SOLICITATION NOTICE
D -- Bioinformatics S/W Services NCI TCGA
- Notice Date
- 6/15/2006
- Notice Type
- Solicitation Notice
- NAICS
- 541511
— Custom Computer Programming Services
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Bldg 427, Room 12, Frederick, MD, 21702
- ZIP Code
- 21702
- Solicitation Number
- S06-261
- Response Due
- 7/7/2006
- Archive Date
- 7/22/2006
- Description
- BACKGROUND A major challenge in cancer research, including the sequencing of ?cancer genes,? lies in its immense complexity. The many different tumor types, each with distinct subtypes, present radically different scientific and clinical challenges. This heterogeneity is in part understood to be related to the dynamic state of the cancer genome and the fact that tumors are complex systems characterized by chromosomal aberrations and nucleotide mutations, by their cellular and biological context and character, and by environmental influences. While certain similarities exist across various forms of cancer, a comprehensive effort to characterize tumor genomes must address the issue of heterogeneity systematically. Consequently, a cancer genome project needs to be multi-institutional, multi-sector, and inter-disciplinary to be successful. In 2004, the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) convened a workshop to consider a project to identify the full set of genetic changes in cancer, as an important step toward the NCI?s 2015 Challenge Goal of the elimination of suffering and death due to cancer. In the same year, Dr. Andrew von Eschenbach, Director, NCI requested that a working group of the National Cancer Advisory Board (NCAB) evaluate the status of advanced technologies in the context of NCI?s challenge goal. This subcommittee presented a series of recommendations to the NCAB that included a proposed genomic characterization and re-sequencing project that would be initiated through a pilot program and subsequently scaled up depending on the outcome of the first phase (http://deainfo.nci.nih.gov/Advisory/ncab/sub-bt/NCABReport_Feb05.pdf). Based on the recommendations from the report, the Directors of the NCI and the NHGRI agreed to pursue a three year pilot cancer genome characterization and sequencing project to determine the feasibility of a large-scale effort to identify most of the genomic changes associated with the wide array of diseases called ?cancer.? The project was subsequently named The Cancer Genome Atlas (TCGA). The aims of the 3-year pilot project are to demonstrate that a reasonably complete genomic characterization of a small number (two or more) of organ site specific tumor types and re-sequencing of selected targets can be efficiently and cost-effectively achieved; and to identify genes and/or regions of interest by combining information from genome analysis technologies and tumor biology (cancergenome.nih.gov). If successful, the results from the pilot program will provide both the basis for genomic analysis of a larger number of tumors, and generate a large set of data that will inform and benefit individual investigator-initiated studies to identify new targets for intervention, patient stratification in therapy, and possibly even prevention. Successful completion of TCGA pilot project, namely the achievement of established success factors and milestones to attain clinical impact, will be required before the concept of an expanded ?production phase? can begin to rapidly and efficiently generate a genomic ?atlas? for all major cancer types. Based on the NCAB Subcommittee?s recommendations and broad input from the scientific community, the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) agreed to support The Cancer Genome Atlas (TCGA) Pilot Project (http://cancergenome.nih.gov/). A joint staff-level planning and management structure for the project, the TCGA Project Management Group, has developed an overall approach and plan for the pilot project based on the NCAB Working Group Report on Biomedical Technology (http://deainfo.nci.nih.gov/Advisory/ncab/sub-bt/NCABReport_Feb05.pdf) and two workshops: Exploring Cancer through Genomic Sequence Comparisons (http://cgap.nci.nih.gov/Info/genomic_comparison) and Toward a Comprehensive Genomic Analysis of Cancer (http://cgap.nci.nih.gov/Info/TCGA_executive_summary.pdf). The overarching goal of the TCGA Pilot Project is to leverage the existing infrastructure, extant knowledge bases, and resources of the NCI and the NHGRI to conduct the high-throughput analysis of tumor genes and regions , from highly defined and annotated human cancer biospecimens of the highest quality. Genes and regions will be chosen based on the analysis and integration of data from multiple genome analysis platforms and informed by the context of the cancer biology conducted in Cancer Genome Characterization Centers. The key programmatic components of TCGA include: a biospecimen core resource (BCR); cancer genome characterization centers (CGCCs); genome sequencing centers (GSCs); a data coordinating center (DCC); technology development; and community portals. A schematic representation of the TCGA project is shown at