FAR 13.5 Single Source or Brand Name Justification Less than SAT.pdf

United States Department of Agriculture Limited Source/Brand Name Justification

FAR 13.106-1(b)(1) – Simplified Acquisitions

1. Identification of the agency and the contracting activity.

Requesting Agency:

United States Department of Agriculture Animal Plant Health and Inspection Service National Bio and Agro Defense Facility (NBAF) Manhattan, Kansas

Contracting Activity:

USDA, APHIS

Marquette Ave, Suite 410 Minneapolis, MN 55401

2. Description of supply or service required to meet the agency’s needs.

The USDA proposes to enter into a limited source brand-name, firm fixed-price contract with Sage Science to procure two (2) PippinHT size selection electrophoresis systems, Item # HTP0001 and three (3) SageELF size selection system electrophoresis systems, Item # ELF0001.

3. The rationale or circumstances for limiting competition.

Sage Science, Inc. is the original equipment manufacturer and the sole supplier of the PippinHT and Sage ELF systems. The PippinHT and SageELF are automated electrophoresis systems that reduce the multiple handling of potentially infectious biological materials as well as eliminating handling of hazardous chemicals for the separation of molecules using electrophoresis. Other systems require working in biological safety cabinets or on the bench top with the potential of exposure to hazardous chemicals in the electrophoresis gels.

SageELF Fractionation System: The SageELF is an electrophoresis system that separates DNA or protein samples by size, and then fractionates the whole sample, or section of sample, into 12 fractions.

The system is equipped with pulsed-field electrophoresis for resolving large DNA. Fractionation ranges are estimated and adjusted in software, and fractions are collected in buffer. One sample is fractionated on a single precast agarose cassette, and one or two cassettes may be processed at one time.

Salient Characteristics:

Reduces the complexity of RNA (cDNA) or protein samples

Allows construction of DNA libraries with multiple insert sizes for improved assembly

Allows sequencing of valuable DNA and retrieving sample for later study Must fractionate DNA or solubilized protein samples using agarose gel electrophoresis.

Must separate DNA or solubilized protein samples by size in an agarose gel column, followed by lateral electro-elution into 12 adjacently placed collection wells.

Fractionation must be undertaken in disposable pre-cast gel cassettes.

Must be able to run up to two gel cassettes simultaneously.

Must have pulsed-field (field inversion) electrophoresis capabilities to enable separation of high molecular weight DNA.

DNA or protein fractionation profiles must be predicted with software.

Must have the ability to optically detect fluorescent dyes within samples.

Must be able to accept sample loads of randomly sheared genomic DNA in amounts up to 10 μg.

Must be able to accept sample loads of protein samples up to 350 μg

PippinHT incorporates the company’s highly regarded sizing technology and increases throughput to 24 samples per run, compared to a maximum of five with Pippin Prep or BluePippin. The instrument offers an efficient, automated solution for scientists running busy sequencing labs, core facilities, and other laboratories producing large-scale sequencing data.

Salient characteristics:

Sample-to-sample reproducibility streamlines research Higher sample quality improves downstream analysis 24 sample capacity meets high throughput sequencing demands Must separate DNA by agarose gel electrophoresis.

Electrophoresis must be undertaken in disposable pre-cast gel cassettes.

Must be capable of running direct current electrophoresis and pulsed-field (also known as field inversion) electrophoresis.

Individual sample lanes must be separated by a physical barrier.

Must accept 1or 2 precast agarose gel cassettes DNA size selection A gel cassette must be able to process (collect a DNA fraction from) up to 12 samples at one time.

The instrument must be able to process 2 cassettes per run, or 24 samples at once.

Each sample lane must be bifurcating and be electrophoretically controlled by three electrodes (one negative and two positive). The positive electrodes must be switchable (one on and one off).

Must electro-elute DNA from agarose filled sample lanes into wells filled with electrophoresis buffer.

DNA fragments size ranges to be collected must be selectable via software.

Must calculate optimal elution timing software DNA elution in a sample by determining migration rates of DNA size ladder used as an internal or external standard.

Electrophoretically mobile dye-labeled DNA must be visible in real-time via monitor.

Must be able to accept sample loads of sheared genomic DNA in amounts up to 1.5 μg.

Must electro-elute fractions with 40-80% efficiency of recovery when compared to input DNA.

Must electro-elute randomly sheared genomic DNA fractions that have size distribution coefficients as low as 8% CV, or + 16% of the median fragment length.

Must be able to extract target fragment sizes between 90 and 2,000 base pairs.

4. A description of the market research conducted and the results or a statement of the reason market research was not conducted.

Market research was conducted in accordance with FAR Part 10. This effort did not yield any sources that can meet the Government’s requirements based on the required characteristics and features.

On-line searching provided only obsolete systems that do not meet the required specifications. Other systems mentioned are tape systems which are becoming obsolete and do not meet the required specifications. The two requested Sage systems cover the rapid results needed by diagnostics and the high throughput which is needed in outbreak ramp up. Using the same system allows better comparison among samples that may have been run at separate times for previously different reasons. Use of this equipment will allow for continuity and transition of the diagnostics and development from Plum Island Animal Disease Center to the newly constructed National Bio and Agro-Defense Facility.

5. Estimated price, including all options, if applicable.

Description The estimated price is less than the simplified acquisition threshold.

6. Recommended source(s).

Sage Science 500 Cummings Center Suite 2400 Beverly MA 01915

Certifications

☒ The information provided for this justification has been reviewed and certified accurate and complete by Patricia S. Glas, Senior Advisor for NBAF Laboratory Logistics

The information contained in this justification is accurate and complete to the best of my knowledge and belief and in accordance with Federal Acquisition Regulation 13.106-1(b)(1), I hereby determine the circumstances described above deem only one source, or limited sources, reasonably available and competition is precluded for the reasons indicated in this document.

Lisa A. Draves Contracting Officer