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FBO DAILY - FEDBIZOPPS ISSUE OF JUNE 30, 2013 FBO #4236
SOURCES SOUGHT

99 -- DNA Sequencing Sytem, Assessories, and Supplies

Notice Date

6/28/2013
 

Notice Type

Sources Sought
 

NAICS

541711 — Research and Development in Biotechnology
 

Contracting Office

Department of Health and Human Services, National Institutes of Health, Office of Administration, 6011 Executive Blvd, 5th Floor, Rockville, Maryland, 20852-3804, United States
 

ZIP Code

20852-3804
 

Solicitation Number

HHS-NIH-OD-OLAO-SS-13-004
 

Point of Contact

Timothy Johnson, Phone: 301402-5450, Foteni - Tiffany, Phone: 301-402-3079
 

E-Mail Address

johnsontim@mail.nih.gov, tiffanyf@od.nih.gov
(johnsontim@mail.nih.gov, tiffanyf@od.nih.gov)
 

Small Business Set-Aside

N/A
 

Description

This Sources Sought Notice is in support of market research being conducted by the National Institutes of Health, National Eye Institute (Bethesda, MD) to identify capable manufacturing or distribution sources for an Illumina HiSeq 1500 Sequencing System, or better, meeting the specifications and capabilities, to be listed below. Compatible accessories, kits, and other supplies are also identified. This Sources Sought Notice is only for the purpose of identifying potential sources as part of NIH's market research mission. NO RFP EXISTS; therefore, do not request a copy of the RFP. This market survey is being conducted to reach the widest possible audience and to gather current market information. A determination by the Government not to compete this proposed contract based on responses to this notice is solely within the discretion of the Government. This is a Sources Sought Notice for information and planning purpose only and is not to be considered as a commitment by the Government. It is market research for a future equipment requirement. Your response to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. Any "Trade-In or Exchange of Government-owned Property" program for prior Illumina equipment products should be included in the vendor's capability responses. CAPABILITY STATEMENTS: JULY 13, 2013 AT 5 PM IS THE CLOSING DATE AND TIME FOR SUBMISSIONS. ALL INFORMATION SUBMITTED IN RESPONSE TO THIS ANNOUNCEMENT (BY EMAIL OR DELIVERY) MUST BE RECEIVED ON OR BEFORE THE CLOSING DATE AND THE DESIGNATED TIME. THE CLOSING DATE FOR RESPONSES IS DUE within 15 days of release of posting at 5PM Eastern Time (EST). Facsimile (faxed) will NOT be accepted. EMAILED CAPABILITY STATEMENTS are authorized (either in Microsoft Word or PDF), but it is the responsibility of the vendor to make certain that the email was received at the email address that follows. The government is not responsible for acknowledging receipt or capability statements sent by email, by mail, or courier. All capability statements, questions, and/or comments must be in writing and may be emailed to Timothy Johnson at johnsontim@od.nih.gov. (REFERENCE: HHS-NIH-OD-OLAO-SS-13-004) Comments and questions will NOT be answered, but will assist in creating a solicitation for this requirement. MAIL SUBMISSIONS: Three (3) copies of the capability statement are required if submission is via mail. Submissions via mail shall be sent to: Timothy Johnson (REFERENCE: HHS-NIH-OD-OLAO-SS-13-004), National Institutes of Health, Office of Acquisitions, 6011 Executive Blvd., Room 529W, (MSC-7663) Bethesda, MD 20892-7663. NOTE: If you are using a courier service, Federal Express, UPS, or Express Mail, the city, state, and zip code should read ROCKVILLE, MD 20852. Further Disclaimers and Important Notes: This notice DOES NOT obligates the Government to award a contract or otherwise reimburse vendors for cost involved with providing a response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work or deliver the required equipment or supplies. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will NOT be considered adequate responses to a solicitation. Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s). DESCRIPTION OF INFORMATION TO INCLUDE IN THE CAPABILITY STATEMENT: The North American Industry Classification System (NAICS) code for this requirement is 541711 (Research and Development in Biotechnology). All interested parties are invited to submit a tailored capability statement. The capability statement should reference Sources Sought Notice HHS-NIH-OD-OLAO-13-004 and should be no longer than 15 pages in length and shall include the following: (1) Name and Address of the organization (2) The size and type of business (3) Points of Contact with name, title, telephone, facsimile number, and email address. (4) DUNS Number (5) Contractor's capability statement that demonstrates the organizations ability, knowledge, and experience to provide equipment specifications that follow. (6) List of organizations and specific contracts specific to this requirement. Also include similar types of equipment, previously provided. Include contract number, dollar value, the name and the phone number of the contracting officer(s). (7) Do not submit