Sole_Source_Justification_-_Sequel_Instrument.pdf

Justification for Other than Fair and Open Competition

1. Contracting Activity:

USDA, ARS, WBSC

1001 Holleman Dr. EAST College Station, TX 77840

2. Nature/Description of Action:

The USMARC intends to award a sole source, firm fixed priced contract, pursuant to FAR Part 12, to Pacific Biosciences for a Sequel DNA sequencing instrument and related hardware and software components, as detailed in quote # 20001212.

3. Description of Supplies/Services:

As per quote 20001212 This purchase is for one Sequel DNA analysis instrument from Pacific Biosciences which included all necessary hardware and software components for DNA sequencing producing long read sequences.

Sequencing chemical are also contained within. Included is three day training of operation and library preparation.

4. Statutory Authority

In accordance with FAR 6.302-1 and 41 USC 253 (1), only one responsible source and no other type of supplies or services will satisfy agency requirements.

Pacific Biosciences is the only vendor of the PacBio Sequel instrument and associated polymerase, and sequencing reagents. The Sequel instrument is covered by numerous patents owned by Pacific Biosciences.

5. Demonstration of Contractor’s Unique Qualifications or Nature of the Acquisition that Requires Use of the Authority Cited The PacBio Sequel instrument is covered by numerous patents owned by Pacific Biosciences. Pacific Biosciences is the only vendor of the PacBio Sequel instrument and associated preparation, polymerase, and sequencing reagents in the United States.

The system is unique in many aspects that are critical to genome assembly. This includes the ability to sequence DNA that has not been amplified by PCR. This helps in the reduction of errors and prevents redundancy which would impact overall output. The Sequel instrument can produce extremely long reads with an average of 8-12 kb and as long as 40 kb. In comparison the Illumina platform can only produce 600 bp read lengths while the Roche 454 or Ion torrent produce variable read lengths of 200- 1200 bp. The system can also detect base modifications such as DNA methylation. In general, with one SMART cell enough DNA sequence is obtained of length and amount that a whole genome of a bacteria can be accomplished with few gaps, in most instances. This is achieved in part due to the long read lengths which help cover gaps missed by other technologies.

6. Federal Business Opportunities (FedBizOps) Announcement/Potential Sources

7. Determination of Fair and Reasonable Cost

The price of this system is comparable to other DNA sequencing systems purchased by USMARC in the past 12 years. This includes the Roche 454 system (~$450K) and the Illumina NextSeq500 ($250k).

Each system has its own unique capabilities based on output amounts and sequence reads. The PacBio Sequel instrument has much greater read length than the other two systems (500-1200 bp compared to 8,000-12,000 bp). As long read length is critical to genome assembly this difference is critical for some analysis.

Deborah.Hughes Typewritten Text $367,500

Deborah.Hughes Typewritten Text

8. Market Survey

USMARC is fully aware of the market trends in DNA sequencing as unit members attend the yearly Plant and Animal Genome meeting, which is the largest genome meeting for agriculture genomics research, trade magazines are read by the unit as is the popular GenomeWeb daily newsletter which reports several times daily on genomics and sequencing research and news. Dr. Smith is considered an expert in the field of genomics and has participated in several international genome efforts. Due to his work and these interactions, he is familiar with the various vendors for DNA sequencers, uniqueness of their products and relative costs on the open market. To the best of his knowledge, the price obtained for this instrument is in keeping with standard market value and represents best value for the U.S. Government.

9. Additional Support

N/A

10. Other Interested Sources

None that have expressed interest. The JOFOC will be posted in FBO.

Certification:

Requirements-Program Office:

I certify the facts and representations under my cognizance included in this justification form are complete and accurate basis for the justification.

Tim Smith, Research Chemist 09 Nov 15 (Signature and Printed Name)____________________________________________________ Name Title Date

Contracting Officer:

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Cindy J. Cose, Contracting Officer Date

Branch Chief:

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Deborah Hughes, Branch Chief Date