Illumina genotyping sequencer bnoe

THIS IS A SOURCES SOUGHT NOTICE. This is not a request for proposals. A solicitation will not be issued at this time. The Department of Veterans Affairs, New Mexico VA Health Care System (NMVAHCS) has a requirement for Brand Name or Equal Genotyping Sequencer. The intent of the procurement is to award a firm-fixed price contract. The below specifications define the minimum salient characteristics of the product to be delivered.
Required Items Brand Name or Equal:
Item
Description
QTY
MiSeq System
Illumina MiSeq System
1
Delivery charge
Delivery charge
1
In-Service
Per statement of work, to include initial installation, testing and standard one day training.
1
Statement of Work:
Background.
The Research Department has a requirement for ongoing VA studies to enhance the quality and delivery of care to the Veteran population through improved research capabilities and tests through improved technology in detecting mutations, microbiomes and RNA abundancies.
Scope.
NMVAHCS investigators and our Personalized Medicine eConsult Service requires developmental sequencing capacity that identifies genotypes, rare mutations, microbiomes and RNA abundancies. These results can then be implemented as CLIA certified clinical assessments at VISN 22 Central Genomics Laboratory. This instrument will benefit clinical and translational researchers from Medicine, Neurology, Behavioral health and Pathology, assist New Mexico Veterans in choosing VA, increase local availability of personalized and precision medicine and aid responses to the Secretary s priorities including overdose and suicide.
Specific Tasks.
This requirement specifically is a benchtop sequencer which allows the processing of samples to data in a relatively brief period of time, depending on the sample and data requirement(s).
Task. The instrument designed specifically for the processing and data collection of samples includes the following:
Instrument
Instrument footprint requires less than two square feet of benchtop space, less then 150lbs
Instrument control computer should be integrated in the sequencer no need for an additional computer purchase
Quad core CPU with 16 GB of RAM included for instrument control, processing images, and performing alignment and variant calling
Operates as a stand alone instrument, does not need to be connected to internet to function
Able to have 8 hour total turnaround time from purified DNA to direct variant reporting with less than 30 minutes total hands-on time
Hands-free, completely automated, on-instrument paired-end sequencing
Supports up to 2 Ã- 300 bp read length
Up to 15 Gb of high-quality data passing filter per 2 Ã- 300 bp run
Accurate variant detection by Sequencing by Synthesis (SBS) chemistry able to provide highly accurate sequencing even through homopolymeric regions. SBS chemistry is the demonstrated leader in data accuracy.
high quality score distributions at every read length [> 90% of bases with Q scores > 30 (1 Ã- 36 bp), 90% of bases with Q scores > 30 (2 Ã- 25 bp), > 85% of bases with Q scores > 30 (2 Ã- 100 bp), > 80% of bases with Q scores > 30 (2 Ã- 150 bp), > 75% of bases with Q scores > 30 (2 Ã- 250 bp), > 70% of bases with Q scores > 30 (2 Ã- 300 bp)]
With multiplexing, prepare >147,000 amplicons in a single day (96 samples Ã- 1536 amplicons per sample = 147,456 amplicons total).
Call variants in >147,000 amplicons in two days using standard lab equipment
Flexible amplicon sizes smaller to enable custom panel support for FFPE, and larger to take advantage of 2 Ã- 300 bp read lengths.
Multiplexed amplicon samples, designed for human and non-human genomes, can be loaded directly onto the machine
Variable length amplicon sequencing spanning hundreds to thousands of base pairs
Greater than 25 million reads per single-end run to enable small RNA sequencing and assay method development.
Greater than 15 Gb of output to allow multiplexed sequencing of viral and bacterial genomes in a single run
22-25 million reads per run (e.g. clusters passing filter)
13.2-15 Gb data per 2 Ã- 300 bp run
Set-up options include single-read or paired-end runs
Set-up options include imaging top, bottom, or both surfaces of flow cell
Flow cell options (e.g. original, micro or nano flow cells) can be used to select image area utilization and thus select data output levels
Read-length is fully adjustable from 36-300 base pairs
Overlapping 2 Ã- 300 bp reads provides ability to generate 550 bp reads on the same fragment
Flow cells
Single flow cell system
Each flow cell is a substrate with a single channel that can be imaged on either the top, bottom, or both surfaces as needed
Flow cells are auto-positioned and held in place by a clamping mechanism
Flow cells are keyed such that there is only one correct orientation
Reagent handling
Machine has a reagent chiller compartment with capacity for one reagent cartridge containing reagents for cluster generation, paired-end chemistry, and up to 600 cycles of sequencing
Reagents arrive pre-mixed in an integrated, RFID enabled, reagent cartridge
Sequencing synthesis chemistry
Uses reversible terminators and a highly efficient DNA polymerase
Use of a DNA polymerase that provides efficient addition of nucleotides with cleavable fluorescent dyes and reversible terminators
Sequencing reactions are performed in a self-contained single channel flow cell environment
Fluorescent dyes on the nucleotides are cleaved after imaging
Reversible terminators are removed to allow chain extension
Sequenced DNA templates are copied to generate complementary strands, enabling paired-end sequencing
Forward DNA strands are selectively washed out of the flow cell
Genomic DNA sample libraries can be prepared in.