pricing information, in response to this Sources Sought Notice. General Specifications: The Illumina HiSeq 1500 Sequencing System, or better, is an integrated platform that uses massively parallel sequencing technology for genetic analysis and functional genomics. It consists of the HiSeq 1500 sequencer, which uses TDI line scanning and dual surface imaging to generate up to 300 GB in a high output mode or up to 90 GB in a rapid run mode. Other components include an onboard template loading station that allows prepped libraries to be loaded directly on the system for rapid runs, an optional cBot template hybridization system, a suite of data collection and analysis software, and dedicated consumables. The onboard cluster generation module provides automated clonal amplification of single molecules randomly distributed on a glass surface, while the optional cBot cluster generation system allows users to double the level of multiplexing by template hybridization of different libraries in separate lanes of the sequencing flow cell. Resulting DNA clusters are sequenced on the HiSeq 1500 using Sequencing by Synthesis (SBS) method with patented reversible terminator chemistry. The Illumina HiSeq 1500 System, or better, will offers: - Scalability from 10 Gb to 300 Gb in a single run to support a broad range of applications and study sizes - Flexibility to switch between rapid run and high output run modes to suit user requirements - Single day runs including on board cluster generation in rapid run mode - Fully automated onboard cluster generation allows the ability to load prepped libraries directly on the instrument for rapid runs - Highest accuracy of any high throughput sequencing system - Proven SBS chemistry with single base extension allows accurate sequencing of homopolymers - Fully automated paired-end sequencing in rapid run mode or high output mode - Flexibility to process one or two flow cells at a time to suit throughput requirements - Greater than 3300 peer-reviewed publications have been published using Illumina SBS sequence data Sequencing by Synthesis (SBS): 1. Data Generation- Number of High Output Mode reads and thoughput: - Up to 1.5 billion clusters passing filter enable the system to generate up to - 1.5 billion reads per single-end run, or up to three billion reads per paired end run - Each channel in the 8-channel flow cell generates up to 375 million paired-read tags - Up to 300 Gb of high-quality passing filter data per 2 x 100 bp run - Up to 35 Gb of sequence data generated per day - Generate 1.5 billion reads in -2 days for 1 x 50 bp run - Generate three billion reads in less than five days for 2 x 50 bp run Number of Rapid Run Mode reads and thoughput: - Up to 300 million clusters passing filter enable the production of 300 million single- end reads or 1.2 billion paired-end reads - Each channel in the 2-channel flow cell generates up to 150 million paired-end reads 2. Instrumentation- - Lasers - A two-laser system with wavelengths at 532 nm and 660 nm for excitation, dynamic focusing, and detection of fluorophores. - Optical system Time Delayed Integration (TDI) line scanning and four CCD sensors provide high- resolution performance and fast imaging rate. Optics enable dual surface imaging, allowing clusters on both the top and bottom of the flow cell to be processed in both high output and rapid run mode - Reagent handling Reagent chiller compartment has capacity for one reagent rack, containing enough reagents for 200 cycles of sequencing plus indexing in high output mode and 300 cycles of sequencing plus indexing in rapid mode..Reagents are premixed and loaded into color coded reagent racks; reagent racks slide into the reagent chiller and are loaded by pulling down a sipper handle. - Flow cell loading Flow cell is held in place by a vacuum with a toggle lever for simplified loading. Flow cell loading dock contains an LED switch with positive feedback to ensure vacuum and fluidics are engaged - Sample loading Rapid run mode allows users to load libraries directly into the sequencer through an onboard template loading station - Instrument control computer Conducts real-time data processing that automatically produces image intensities and quality-scored base calls directly on the four-processor instrument computer. Sequence output contains accurate base calls and quality scores derived directly from intensity data and not from a reference, sequence-based, or multiple-color encoding scheme - Flow cells - A single flow cell system that can be upgrade to dual flow cell system. System operates in high output mode or rapid run mode. The flow cell can be stopped and started at any time. Sequencing reactions on up to 96 samples per flow lane are performed in a self-contained 2-channel or 8-channel flow cell. Each flow cell is a glass substrate with either two or eight channels for samples, providing physical separation without gaskets and without any reduction in sequencing output. Sequencing by synthesis chemistry uses reversible terminators and a highly efficient DNA polymerase modified to accept reversible terminator nucleotides. 