Sole_Source_Synopsis_-_FedBizOpps.docx

NAICS: 334516 (Analytical Laboratory Instrument Manufacturing)

PSC: 6640 (LABORATORY EQUIPMENT & SUPPLIES)

Proposed Vendor: Illumina Duns# 033305264 Synopsis: THIS IS NOT A REQUEST FOR COMPETITIVE QUOTES. This is a notice of intent to award a sole source purchase order under Federal Acquisition Regulation Part 13.106-1(b). The Environmental Protection Agency (EPA), National Health and Environmental Effects Research Lab (NHEERL), Western Ecology Division (WED) intends to purchase The MiSeq System and MiSwq reagents/kits from Illumina Inc.

The EPA currently has a MiSeq System integrated workstation within the Research Core Unit (RCU) that is being utilized in experiments conducted by the Western Ecology Division (WED). An additional MiSeq System is now needed at WED in order to expand experimental capability while maintaining compatibility, Quality Assurance and Quality Control of data generated at the RCU and WED. The MiSeq is designed specifically for automated generation of DNA clonal clusters by bridge amplification, sequencing, primary and secondary analysis. The system includes an embedded touchscreen monitor and on-instrument computer, dual surface imaging capability, MiSeq Software Suite, installation, installation kits, standards, training, and a 12 month warranty.

Salient Characteristics required are as follow:

1) The system must be a single integrated workstation that performs clonal amplification, sequencing, and data analysis (e.g. basecalling, alignment, variant calling, and reporting).

2) The instrument footprint ≤ two square feet of benchtop space.

3) The system shall not require dedicated ancillary amplification system or computing/IT infrastructure.

4) The system must have an 8 hours or less turnaround time from purified DNA to direct variant reporting and less than 30 minutes hands-on time.

5) The system must have accurate variant detection enabled by proven chemistry.

6) The system must support up to 2 X 300 bp read length.

7) The system must have throughput capability per run of 13.2-15 Gb (on 2 × 300 bp runs).

8) The system must be capable of producing data with Quality (Q) scores of > 85% of bases with Q scores > 30 (on 2 × 100 bp runs) and > 70% of bases with Q scores > 30 (on 2 × 300 bp runs).

9) The system must have a proven track record in the industry and use in peer reviewed publications.

10) The system must have a fully optimized, highly multiplexed amplicon and sample assay for targeted resequencing.

11) The system must have software for real-time, on instrument image processing and base calling, with a built-in web server with compatible web browsers for Windows 7 platforms.

12) Reagents needed for the systems operation must be ready to use and must enable paired-end reads.

13) The system and all applicable reagents must support solid-phase isothermal amplification. A single operator must be able to amplify up to 96 samples or more on a single channel flow cell in one hour.

14) The system must support whole-genome sequencing, targeted resequencing, de novo sequencing, metagenomics, paired-end mRNA sequencing, custom amplicon sequencing and detection of genomic changes in methylation patterns.

15) Output standard file formats must be compatible with most third party software (i.e. fastq, bam, vcf, text).

Extensive market research was undertaken to see if another product existed which would also meet the requirements listed in (c) above. Aside from reaching out to industry, this also included extensive google searches of keywords such as “next-generation DNA sequencers”, “next-generation sequencers” and “Illumina competitors”. All products from companies besides Illumina did not meet the above criteria. They failed for various reasons including: ancillary amplification systems, ancillary servers, external gas sources, insufficient throughput, use of non-Windows operating systems, excessive run times and exceeding the funds available for the purchase.

Any interested vendors that believe they can satisfy this requirement, may submit their capabilities, qualifications and product literature fully supporting that their product meets all of the specifications mentioned above by e-mail to Brian Nelson-Palmer no later than 10:00 a.m. EDT, on 09/04/2015. A determination by the Government not to compete this proposed purchase order based upon responses to this notice is solely within the discretion of the Government. Information received will normally be considered solely for the purpose of determining whether to conduct a competitive procurement. The contact information is as follows:

Brian Nelson-Palmer Nelson-Palmer.Brian@epa.gov