Title: Illumina HiSeq 2000

THIS IS A COMBINED SYNOPSIS / SOLICITATION NOTICE. This is a combined synopsis / solicitation for commercial items, prepared in accordance with the format of FAR 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued.

The reference solicitation number is: NHLBI-CSB-(AR)-2011-169-CRS.

This solicitation is issued as a request for quotation (RFQ).

This acquisition is being conducted under the procedures in accordance with FAR 13.3 Simplified Acquisition Methods, and FAR Part 13.5 - Test Program for Certain Commercial Items.

The resultant purchase order will include all applicable provisions and clauses in effect through the Federal Acquisition Circular 05-50 April 15, 2011. The total contracted dollar amount, including options will not exceed $5 million.

The acquisition is being conducted as Full and Open Competition. The North American Classification System (NAICS) code applicable to this requirement is 334516, and the associated small business size standard is 500 Employees.

The National Institutes of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI), Office of Acquisitions (OA), on behalf of the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), intends to award a single, fixed priced contract for the purchase of the Illumina HiSeq 2000.

Description and Features - Sequencing by Synthesis:

Data Generation                 
Number of Reeds
•Up to one billion clusters passing filter enable the system to generate up to one billion reads per single-end run, or up to two billion reads per paired end run
•Each channel in the 8-channel flow cell generates up to 125 million paired-read tags

Throughput
•Up to 200 Gb of high-quality passing filter data per 2 x 100 bp run
•Up to 25 Gb of sequence data per day
•Generate one billion tags in less than two days for 1 x 50 bp run
•Generate two billion tags in less than five days for 2 x 50 bp run

Instrumentation
HiSeq 2000 physical specifications
• Benchtop instrument; W×D×H: 118.6 cm × 72.6 cm × 94.7 cm
Lasers
• A three-laser system with wavelengths at 532 nm, 660 nm, 780-840 nm for excitation and detection of fluorophores and autofocus calibration
Optical system
• Time Delayed Integration (TDI) line scanning and four CCD sensors provide high-resolution performance and fast data rate
• HiSeq 2000's optics enable dual surface imaging, allowing clusters on both the top and bottom of the flow cell to be processed
Reagent handling
• Reagent chiller compartment has capacity for two reagent racks, each containing enough reagents for 200 cycles of sequencing and indexing, plus capacity for paired-read reagents
• Reagents are premixed and drop 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 cells are held in place by a vacuum with the flip of a switch for simplified loading
• Flow cell loading dock contains a LED switch with positive feedback to ensure vacuum and fluidics are engaged
Instrument control computer
• Conducts real-time analysis 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 qualities derived directly from intensity data and not from a reference sequence-based, multiple-color encoding scheme
Flow Cells
• HiSeq 2000 can be operated in single or dual flow cell mode
• Each flow cell can be operated independently with different read lengths and run parameters
• Each flow cell can be stopped and started independently of the other flow cell
• Each flow cell is a substrate with eight channels for samples, providing physical separation without gaskets and without any reduction in sequencing output

Chemistry
• Sequencing reactions on up to 12 samples per flow lane is performed in a self-contained 8-channel flow cell environment
-HiSeq 2000 can simultaneously process 2 flow cells
• Competitive addition from a pool of all four reversible terminator nucleotides labeled with four different fluorescent dyes 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 be copied to generate complementary strand, enabling paired-end sequencing
• Forward DNA strands are be selectively washed out of the flow cell Sequencing reagents can be prepared in less than 15 minutes

Quality Control
• DNA sequence quality is ensured by integrated quality control steps upon incorporation of the first base

Sequencing Flexibility
• System can process two flow cells in parallel or independently with the same or different run parameters/read lengths
• Each flow cell can be stopped and started independently of the other
Sequential interrogation of bases allows flexible adjustment of read length during a run
• Supports read lengths up to 2 × 100 bp run on two paired-end flow cells

Sequencing Run time
Sequencing runs can be completed in:
• 1.5 days for a 36 bp single-read sequencing run
• 4 days for a 2 × 50 bp paired-read sequencing run
• 8 days for a 2 × 100 bp paired-read sequencing run

Daily throughput
• Up to 25 Gb of high-quality filtered bases per day on the sequencer (2 x 100 bp reads)

Instrument Control Software
• HiSeq Control Software (HCS) offers a simple interface to configure, launch, and monitor runs.
• HCS includes real time analysis (RTA) functionality that automatically produces image intensities and quality-scored base calls directly on the instrument computer.

