SOLICITATION NOTICE
99 -- DNA Sequencing System, Accessories, and Supplies
- Notice Date
- 7/26/2013
- Notice Type
- Presolicitation
- 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
- NIHOD2013437
- 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
- The National Institutes of Health (NIH), Office of the Director, on behalf of the National Institute on Deafness and Other Communication Disorders (NIDCD), intends to solicit and negotiate on a non-competitive basis, with only one source, Illumina, 5200 Illumina Way, San Diego, CA 92122 for a DNA Sequencing System, Accessories, and Supplies. The cited authorities are 41U.S.C. 253(c) (1), as set forth in FAR 6.302-1. The National Institute on Deafness and Other Communication Disorders (NIDCD) currently performs genome-wide linkage scans and RNA expression array studies using an Illumina Bead Array Reader. Organizations having demonstrated experience in providing this type equipment above requirements are invited to submit capability statements. Capability statements must document the following: 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, or better, using Sequencing by Synthesis (SBS) method with patented reversible terminator chemistry. The Illumina HiSeq 1500 System, or better, will offer: - 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. - TRADE-INs: Customer (NIDCD) is to be granted trade-in values for the following: 1. AB Solid 5500, Sequencer, 2. Illumina 11182022 Bead Array Reader System; Reader/Analyzer 3. Two (2) computers and two (2) monitors. Delivery: The government requires delivery to made within 90 days from the date the contractor receives an order. Capability Statements submitted in response to this notice that do not provide sufficient information for review will NOT be considered. This is NOT a Request for Proposals (RFP), and responses should NOT include budgetary information. Respondents to this notice shall provide capability statements (one original and three (3) copies) no later than 5:00 p.m. EST on Aug 2, 2013 to Timothy Johnson (Ref. NIHOD2013437), National Institutes of Health, Office of Acquisitions, 6011 Executive Blvd., Room 529W (MSC 7663) Bethesda, MD 20892-7663. PLEASE NOTE: If you are using a courier service, Federal Express, or UPS, the city, state, and zip code should read ROCKVILLE, MD 20852). Please be aware that the U.S. Postal Service's "Express Mail" DOES NOT deliver to the Rockville, Maryland address AND delivery to the Bethesda, Maryland address will result in a delayed delivery to our office in Rockville, MD (up to 3 - 5 days). Email and facsimile copies will not be accepted. Note: This synopsis follows Sources Sought Notice HHS-NIH-OD-OLAO-SS-13-004 that was released on June 28, 2013. Disclaimer: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Respondents are advised that the Government is under no obligation to acknowledge receipt of information received or provide feedback to respondents with respect to any information submitted.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/OoA/NIHOD2013437/listing.html)
- Place of Performance
- Address: National Institutes of Health, Bethesda, Maryland, 20892, United States
- Zip Code: 20892
- Record
- SN03128515-W 20130728/130726234637-96102815db43bb36411e537e86a3468d (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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