3. Chemistry - - Competitive addition from a pool of all four reversible terminator nucleotides labeled with four different fluorescent dyes nearly eliminates homopolymer errors. - The DNA polymerase is modified for efficient addition of nucleotides with cleavable fluorescent dyes and reversible terminators. - Fluorescent dyes on the nucleotides are cleaved after imaging. - The reversible terminators are removed to allow chain extension. - Sequenced DNA templates are copied to generate complementary strand, enabling paired-end sequencing. - Forward DNA strands are selectively washed out of the flow cell. - Sequencing reagents can be prepared in less than 20 minutes. 4. Sample Preparation Kits - - Ready-to-use kits are available to prepare samples for DNA sequencing (single or paired-end reads and mate pairs) - Exome sequencing - Transcriptome sequencing (mRNA-Seq) - Directional RNA sequencing. - Sample multiplexing with up to 96 indexes per lane currently supported in TruSeq and Nextera Sample Prep kits. - Plus, support additional applications as developed. 5. Paired-End Read Support - - Kits enable a unique combination of paired-end insert size ranges: 200--500 bp (short insert paired-end) 3-15 kb (long insert mate pairs) 6. Low Sample Input - - Less than 1 g DNA for genomic DNA sequencing applications (as low as 100 ng for many genomic DNA samples) - 1 ug DNA with TruSeq DNA Sample Prep v2 - 50 ng DNA with Nextera DNA Sample Prep - 1 ng DNA with Nextera XT DNA Sample Prep - As low as 10 ng DNA for ChiP-Seq applications - 1 ug Total RNA for TruSeq Small RNA Sample Prep - < 1 g Total RNA for TruSeq RNA v2 Sample Prep Kit (mRNA-Seq) - 0.1ng-10 ng of total RNA with Smarter TM Ultra Low RNA Kit - < 1 g DNA for bisulfite-converted DNA sequencing applications Amplification: 1. Amplification Method - Solid-phase isothermal amplification to produce clonal single-molecule array clusters is completely automated, requiring no user intervention. No need for emulsion PCR. 2. Amplification Time - A single operator can amplify up to 96 samples per lane on the flow cell in -1.5 hours using onboard cluster generation. Amplification can be accomplished with less than 20 minutes of hands-on time, including reagent preparation. A single operator can amplify up to 768 samples or more on an 8-channel flow cell in four hours using a single cBot instrument. Amplification can be accomplished with less than 10 minutes of hands-on time, including reagent preparation. 3. Cluster Generation - The cBot and onboard clustering modules perform automated simultaneous clonal amplification of hundreds of millions of single molecule DNA templates producing clusters containing approximately 1,000 identical copies of each original DNA sequence. Applications: Targeted resequencing including, but not limited to the following methods: • Illumina TruSeq Exome Enrichment • Illumina TruSeq Custom Enrichment • Whole genome resequencing • Microarray pull-out (Agilent or Nimblegen assays) • Long-range PCR • Molecular inversion probes • De novo sequencing • De novo SNP discovery sequencing • ChiP-Seq of sequence-specific DNA binding proteins • ChiP-Seq of histone modifications and epigenetic marks • Sequencing of bisulfite-treated DNA to study DNA methylation • Metagehomics • Single cell sequencing • Full transcriptome analysis • Full-length mRNA sequencing • Tag-based gene expression • Small RNA profiling and discovery • Ribosome profiling • DNAse 1 hypersensitivity site mapping • Nucleosome positioning and chromatin structure studies • CLiP-Seq: studying sequence specific protein-RNA interactions • CNV-Seq: measuring copy number variation with sequencing • GRO-Seq: studying RNA polymerase initiation events • Prenatal screening from maternal blood • Sequencing of ancient DNA samples • Paired-end mRNA sequencing to study gene fusions in cancer • DNA imprinting and allele specific expression (Plus, additional applications, as developed.) Installation: Installation shall be included, within the capability statements. Delivery: The government requires delivery to made within 90 days from the date the contractor receives an order. The government will evaluate, as regards to time of delivery, offerors that propose delivery within the applicable delivery period specified above. Offeror's that propose delivery that will not clearly fall within the applicable anticipated delivery period specified above will also be considered. The Government reserves the right to award either the anticipated delivery schedule or the proposed delivery schedule.
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/OoA/HHS-NIH-OD-OLAO-SS-13-004/listing.html)
 

Place of Performance

Address: National Institutes of Health, Bethesda, Maryland, 20892, United States

Zip Code: 20892
 

Record

SN03103165-W 20130630/130628235142-a4c4cf63d88285266ed177810ca3da81 (fbodaily.com)
 

Source

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

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