http://cancergenome.nih.gov/media/process.asp. This SOW describes the requirements for the data coordinating center (DCC) component of the TCGA program. The DCC will be expected to adopt and implement systems and standards from the NCI?s Cancer Biomedical Informatics Grid (caBIG?) program (http://cabig.nci.nih.gov). caBIG? aims to create a broad federated network of interoperable biomedical information systems. The requirements for interoperability are defined in the caBIG? Compatibility Guidelines, which can be found https://cabig.nci.nih.gov/guidelines_documentation. Detailed requirements for caBIG Compatibility are given in TASKS below. OBJECTIVES This statement of work (SOW) describes four major objectives: In collaboration with representatives from TCGA data collection centers, including Genome Sequencing Centers (GSCs), Cancer Genome Characterization Centers (CGCCs), and Biospecimen Core Resource (BCR), establish and execute standard operating procedures for data transmission to the Data Coordinating Center. Design and implement data analysis procedures that perform quality checks on incoming data and report anomalies to the data source sites. Implement a data management pipeline to process data and prepare it for public distribution in formats and systems that are consistent with compatibility guidelines defined by the caBIG? program. Post the processed data to the publicly accessible distribution points immediately after quality checks and processing are completed. OVERALL TASKS The Contractor shall furnish the National Cancer Institute with professional service experts to create and support the activities of the TCGA Data Coordinating Center. These experts will work directly with representatives from other TCGA program centers to establish and execute program-wide procedures for data transmission, quality assurance checks, compliance with requirements for adoption of data standards, and other requirements related to the management, processing, aggregation, and distribution of TCGA program data. The Contractor staff will raise issues, conduct discussions, perform analyses, make recommendations, forge consensus, produce documentation, implement processes, and use their skills to achieve the Objectives of this SOW. The experts are expected to have knowledge and past experience with life science data analysis and management, including data from clinical annotations, tissue pathology reports, genetics, genomics and gene expression. Experience with high throughput methods for data quality analysis and compliance with data standards will be essential. Two categories of software are anticipated to be needed to carry out the tasks in this SOW. The first category includes scripts and programs to support data processing, analysis, and transformation, quality checks, and reporting. The Contractor will be expected to re-use existing public scripts, programs and software tools to carry out these functions, and develop new scripts, programs and tools as needed. Since this category of software is for internal processing purposes only, it is not expected to conform to caBIG? interoperability standards, though the data that is disseminated by the DCC will be need to be compliant (see ?caBIG Compatibility for Data Sets?, Section 7, below). The second category of software includes data management systems to support public access to the data after it has been fully processed by the DCC. This category of software will be expected to conform to caBIG? compatibility guidelines at the Silver level of compatibility. The DCC is expected to adopt existing caBIG compliant software systems that are currently being hosted at the NCI Center for Bioinformatics (NCICB). In cases where the NCICB is not already hosting a needed system, an existing caBIG?-compatible product with suitable functionality should be adopted and instantiated. These existing caBIG?-compatible software products may need to be extended to support TCGA requirements, in which case the Contractor shall leverage the caBIG? development methodology and tools associated with the caCORE Software Development Kit (SDK), which can be found at http://ncicb.nci.nih.gov/NCICB/infrastructure/cacoresdk. Entirely new software systems in this category are not in scope for this SOW. Any software developed with funding under this project must be released under an open-source license that complies with caBIG? licensing guidelines https://cabig.nci.nih.gov/working_groups/DSIC_SLWG/index_html/document_view The DCC may also deposit certain data types in non-caBIG? public repositories, such as those hosted by the National Center for Biotechnology Information (NCBI). Decisions about deposition in such non-caBIG repositories will be made in conjunction with the COTR and with NCI and NHGRI TCGA program management. To request a copy of this Request for Proposal (RFP), please contact Ms. Jane Wells, jwells@ncifcrf.gov.
- Place of Performance
- Address: NCI Center for Bioinformatics, 6116 Executive Blvd., Rockville, MD 20850
- Record
- SN01070464-W 20060617/060615220739 (fbodaily.com)
- Source
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