SOLICITATION NOTICE
Q -- Microarray and Microarray Services
- Notice Date
- 8/14/2006
- Notice Type
- Solicitation Notice
- NAICS
- 621511
— Medical Laboratories
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, Nat'l Institute of Diabetes, Digestive, & Kidney Diseases, 2 Democracy Plaza, Suite 700W 6707 Democracy Blvd., MSC 5455, Bethesda, MD, 20892-5455
- ZIP Code
- 20892-5455
- Solicitation Number
- NIH-NIDDK-06-925
- Response Due
- 8/28/2006
- Archive Date
- 9/12/2006
- Description
- This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate written solicitation will not be issued. This solicitation number is NIH-NIDDK-06-925, and is issued as a Request for Quotation (RFQ). The solicitation/contract will include all applicable provisions and clauses in effect through Federal Acquisition Circular 2001-27. The North American Industry Classification (NAICS) Code is 621511 and the business size standard is $11.5 million. This acquisition is being conducted using Simplified Acquisition Procedures in accordance with FAR Part 13. However, this solicitation is not set aside for small business. It is the intent of the National Institutes of Health (NIH), National Institute of Child Health and Human Development (NICHD) to procure Microarray and Microarray Services for the NICHD Microarray Core Facility, from George Washington University c/o Yan A. Su. Scope of Work Microarray, Database and Bioinformatics for Gene Expression and Mutation Analyses 1. Microarray, Database and Bioinformatics Yan A. Su, Associate Professor of Biochemistry and Molecular Biology and Associate Director of Catherine Birch McCormick Genomics Center, the Department of Biochemistry and Molecular Biology, the George Washington University the School of Medicine has provided microarray, database, and bioinformatics services to the NICHD investigators for more than five years. Below are resource and work-scope established in Dr. Su?s laboratory for NICHD investigators conducting microarray, database and bioinformatics analysis of mRNA and protein expression, gene amplification and deletion, DNA methylation, promoter DNA-protein interaction, regulatory micro-RNA expression, and gene mutation studies. Dr. Su is responsible for maintaining his laboratory at the cutting edge in these fields, for developing resource, designing and fabricating microarrays for the NICHD investigators, and for developing, maintaining and updating algorithms, databases and bioinformatics tools for a large-scale analysis of gene expression and mutation in healthy and diseased cells. In addition, Yan A. Su and his colleagues are available to assist the NICHD investigators in microarray data analysis and technical assistance upon requests. The methods for the microarray technologies developed in Yan A. Su?s laboratory have been described in the recent publications1-4. 2. E.coli DH5 strain, Plasmid and PCR DNA Clones Related to Human and Mouse Genes for Microarrays Clones are available to NICHD investigators: 40,000 cDNA clones of human genes were purchased from Invitrogen (previous Research Genetics, Inc). The Contractor will update bi-monthly the gene names and descriptions corresponding to these clones based on Human Unigene database that is constantly updating as the Human Genome Project progresses. All the clones were sequence-verified by Research Genetics and do not need further verification for their sequence identities. Due to constant updates of Human Unigene database, it is recommend for researchers to verify the sequence and clone identities following the microarray identification of candidate genes. The NIA 15,000 and 7,400 mouse cDNA clones have been used to produce cDNA microarrays for the NICHD investigators. The mouse gene lists and information are available to the NICHD investigators and have been deposited into the NICHD Gene Expression Server, which is available by contacting Stanley Hornyak, the Computer Support Services at the NICHD. Gene lists and information will be sent to the investigators directly, upon requests. For genes not present in the collection, the NICHD investigators will have to provide DNA clones for microarrays. 9,000 CpG island DNA clones of human promoter sequences have been utilized to develop promoter DNA microarrays for the NICHD investigators to study transcription factor-promoter interactions, gene expression regulation, and DNA methylation on gene expression control, etc. NIH-BMAP Non-Redundant 38,000 mouse ESTs (37,459 clones) generated by the Brain Molecular Anatomy Project (BMAP) which is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major goals: (i) gene discovery: to catalog all of the genes expressed in the nervous system, under both normal and abnormal conditions. (ii) Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage and physiological state, and thus gain insight into gene function. In pursuit of these goals, M. Bento Soares has developed cDNA libraries from 10 regions of adult mouse brain, spinal cord, and retina. From these libraries, over 50,000 EST clones have been sequenced and clustered. The resulting 37,459 unique clones have been arrayed into the BMAP non-redundant collection. NIH-BMAP Non-Redundant 12,000 mouse Retina ESTs (11,864 clones). The mouse retina non-redundant set was generated for the NIH - University of Iowa Brain Molecular Anatomy Project: NIH-BMAP (M. Bento Soares, Thomas L. Cassavant, Val C. Sheffield). The clones in this set were chosen by applying the