Illumina NextSeq 2000 Sequencing System

THIS IS A PRE-SOLICITATION NON-COMPETITIVE (NOTICE OF INTENT) SYNOPSIS TO AWARD A CONTRACT WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION.

This acquisition is conducted under the authority of 41 U.S.C. 253(c) under provisions of the statutory authority of FAR subpart 6.302-1. 

The National Heart, Lung, and Blood Institute (NHLBI) intends to award without providing for full and open competition to Illumina, Inc for the Illumina NextSeq 2000 Sequencing System

It is anticipated that one award will be made from this notice.

BACKGROUND

The National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) Genomic Technology Section (GTS) is charged with providing genome-scale, high throughput data generation for researchers within the Institute.  The Core Facility, like most other Institutes at NIH and sequencing centers around the world, adopts new emerging technologies to maintain the leading edge on genomics and epigenomic research areas. Among them are Illumina platforms introduced in 2017 to support the program’s sequencing needs. 

Currently, the Core Facility has the three (3) Illumina sequencers, the NovaSeq 6000, MiSeq and NextSeq 550.  All can accommodate different sequencing size runs and applications. The MiSeq, the NextSeq 550 and the NovaSeq 6000 support a data output of 15, 340 and 6000 Gigabases (GB) respectively while sharing the same patented technology and sequencing chemistry. The sequencers  are 100% compatible with NIAMS existing infrastructure, space, previous data, and computational needs. Due to the increase demand for sequencer allotted times and data output, GTS is proposing to replace Illumina’s NextSeq 550 purchased in 2019 (75N2019P00304) with  Illumina’s NextSeq 2000.

Throughout the years, the Illumina technology has proven to ideally serve the needs of NIAMS investigators due to the variety of applications supported by the manufacturer and the variable demands of GTS program researchers. Illumina is the dominant sequencing technology on the market today without comparable equipment, and the only known equipment that meets the needs of NIAMS investigators. GTS is procuring the Illumina NextSeq 2000 Sequencing System because of its capability delivering higher daily throughput (up to 360 GB) at a fastest pace and lower price per sample without the need of additional space, when compared to the NextSeq 550, but also due to the variety of applications supported and difference in maximum data output, in contrast to the NovaSeq 6000 and the MiSeq.  GTS intends to trade-in the existing Government-Owned Illumina NextSeq 550 for the purchase of the Illumina NextSeq 2000 Sequencing System. 

TYPE OF ORDER

This will be a Firm Fixed-Price Purchase Order.

SPECIAL ORDER REQUIREMENTS

The Contractor must accept the existing equipment for trade-in.

Brand: Illumina

Model: NEXTSEQ550

S/N: HFJZJBGXC

PRODUCT FEATURES/SALIENT CHARACTERISTICS

The following product features/characteristics are required for this requirement:

Single, integrated instrument

Single instrument performs clonal amplification, sequencing, paired-end turn and primary data analysis (e.g. base calling)

Alignment, variant calling, and reporting are supported in BaseSpace

Footprint requires less than two square feet of benchtop space

No need for dedicated ancillary amplification system or computing/IT infrastructure

Hands-free, completely automated, on-instrument paired-end sequencing

Run Times

11 hour total sequencing with less than 10 minutes total hands-on time

10 minutes hands-on time for run set up (amplification, paired-end sequencing)

11-hour sequencing time (1 × 50 bp) including on-instrument cluster generation, sequencing run and automated post-run wash

Output

360 Gb data per 2 × 150 bp run using (P3) High Output flow cell and reagents

120 Gb data per 2 × 150 bp run using (P2) Mid Output flow cell and reagents

30 Gb data per 2 × 150 bp run using (P1) Low Output flow cell and reagents

Up to 1.2 billion reads per run (e.g. clusters passing filter) using High Output flow cell

Up to 100 million reads per run (e.g. clusters passing filter) using Low Output flow cell

Capable of sequencing a 30× human genome in a single run

Flexibility

Multiple flow cell and reagent configurations enable sequencing of 30–360 Gb per run

Up to 2.2 billion single read clusters (2.4 billion paired-end reads) passing filter in the High Output configuration enable up to 360 Gb per run in a single run

Up to 400 M single-read clusters (800 M paired-end reads) passing filter in the Mid Output configuration enable up to 120 Gb per run

Up to 1.2 B single reads enables gene expression profiling and cytogenetic applications

Variable length amplicon and enrichment panels spanning hundreds to thousands of base pairs

Cost-effective, flexible options for sequencing runs with smaller number of samples using Mid Output kits

Set-up options include single-read or paired-end runs

Flow cell options (e.g. Low, Mid, or High Output flow cells) can be used to select data output levels

Read-length is fully adjustable up to 300 base pairs

Accurate data quality

Accurate variant detection- competitive nucleotide addition with a proprietary reversible terminator technology allows for highly accurate sequencing, even though homopolymeric regions.

High-quality score distributions- > 85% of bases with Q scores > 30 (2 x 150 bp)

Physical specifications

Desk-top instrument; W×D×H: 60 cm × 65 cm × 60 cm

Weight: 83 kg (310 lbs)

Illumination

12 light-emitting diodes at 449nm, 523 nm, 820 nm

Reagent handling

Reagent compartment has capacity for two reagent cartridges containing reagents for cluster generation, paired-end chemistry, and up to 300 cycles of sequencing

Reagents arrive pre-mixed in an integrated, RFID enabled, reagent cartridge

Sample loading

Libraries are loaded directly into the sequencer through an onboard template loading station

Flow cells and loading

Dual flow cell system

Each flow cell is a substrate with a single channel that can be imaged on both the top and bottom surfaces

Flow cells are auto-positioned

Flow cells are keyed such that there is only one correct orientation

Instrument control computer

Instrument control computer is integrated in the sequencer—no additional computer purchase is required

Base Unit: 2U Microserver

Memory: 288 GB

Hard Drive: 3.8 TB SSD

Operating System: Linux CentOS 7.6

Conducts real-time analysis processing that automatically produces image intensities and quality-scored base calls directly on the instrument computer

Sequence output contains accurate base calls and qualities derived directly from intensity data and not from a reference, sequence-based, or multiple-color encoding scheme

Operational environment

Temperature: 15℃ to 30℃

Humidity: Non-condensing 20-80% relative humidity

Power Requirements

Instrument Input Voltage: 100-240 VAC

Instrument Input Frequency: 50/60Hz, 10A

DELIVERY / INSTALLATION

Equipment must be delivered and installed at the address below within 30 days of purchase order award.

POC: Will be provided at the time of award

            Address: NIAMS / Genomic Technology Section

            Building 50, Room 1342

            9000 Rockville Pike, Bethesda, MD 20892

TRAINING

Instrument training should occur within seven days of installation for four (4) users

PAYMENT

Payment will be made after equipment, installation and training is accepted and within 30 days after invoice is received.

CLOSING STATEMENT

This synopsis is not a request for competitive proposals.  However, interested parties may identify their interest and capability to respond to this notice.

A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government.  The information received will normally be considered solely for the purposes of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement.  

All responses must be received by July 12, 2022 by 12:00PM EST. Responses must be submitted via electronic mail to Kimesha Leake, Contracting Officer at Kimesha.leake@nih.gov Please include notice number 75N92022Q0388 in the subject line of the communication.