SPECIAL NOTICE
B -- Bio-Marker in MS
- Notice Date
- 12/14/2004
- Notice Type
- Special Notice
- NAICS
- 541690
— Other Scientific and Technical Consulting 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
- S05-010
- Response Due
- 12/27/2004
- Archive Date
- 1/11/2005
- Description
- Bio-marker in Multiple Sclerosis General Information Document Type: S = Special Notice Solicitation Number: SO5-010 Posted Date: DEC 14, 2004 Response Date: DEC 27, 2004 Archive Date: JAN 04, 2005 Classification Code: B -- Special studies and analysis - not R&D NAICS Code: 541990 Set Aside: N/A Contracting Office Address SAIC Frederick, Inc. P.O. Box B Frederick, Maryland Description SAIC Frederick Inc. intends to award Translational Genomics Research Institute a contract in support of The Biomarker in Multiple Sclerosis Study (BIO-MS) sponsored through NINDS. This study will be performed as anancillary study to a double-blind, multicenter (77 centers) combination treatment trial in MS patients. The trial will study 1000 patients over three years. Patients will be randomized after a baseline visit into treatment arms with interferon-beta (Avonex?), glatiramer-acetate (Copaxone?)(both approved therapies in MS; 250 patients in each arm) or the combination of the two drugs (500 patients). The Bio-MS study will address a number of questions that are related to identifying biomarkers that reflect the complex disease pathogenesis and clinical heterogeneity in MS patients, and also the treatment responsiveness or non-responsiveness. The main aspects of the intended award are: 1. Single nucleotide polymorphism polymorphism mapping with the largest available SNP platform (all 1000 patients; one examination); performed at TGen, Arizona 2. Gene expression profiling with the Affymetrix 133-Plus microarray platform (all 1000 patients, 4 time points); TGen, Arizona 3. Protein expression profiling by a combination of SELDI-TOF and LC-MS/MS (1000 patients, 4 examinations); performed at SAIC, Frederick 4. HLA-typing (class I and class II) (1000 patients, one examination); performed at the Department of Transfusion Medicine, Clinical Center, NIH 5. Storage of samples for additional studies on autoantibodies or other components. Performed at SAIC, Frederick; aliquoting of samples into multiple tubes necessary. 6. Data analysis of biomarker studies and linking with clinical and MRI data from the combination therapy trial (Combi-Rx). Performed by the IT Branch, NINDS, NIH. Notes: SAIC to handle Proteomics 1. SNP Genotyping SNP genotyping by internationally recognized field leaders (development site and/or center of excellence preferred) is required for a single 1,000 baseline clinical trial sample set. The platform of choice is the Affymetrix GeneChip? Mapping 100K Set. Samples will be provided from a repository facility, in accordance with the clinical trial schedule. The work scope is to include DNA isolation through to capture and analysis of data from the hybridized array chips using standard techniques. 2. Gene Expression Microarrays Gene expression profiling by internationally recognized field leaders (development site and/or center of excellence preferred) is required for a 1,000 baseline clinical sample set and two 1,000 sample time points at six months and one year. Appropriately stabilized samples will be provided from a repository facility in accordance with the clinical trial schedule. The work scope is to include RNA isolation through to capture and analyzed data from the hybridized array chips using standard techniques. 3. Data Processing/Interpretation a. Database Design The selected vendor should have extensive experience designing databases and processes for significant clinical trials with a genotyping component. The vendor should have worked with hospitals and other organizations involved with clinical trial data to ensure secure storage and transfer of confidential information. b. Microarray Data Management The selected vendor should have demonstrated industry leading storage and analysis capabilities for microarray experiments including gene expression and SNP genotyping. Expertise with automated methods that can re-annotate expression and microarray chips by integrating data from OMIM, LocusLink, dbSNP, TIGR?s Resourcerer System, and Vendor-annotations are required. c. Data Analysis The ability to integrate SNP and expression data is required. Any algorithms developed for such data integration should have been published and have demonstrated utility in the biomedical research community, particularly those members involved with clinical trials. For this purpose, the selected vendor will posses some or all of the following mathematical tools: small feature classifiers; biological context mining; discriminant predictors; multivariate clustering; coefficient of determination; correlation classification of SNP data; and genotyping methods including standard LOD, LD, and LOH analyses; advanced susceptibility analyses. Access to a highly parallel supercomputer for performing combinatorial and iterative calculations in a reasonable time frame is also required. d. Database Management The selected vendor?s analytical approach should include a federated biomedical database system that provides a local instance of relational databases for microarray expression, SNP, clinical, epidemiology, and others. This federation should use a metathesaurus like that of the NCI (http://ncimeta.nci.nih.gov/indexMetaphrase.html) to ensure consistency in biological and medical terms, and to provide a robust and cross-discipline database system. Ideally the selected vendor should be involved in or at least follow the NCI caBIG initiative, and when applicable adopt the standards being developed there. Primary Point of Contact Jane Wells, Senior Contract Specialist, Phone (301) 228 - 4023, Fax (301) 228 - 4003, Email jwells@mail.ncifcrf.gov Annette Bishop, Deputy Manager, Research Contracts, Phone (301) 644-2003, SAIC Frederick, Inc. P.O. Box B Frederick, Maryland Please Note; All questions must be submitted in writing.
- Place of Performance
- Address: SAIC Frederick, Inc. P.O. Box B Frederick, Maryland
- Zip Code: 21702
- Country: United States
- Zip Code: 21702
- Record
- SN00720976-W 20041216/041214211855 (fbodaily.com)
- Source
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