36C26218U0177-002.docx

ATTACHMENT A - STATEMENT OF WORK

VISN 22 Molecular Next Generation Sequencing Platform Capital Purchase

1. DESCRIPTION/SPECIFICATIONS/STATEMENT OF WORK

1.1. GENERAL REQUIREMENTS:

1.1.1. Primary analyzer(s) - Base equipment offered that shall fully support the scope of operations (minimal requirements). Depending upon the technical functionality and the capabilities of the individual manufacturer’s instrumentation, one analyzer or multiple analyzers may be required to meet the productivity specifications defined herein. In those instances, the additional analyzer(s) shall, likewise, be considered primary instrumentation and shall meet all of the technical specifications of this solicitation.

Meets the minimum requirement described in Section above (y/n)?

Describe how the minimum requirement is met or exceeded:

File name of Contractor’s attachment, if providing additional supporting documentation:

1.1.2. Operational Features - The instrumentation offered shall have the following:

1.1.2.1. The capability of performing next generation sequencing.

1.1.2.2. The capability of automating DNA and RNA library preparations.

1.1.2.3. Sufficient capacity and throughput to meet the volume and service demands of 3,000 samples per year.

1.1.2.4. Safety features to avoid unnecessary exposure to biohazardous and chemical material. The exposure to and the volume of biohazardous and chemical material generated by the equipment shall be minimal and require a minimum amount of handling.

1.1.2.5. Minimal daily, monthly, and periodic maintenance.

1.1.2.6. Ability to store and retransmit records (24 hours of maximal instrument throughput) in case of interface outage.

Meets the minimum requirement described in Section above (y/n)?

Describe how the minimum requirement is met or exceeded:

File name of Contractor’s attachment, if providing additional supporting documentation:

1.1.3. Technical Features -

1.1.3.1. Ability to read 100-130 million reads at 200 base pairs (40-50Gb) in 12 hours on an Ion 550 Chip

1.1.3.2. Ability to read 100-130 million reads at 200 base pairs (20-25Gb) in 8.5 hours on an Ion 550 Chip

1.1.3.3. Ability to read 60-80 million reads at 200 base pairs (20-30Gb) in 10 hours on an Ion 540 Chip

1.1.3.4. Ability to read 60-80 million reads at 200 base pairs (10-15Gb) in 6.5 hours on an Ion 540 Chip

1.1.3.5. Ability to read 9-12 million reads at 600 base pairs (1.5-4.5Gb) in 7 hours on an Ion 530 Chip

1.1.3.6. Ability to read 15-20 million reads at 400 base pairs (6-8Gb) in 2 hours on an Ion 530 Chip

1.1.3.7. Ability to read 15-20 million reads at 200 base pairs (3-4Gb) in 4 hours on an Ion 530 Chip

1.1.3.8. Ability to read 3-4 million reads at 600 base pairs (0.5-1.5Gb) in 5.5 hours on an Ion 520 Chip

1.1.3.9. Ability to read 4-6 million reads at 400 base pairs (1.2-2Gb) in 5.5 hours on an Ion 520 Chip

1.1.3.10. Ability to read 4-6 million reads at 200 base pairs (0.6-1Gb) in 3 hours on an Ion 520 Chip

1.1.3.11. Ability to read 2-3 million reads at 400 base pairs (0.6-1Gb) in 5 hours on an Ion 510 Chip

1.1.3.12. Ability to read 2-3 million reads at 200 base pairs (0.3-0.5Gb) in 3 hours on an Ion 510 Chip

1.1.3.13. Automated workflow of DNA and RNA library preparation for up to 8 samples.

1.1.3.14. Automated library preparation that requires 45 minutes or less of hands on time.

1.1.3.15. Automated library preparation that performs amplification and ISP recover and enrichment.

1.1.3.16. Ability to accommodate the use of third party reagents for specialized testing.

Meets the minimum requirement described in Section above (y/n)?

