to the same standard principles of scientific etiquette that apply to use of unpublished findings from other sources. Below is the list of tumor datasets that are available for use now. The list will be updated when the first global manuscript for each tumor is accepted for publication. For questions, do not hesitate to contact firstname.lastname@example.org.
|Tumor Type/ Data Use Limitation||Subproject Status||Data Availability Status|
|Burkitt lymphoma/ general research use (Data Use Limitations for some cases are being confirmed.)||Pediatric BL study is complete. Adult cases are in progress.||Pediatric whole genome sequencing, RNA-seq and miRNA-seq data are available at NCI's Genomic Data Commons (GDC) and OCG Data Coordinating Center (DCC). EBV sequences are available as BAM alignments from the public directory at the DCC.|
|Non-Hodgkin lymphoma/ cancer research only||Complete||Open access (analyzed) and controlled access (upper level files e.g. VCF or MAF) mRNA-seq data, whole exome, and whole genome sequencing data are available at OCG DCC. Controlled access aligned sequence reads (BAM files) from mRNA-seq, whole exome and whole genome sequencing data are available at NCBI’s Sequence Read Archive (SRA).|
|HIV+ associated cervical cancer/ general research use||Complete||
Controlled-access whole genome sequencing, RNA-seq, miRNA -seq and targeted sequencing data are available at NCI's Genomic Data Commons (GDC). Controlled-access ChIP-Seq data and open-access methylation array data are available at the DCC. Both open and controlled-access higher level (analyzed) sequencing data are available at OCG DCC.
Note: The project includes cases from both HIV+ and HIV- cervical cancer patients.
|HIV+ associated lung cancer/ general research use and cancer research only||In progress||To be determined.|
|HIV+ associated diffuse large B cell lymphoma/ general research use||In progress||To be determined.|
Use of CGCI Data in Manuscripts After Each Initial CGCI Disease-Specific Global Analysis Publication
There are no restrictions on the use of CGCI data in manuscripts after the initial CGCI global analysis publication if the data are used specifically within the Data Use Limitations.
If data are used within the Data Use Limitations, there are no restrictions on the use of CGCI data for legitimate research purposes not involving publication or public presentation. For example, researchers may use CGCI data in research grant applications at any time with appropriate acknowledgement (see below), regardless of whether the initial CGCI disease-specific global analysis has been published.
OCG requests that authors who use data from CGCI acknowledge the appropriate subproject team(s) in their work by referencing the CGCI dataset in accordance with the CGCI Data Use Certification at dbGaP. Inclusion of CGCI subproject team members as authors is not required.
If investigators desire to collaborate with CGCI members, they should contact the specific subproject team. Authors are also encouraged to recognize the contribution of the appropriate specimen donors and research groups via the acknowledgements section in their publication. Similarly, OCG requests that journal editors and reviewers attempt to ascertain if CGCI is cited and if appropriate acknowledgements are made.
For questions, please contact the OCG by emailing email@example.com.