University of Iowa clustering method to sequences generated from Soares non-normalized, normalized, and serially subtracted cDNA libraries constructed from mouse neonatal, embryonic, and adult retina specific tissues. Tissues were provided by Dr. Xin-Yuan Fu, Yale School of Medicine. Therefore, we have a total of 40,000 human genes, 9,000 human gene promoter clones, and 72,000 mouse genes for DNA microarrays. Many of these clones have been used to designed and fabricate microarrays. In this case, plasmid DNA and PCR products are available for fabrication of microarrays. Clones are for gene mutations and/or polymorphisms: 287 customized oligos have been designed, synthesized and printed on glass slides for simultaneous detection of multiple gene mutations and/or polymorphisms, as requested by the NICHD investigators. Antibodies for protein microarrays: 10 antibodies against human proteins were purchased from commercial resource and have been used to develop protein microarrays, as approval of the principle study. Upon requests by NICHD investigators and approval by the NICHD Scientific Director, the contractor will be able to design and fabricate microarrays with customized antibodies for research projects. 3. Available Microarrays for Gene Expression and Mutation Analysis To support investigator's research projects, the contractor will have designed and fabricated high quality mouse and human cDNA microarrays. cDNA microarrays with mouse genes including: Generic arrays with the NIA mouse 23K sequence verified genes; Generic arrays with the NIA mouse 15K sequence verified genes; Generic arrays with the NIA mouse 7.4K sequence verified genes; cDNA microarrays with human genes including: Generic arrays with 40,000 human genes Generic arrays with 25,000 human gene Generic arrays with 12,288 human genes Generic arrays with 6,336 human genes Generic arrays with 1,056 cancer and proliferation related human genes Practice arrays with 288 human genes Customized arrays with 768 human cancer related genes Customized arrays with 244 human cell cycle related genes Customized arrays with 288 human hemostasis and thrombosis research Human XY chromosome gene chips for study of physiology and pathology Mouse XY chromosome gene chips for study of physiology and pathology Customized arrays with 400 human mitochondria-focused genes (hMito1) Customized arrays with 592 human mitochondria-focused genes (hMito2) Customized arrays with 1K human mitochondria-focused genes (hMitChip3) Microarrays with CpG island promoter DNA sequences of human genes: Generic arrays with 9K human CpG island promoter DNA clones Microarrays with oligo DNA of zebrafish genes: Customized arrays with 96 zebrafish gene Customized arrays with 16 zebrafish genes Microarrays with oligo DNA of genes for mutation analysis: Customized oligo DNA microarrays for simultaneous analysis of 28 mutations in 7 genes Microarrays with mirVana miRNA probe DNA for human and mouse MicroRNAs: MicroRNAs (miRNAs) are small, RNA molecules encoded in the genomes of plants and animals. They are highly conserved, approximately 21-mer RNAs regulate the expression of genes by binding to the 3'-untraslated regions (3'-UTR) of specific mRNAs. The mirVana miRNA probe set is a collection of 200 amine-modified DNA oligonucleotides complementary to every known human and mouse miRNA. Using the miRNA microarrays, one can analyze global miRNA expression profiles. Protein arrays with antibodies to human proteins: Customized arrays with 10 antibodies; The microarray images have deposited to the NICHD Gene Expression Server that demonstrate the quality of gene chips, that is, high signal intensities, low background signals, high signal to noise ratio, and broad distributions of signal intensities. 4. Databases and Data Analysis for Profiling Gene Expression Equipped with expertise, computer and software, we assist in database construction and expression data analysis outlined in the following sections: i) Expression database for data analysis. After obtaining a microarray image, the first step is to extract the expression ratio accurately. A widely used expression intensity and ratio extraction technique 5 has been successfully employed in many of studies 6-8 including studies conducted in Dr. Su's laboratory 1,2. Briefly, the expression data files contain bio-information including gene name, gene title, gene identification number, plate and array positions of genes, expression signal intensities, mean values, standard deviations, background intensities, signal to noise ratios, array qualities, hybridization qualities, expression ratios and calibrated ratios, and many others. The individual expression data file is linked to a master database for each research project. The master expression database is a relational database linked to the corresponding expression data files and unigene databases (human or mouse), and the public databases as well to facilitate high throughput analysis of gene expression. ii) Computing algorithm and software. The Contractor will develope a computing algorithm termed the local maximum clustering method that is applied for clustering analysis of microarray gene expression data.3 Based on this algorithm, the contractor developed software "LocaMaxCluster" for automated clustering analysis of gene expression profiles. In addition, we have developed computing tools including UniGDatabaseConverter v.l.0 and ArrayDataMiner v1.0 to facilitate high-throughput