Describe how the minimum requirement is met or exceeded:

File name of Contractor’s attachment, if providing additional supporting documentation:

1.1.4. Hardware Features - The instrumentation shall have the following:

1.1.4.1. Next Generation Sequencer

1.1.4.1.1. Utilize simple Ion Torrent semiconductor sequencing that requires no complex optics and employs natural nucleotides to enable highly accurate variant detection, extremely uniform coverage, and sensitivity to detect low-frequency variants

1.1.4.1.2. Provide simple and integrated tools for tertiary data analysis, with Ion Reporter™ Software for DNA variant detection and characterization across paired samples

1.1.4.1.3. Include a complete end-to-end solution from base calls to variants with the built-in Ion S5™ Torrent Server and Torrent Suite™ Software

1.1.4.1.4. No fluorescence, no cameras, no lasers, no LEDs, no optical elements

1.1.4.1.5. Sequencing reactions are performed in a self-contained semiconductor chip environment

1.1.4.1.6. The DNA polymerase exhibits optimal processivity and high fidelity in a buffer-free environment

1.1.4.1.7. Nucleotides are sequentially flowed over the semiconductor chip via a proprietary flow order algorithm that enables phase-error correction

1.1.4.1.8. Washes are programmed to flush any residual unincorporated nucleotides prior to the application of the next nucleotide

1.1.4.1.9. Protons are cleaved from the 3/-hydroxyl moiety following nucleotide incorporation

1.1.4.1.10. Proton concentrations are precisely measured and are directly proportional to the number of nucleotides incorporated during any discrete flow cycle

1.1.4.1.11. Generation of increasingly long read lengths with high-fidelity base calls

1.1.4.1.12. High uniformity of coverage and sensitivity to detect low-frequency variants

1.1.4.2. Library Preparation Features

1.1.4.2.1. Genomic DNA sample libraries can be prepared in approximately 2 hours of total time by a single person, generating libraries of 100–400 base reads.

1.1.4.2.2. Enzymatic fragmentation module eliminates the need for physical shearing and is automation compatible (AB Library Builder System and off-the-shelf automation)

1.1.4.2.3. Generation of amplification-free libraries from as little as 100 ng of input DNA

1.1.4.2.4. Sample multiplexing is supported via up to 96 indexes per Ion Torrent chip; these barcodes enable highly multiplexed amplicon sequencing, allowing interrogation of thousands of gene targets per sample.

1.1.4.2.5. As little as 1 ng of input DNA or RNA from formalin-fixed, paraffin-embedded (FFPE) samples combined with ultrahigh PCR multiplexing

1.1.4.2.6. Simple and fast custom designs with the Ion AmpliSeq™ Designer tool for any genome

1.1.4.2.7. Simplest and fastest target selection method with automated primer design requiring only minutes of hands-on time

1.1.4.2.8. Helps increase lab efficiency and processing of time-sensitive samples with a workflow consisting of two 8-hour working days from genomic DNA to variants

1.1.4.2.9. Scalability with 12–6,144 amplicons per tube and 96 barcodes for processing up to 96 samples per run

1.1.4.2.10. Easy PCR workflow with no additional equipment needed

1.1.4.2.11. Flexibility with both customized panels and convenient ready-to-use panels

1.1.4.2.12. Ion Library Equalizer™ Kit normalizes Ion Torrent DNA libraries without the need for dilution, quantification, or any additional equipment

1.1.4.2.13. Target over 20,000 genes to survey gene expression changes

1.1.4.3.

1.1.4.3.1. An on-board monitor/screen that is easily readable.

1.1.4.3.2. A printer that has the capability of printing a patient report with patient demographic information that includes minimally the accession or unique identifier number (UID).

1.1.4.3.3. An uninterruptible power supply with line conditioner for each instrument provided.

Meets the minimum requirement described in Section above (y/n)?

1.1.5. Reports - The Contractor shall provide to the Contracting Officer and other individuals (designated post-award) a copy of a quarterly report of sales, by ordering facility, within 30 calendar days after the close of each quarter’s business. Reports are to reflect, at a minimum, total net sales amounts before discount, and discount amounts by ordering facility as well as the raw data used to develop these reports. These reports shall be used to monitor the commitment of each facility, reporting the savings realized and shall be shared with each participating facility, personnel associated with acquiring the products, and respective laboratory personnel. Additional invoice charges associated with reagent and/or supply wastage or repair parts included at no charge (per FSS awarded contract) shall not be accepted. There will be no additional charges for any reports required as part of the contract.

Meets the minimum requirement described in Section above (y/n)?