Data Analysis Software
The RTA (Real Time Analysis) module in HCS (HiSeq Control Software) provides run-time feedback and generates base calls and quality scores as the run completes.
CASAVA (Consensus Assessment of Sequence and Variation) software produces consensus SNP and indel calls and RNA counts or aggregated data from many lanes of multiple flow cells.
GenomeStudio® software provides a single intuitive, graphical environment for analyzing data from a variety of sequencing and microarray applications including:
• DNA resequencing
• ChIP sequencing
• mRNA sequencing and transcriptome profiling
• Array-based DNA copy number analysis
• Array-based gene expression
• Genotyping

Sample Preparation
Same Preparation requirements
Genomic DNA sample libraries can be prepared in one 8-hour day or less by one full-time employee (FTE) for both single and short-insert (<500 bp) paired-end runs.
Sample Preparation Kits
Ready-to-use kits are available to prepare samples for:
• DNA sequencing (single or paired-end reads and mate pairs)
• Transcriptome sequencing (mRNA-Seq)
• Sample multiplexing with an unlimited number of index capabilities- 12 indexes per lane currently supported
Plus additional applications as developed.
Paired-End Read Support
Kits enable a unique combination of paired-end insert size ranges:
• 200-500 bp (short insert paired-end)
• 2-10 kb (long insert mate pairs)
Low Sample Input
• <1 μg DNA for genomic DNA sequencing applications (as low as 100 ng for many genomic DNA samples)
• As low as 10 ng DNA for ChIP-Seq applications
• <1 μg total RNA for small RNA sequencing applications
• <1 μg Total RNA for mRNA-Seq applications (as low as 100 ng for many total RNA samples)
• <1 μg DNA for bisulfite-converted DNA sequencing applications

Amplification
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
Amplification Sample Throughput
Genomic DNA sample library can be prepared in one 8-hour day or less by one full-time employee (FTE) for both single and short-insert (<500 bp) paired-end runs
Amplification Time
A single operator can amplify up to 96 samples or more on an 8-channel flow cell in 4 hours using a single cBot instrument. Amplification can be accomplished with less than 10 minutes of hands-on time, including reagent preparation
Cluster Generation
cBot performs 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
Whole-genome resequencing
Targeted resequencing including, but not limited to the following methods:
• Agilent SureSelect
• Microarray pull out (Agilent or Nimblegen arrays)
• 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
Metagenomics
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.

Evaluation Criteria
1. Provide preventive and corrective maintenance during the first year at no cost. (15 points)
2. Documentation provided on how the company will use original parts for replacement if needed. (15 points)
3. Provide technical support 24/7/365. (15 points)
4. An application field scientist is requested on NIH campus during weekdays. (15 points)
5. It is requested, that the company have the kits used for clustering and sequencing, in stock, and ready to ship, within 24 hours. (10 points)
6. The Contractor should be able to deliver the instrument on time, and schedule installation and calibration, within one week after receiving. (10 points)
7. It is requested, that the company take an Illumina GAIIx sequencer, and a Cluster Generation Station, as a trade-in for the purchase of the Illumina HiSeq2000. (20 points)

The Government's anticipated delivery date is May 2011. The FOB terms are "Destination" and Net 30.
The Government's delivery point is the National Institutes of Health (NIH), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, Maryland 20892.

The award will be made to the Offeror whose product meets the Government's minimum performance specifications, functional specifications, and delivery date. A best buy analysis will be performed taking into consideration price, shipping points, technical specifications, special features, trade-in considerations, probable life of the item selected as compared with that of a comparable item, warranty considerations, maintenance availability, environmental and energy efficiency considerations, delivery terms, and past performance. In addition to a price quote, the Offeror must submit descriptive literature of the product proposed, a commercial price list, warranty provisions, and any other information the Offeror considers relevant to the Government's evaluation of the product proposed. The Government intends to evaluate the quotes and award the purchase order without discussion with Offerors. Therefore, the initial offer should contain the Offerors best terms for a technical and price standpoint. However, the Government reserves the right to conduct discussions, request product samples or demonstrations, if later determined by the Contracting Officer to be necessary. The Government may reject any and all offers if such action is deemed necessary. The Government may also waive informalities and minor irregularities in the offers received.

NOTE: The Offeror must be registered in the Government's Central Contractor Registry (CCR) System, which is available at www.ccr.gov, in order to receive an award from the NIH, NHLBI.

FAR provisions and clauses that apply to this acquisition are: FAR 52.212-1, Instructions to Offerors-Commercial Items (JUN 2008); FAR 52.212-2 Evaluation - Commercial Items (JAN 1999); FAR 52.212-3, Offeror Representations and Certifications - Commercial Items (AUG 2009); FAR 212-4 Contract Terms and Conditions - Commercial Items (JUN 2010); FAR 52-212-5, Contract Terms and Conditions Required to Implement Statues or Executive Orders - Commercial Items (JUL 2010) is included with the following additional clauses: FAR 52.232-33, Payment by Electronic Funds Transfer - Central Contractor Registration (OCT2003); and FAR 52.204-7, Central Contractor Registration (APR2008).

The clauses are available in full text at http://www.arnet.gov/far.

Quotations will be due twelve (10) calendar days from the publication date of this synopsis or by May 13, 2011 9:00am, Eastern Standard Time. The quotation must reference Solicitation Number NHLBI-CSB-(AR)-2011-169-CRS. All responsible sources may submit a quotation/proposal, which if timely received, shall be considered by the agency. Interested vendors capable of furnishing the government with the item specified in this synopsis should submit their quotation to the below address. National Heart, Lung, and Blood Institute, 6701 Rockledge Blvd., Room Suite 6150B, Bethesda, Maryland 20892, Attention: Caitlin Savina. Emails will be accepted at [email protected].