analysis of gene expression. iii) Analysis of expression data. To explore the similarity and dissimilarity between samples and genes, unsupervised and supervised clustering algorithms were applied 8,9. Briefly, genes in each microarray experiment were first filtered according to their measurement quality. After data filtering, standard hierarchical clustering algorithm 9 was applied and the clustering results were visualized by multidimensional scaling and dendrograms displaying techniques so as to give biologists intuitive information on relationship between samples and between genes. Applying the clustering algorithm to all samples in the given experiments may reveal multiple relationships between the samples under study. Clustering of genes based on their expression profiles will provide more hints for understanding of gene function and regulatory pathways. Results derived from the clustering algorithm can be validated by random permutation of sample labeling and/or leave-one-out cross-validation. The robustness of clustering results may be evaluated by adding additional noise into the data set and then observing the change of grouping effect. iv) Development of new algorithms. The Contractor developed hMitChip3, the third generation human mitochondria-focused gene chip4. To efficiently analyze expression profiles of data generated by use of the gene chips, contractor also developed customized computing procedures for extracting informative gene expression data from raw data4. The software is available to the NICHD investigators upon requests. The contractor also developed mutation gene chips for the NICHD investigators and we are going to develop algorithms and software for the gene chips to facilitate automated data analysis. v) Development of new database. All gene chips developed in my laboratory are unique, of which availability of database would accelerate data analysis. For example, contractor developed data files and database for hMitChip3 gene chips and database for hMitChip3 gene informatics to facilitate interpretation of microarray results4. All databases are for analysis of microarray gene expression or mutation and will be available to the NICHD investigators upon requests. 5. Available Database, algorithm and Software for Analysis of Gene Expression Data The computers, ScanArray microarray scanner and software (Microsoft Office, IPLab, FileMaker Pro, GeneSpring, Timbuktu Pro, MATLAB, ScanArray Express, and so on) have been provided by NICHD to Dr. Su?s laboratory. These resources will be used to acquire microarray images, to generate GAL, GIPO, or related files, to perform microarray quality tests, to generate gene databases, gene expression databases and to conduct gene expression data analysis. Because the equipment and procedures used in Dr. Su?s laboratory will be the same as those used in the NICHD and NCCAM laboratories, the variance from equipment and procedures will be minimized in order to increase the quality of the microarray data. To facilitate gene expression data analysis, the following microarray related information is available to investigators: (1) As our collaboration proceeding, the PI will develop and archive the information on DNA clones, genes, array configuration, GAL files and Gipo files for all DNA microarrays onto the NICHD gene expression server to assist the NICHD investigators in their research projects. (2) The materials, methods, and references for DNA microarrays will be archived on the NICHD gene expression server for investigators preparing their publications. In addition, upon requests, Dr. Su is available to offer training course to the NICHD investigators. The training information will be available to those who have no chance to attend training. (3) The information, templates, examples and quality controls for expression database and data analysis, along with brief instructions, were and will be stored onto the NICHD gene expression server to facilitate the research activities. (4) Databases for microarray data analysis include: Human unigene database Human unigene and clone ID link Human 46K gene database Mouse unigene database Mouse unigene and clone ID link Mouse 30K gene database Human mitochondria-focused microarray gene expression database Human and mouse XY-encoded gene database Human apoptosis, mitochondria and chromosome 6 gene expression database Human apoptosis, mitochondria and chromosome 17 gene expression database Human breast cancer gene expression profiling database Master database and individual data files tailored for rapid adaptation to investigator-initiated gene expression experiments analysis. hMitChip3 data files and database for compiling, filtering, browsing, displaying and visualizing gene expression profiles originated from data measured by using hMitChip3 gene chips. GenInform database for compiling, browsing, displaying and visualizing gene informatics including molecular functions, biological processes, cellular components, KEGG pathways, reactome events, genetic disorders, and PharmaGKB drug targets. The database relates gene expression changes to gene informatics, therefore it facilitates interpretation of microarray results. (5) Softwares for data analysis include: hMito2 gene expression data macro for automated filtering and extracting significantly differentially expression genes from microarray gene expression database; LMCI v1.0 to cluster gene expression profiles; Microarray gene expression