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FBO DAILY ISSUE OF MAY 15, 2003 FBO #0532
SOLICITATION NOTICE

B -- Analysis and database of human genes with potentially destabilizing structures

Notice Date

5/13/2003
 

Notice Type

Solicitation Notice
 

Contracting Office

Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Research Contracts Br., 6120 Executive Blvd. EPS Suite 600, Rockville, MD, 20852
 

ZIP Code

20852
 

Solicitation Number

NCI-30056-NG
 

Response Due

5/28/2003
 

Archive Date

6/12/2003
 

Point of Contact

Malinda Holdcraft, Purchasing Agent, Phone (301) 402-4509, Fax (301) 402-4513, - Renita Smith, Contract Specialist, Phone 301-496-8612, Fax 301-480-0241,
 

E-Mail Address

holdcram@exchange.nih.gov, rs442i@nih.gov
 

Description

The National Cancer Institute (NCI) Center for Cancer Research (CCR), Laboratory of Biosystems and Cancer (LBC) plans to procure services for analysis and preparing a database of human genes with young small interspersed elements (SINE) and large interspersed elements (LINE), evaluating age of the elements and annotating evolutionary young interspersed elements in available sequences of non-human primates. with Genetic Information Research Institute, 1190 Eureka Ave., Los Altos, California, 94024. The supplies and services herein are being prepared in accordance with the authority authorized in FAR Part 13. The North American Industry Classification System Code is 541380 and the business size standard is $6M. Alu family of short interspersed elements (SINEs) is a large family of mobile elements that have expanded to a copy number of 1,500,000 within the last 65 million years of primate evolution. Two of the most recently formed subfamilies of Alu elements have been termed Ya5 and Yb8. Alu transposition is an ongoing process that continues this very day. One of the main projects in LBC relates to Human Genome Initiative and includes isolation and characterization of gene homologs from great apes. The goal of this project is to study gene evolution in primates and to clarify a role of Alu repeats and other types of repetitive DNAs in genome stability, gene expression, and predisposition to certain diseases. To achieve these goals preparing a database of human genes with young Alu and LINE integrations, evaluating age of the repetitive elements and annotating Alu and other young elements in available sequences of non-human primates is required. In addition, comparative analysis of entire gene homologs from primates is needed for specific genes containing young Alu integration. Detailed analysis of these DNA sequences will shed light on the gene evolution in primates and also provide information on role of Alu elements and other type of repeats in gene expression and stability. More than one million SINE and LINE sequences will be analyzed. Contractor Requirements: The analysis includes the following steps: 1) Prepare a database of human genes with potentially destabilizing structures resulting from: integration of young Alus and LINEs elements. From this dataset two sets shall be selected: (i) all genes with recent insertion of transposable elements and (ii) all genes harboring two or more highly similar copies of repetitive elements. The database shall contain gene annotation and detailed description of potentially destructive interspersed repeats. The database shall be prepared in two formats: in the simple text format and in the standard database format SQL. The contractor shall use a public database system MySQL, widely used in genome annotations including Ensembl and UCSC GoldenPath; 2) Evaluate approximate age of all Alu Y elements in human genome and determine genes that have been targeted by retransposons approximately 5 Myr ago (date of divergence between human and chimpanzee), and after. For this purpose a dataset from contractor requirement (1) shall be used. For every recent elements (Alu, LINE1, endogenous retroviruses) contractor shall estimate the age using divergence from the family consensus sequence (Alu, LINE1) or divergence between two long terminal repeats (retroviruses). In the case of Alu elements, CpG content shall be evaluated. This shall be combined with data on polymorphisms of repeats in the population, if available, using published works. The database shall be prepared in the simple text and SQL database formats; 3) Annotate Alu and other young repetitive DNA elements in available sequences of non-humanprimates. Genomic sequences of other primates will be annotated for repetitive elements using Censor with Repbase Update libraries. The data shall be released as text and SQL. All genomic segments from primates shall be aligned with human genomic DNA. These alignments will be a basis for detection of all point mutations and indel breakpoints. The alignments shall be prepared by programs tailored for large genome alignments such as AVID or OWEN and; 4) Prepare a detailed annotation and analysis of repetitive DNA and unstable regions in human genes based on comparison with great apes gene homologs isolated in LBC, CCR, NCI. The annotation shall include the following human disease genes: DRD3 gene encoding dopamine receptor D3, breast cancer genes BRCA1 and BRCA2, NBS1 gene responsible for Nijmegen breakage syndrome, tumor suppressor TP53, and ASPM gene that is a major determinant of cerebral cortical size. The analysis shall be prepared as in (contractor requirement 3): first, identification of repetitive elements by Censor, then multiple sequence alignment with AVID or OWEN. The data shall be produced as text and SQL and alignment in the multiple Fasta format. All mutations and indels shall be highlighted and annotated in detail. This strategy should predict majority of potential at-risk motifs in the genes of interest. Genetic Information Research Inc. is the only source known to the NCI that can provide the aforementioned services. Dr. Jerzy Jurka is the Director of Genetic Information Genome Institute. Dr. Jurka is a world-recognized expert on interspersed elements in mammals. Based on his pioneering works, SINE and LINE groups of small and large interspersed elements were identified in human and mouse genomes and further were classified. This notice of intent is not a request for competitive quotations. However, if any interested party believes it can meet the above requirements, it may submit a statement of capabilities. The capability statement and any other furnished information must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can fully meet the requirements herein. Capability statements must be received in the contracting office by 1:00 PM EDT (local Washington DC time) on May28, 2003. If you have any questions, please contact Malinda Holdcraft, Purchasing Agent via electronic mail at holdcram@exchange.nih.gov or by fax 301-402-4513. A determination by the Government not to compete this proposed requirement based on responses to this notice is solely within the discretion of the Government. Information received shall be considered solely for the purpose of determining whether to conduct a competitive requirement. No collect calls will be accepted.
 

Place of Performance

Address: NIH/NCI, Bethesda, MD

Zip Code: 20892

Country: USA
 

Record

SN00322972-W 20030515/030513213333 (fbodaily.com)
 

Source

FedBizOpps.gov Link to This Notice
(may not be valid after Archive Date)

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