data macro for standardized and automated filtering and extracting informative data from row data; UniGDataConverter v1.0 to fetch bio-information from unigene database in any combinations; LocalMaxCluster v1.2 to cluster gene expression profiles; ArrayDataMiner v1.0 to evaluate microarray data and to extract informative data from row data for further analysis of gene expression profiles; ArrayDataMiner v1.2 to evaluate microarray data and to extract informative data from row microarray data for further analysis of gene expression profiles hMitChip3 DataExtractor v1.0 to compute and extract informative gene expression patterns from microarray data measured by using hMitChip3 gene chips 6. Microarrays, Database, Algorithm and Software to be developed Under this research agreement/contract, contractor will develop customized gene chips requested by the NICHD investigators upon approval by the NICHD Scientific Director, Dr. Owen Rennert. In order to maintain our competitiveness in the cutting edge microarray technology, contractor would like to develop the following microarrays and relevant bioinformatics tools. We would like to develop microarrays for study of human mitochondrial diseases. After successful development of human mitochondrial gene expression chips (hMitEChip) for study mitochondrial diseases relevant to changes in gene expression, we would like to develop human mitochondrial gene mutation chips (hMitMChip). Our preliminary searching for public database indicated that there are 300 ? 500 genes with genetic disorders related to human diseases. The mutations of these genes will be selected, designed, printed and tested for hMitMChip. In addition, we would like to develop human mitochondrial siRNA gene chips (hMitSChip) to regulate gene expression on chips in cell culture so that effects of changes in a particular gene expression can be measured in a high-throughput fashion. Database, software and gene informatics for hMitEChip are in tests and will be published soon. Bioinformatics tools relevant to hMitMChip and hMitSChip ought to be developed along the corresponding microarrays. To increase an efficiency of research and reduce slide-to-slide variance, we would like to develop expression microarrays with approximately 30K non-redundant human genes per slide and approximately 30K non-redundant mouse genes per slide, and their related database, algorithm and software as well. One advantage of these microarrays is containing the almost entire genes of one species on the single gene chips and therefore, reduces slide-to-slide variance that would exist if these genes were printed on the separate chips. The contractor tested antibody arrays with commercial antibodies to detect protein expression. The technology will be used to make customized antibody microarrays if the investigators request and provide antibodies for. The contractor would like to develop genomic DNA microarrays for as many as 10K promoter DNA clones of known genes for research projects such as transcription regulation, gene-promoter interactions, and DNA methylation, etc. The related database and software will allow importing, exporting, organizing, displaying, browsing of promoter DNA sequences, controlled genes and their relationships. Contractor has also been developing diagnostic microarrays for expression and/or mutation analysis for translational research projects. Contractor would like to develop ?functional? microarrays to regulate gene expression on chips in cell culture at a large-scale in order to screen and categorize gene functions. This notice of intent is not a request for competitive quotations however, all responses received, within 15 days from the date of publication of this synopsis will be considered by the Government. A determination by the Government not to compete this proposed acquisition is based upon responses to this notice and is solely for the purpose of determining whether to conduct a competitive acquisition. The offeror must include a completed copy of the provision of FAR Clause 52.212-3, Offeror Representations and Certifications ? Commercial Items with its offer. The provisions of FAR Clause 52.212-4, Contract Terms and Conditions ? Commercial Items, applies to this acquisition. The addenda to the clause reads as follows: The offeror must include in their quotation, the unit price, the list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. The FAR Clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders ? Commercial Items ? Deviation for Simplified Acquisitions, applies to this acquisition. The clauses are available in full text at http://www.arnet.gov/far. Interested vendors capable of furnishing the government with the item specified in this synopsis should submit their quotation to the below address. Quotations will be due fifteen (15) calendar days from the publication date of this synopsis or August 28, 2006. The quotation must reference ?Solicitation number? NIH-NIDDK-06-925. All responsible sources may submit a quotation, which if timely received, shall be considered by the agency. Quotations must be submitted in writing to the National Institute of Diabetes and Digestive and Kidney Diseases 6707 Democracy Blvd., Room 775, Bethesda, Maryland 20817, Attention: Patricia Haun. Faxed copies will not be accepted.
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- SN01114113-W 20060816/060814220304 (fbodaily.com)
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