United States - Sanger DNA Sequencing

Description

Added: Jun 24, 2019 12:42 pm

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued.

1. This solicitation 12639519Q0158 is a request for quotations (RFQ).
2. The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2019-03.
3. This solicitation is set aside for small business only. The associated North American Industrial Classification System (NAICS) code for this procurement is 541380 - Laboratory Testing with a small business size standard of $15 million.
4. The government intends to award a fixed price Indefinite Delivery, Indefinite Quantity (IDIQ) contract with 1 base year and 4 option years as a result of this combined synopsis/solicitation that will include the terms and conditions set forth herein.
5. The United States Department of Agriculture (USDA), Animal Plant Health Inspection Service (APHIS), Otis Molecular Laboratory in Buzzard Bay, MA has a requirement for DNA sequencing service of insect, fungus, and pathogen DNA. The Otis Molecular Laboratory conducts molecular activities for the United States Department of Agriculture's Animal and Plant Inspection Services (APHIS) in order to prevent the entry, spread, and establishment of agricultural pests and diseases. The lab is located at 1398 West Truck Road, Buzzards Bay MA, 02542 on Joint Base Cape Cod.
Laboratory research includes molecular identification of unknown insect pest and biological control agents, population genetics of economically important forest pests, and method development for molecular diagnostic assays. DNA sequencing can be used to directly identify a specimen through DNA barcoding-comparing the specific nucleotide sequence of a highly conserved region of mitochondrial DNA to those of known species that are available in public databases. DNA sequencing is also crucial to the development of DNA-based diagnostic assays and is necessary in studying the changes in population genetics over time.
We require a DNA sequencing service that implements Standard Operating Procedures as well as quality control at every step of the process to ensure that results are reliable and repeatable. The facility should be equipped with a high-quality DNA sequencing instrument such as the ABI3730XL DNA Analyzer or a comparable instrument.
Purified PCR DNA samples along with relevant primers will be prepared at the Otis Laboratory. The sequencing facility must be equipped to process sample submissions prepared either in 96-well PCR plates or in snap-cap microcentrifuge tubes. Additionally, we require a facility that is able to receive submissions that are shipped overnight at room temperature. Samples will only be shipped Monday-Thursday, allowing for samples to arrive at the facility during a weekday.
 
Upon arrival at the sequencing facility, we require that samples be processed and results be provided within approximately 24 hours (on business days only) due to the processing of important regulatory samples.
The length of DNA reads should range between 700-1000 base pairs. Once analysis is complete, an E-mail notification should be sent to the primary investigator to notify that results are available. Results should be made available in a download link through secure web based access in the form of chromatogram, sequence text file, and base call quality files.
An online interface for submitting orders, checking order status, and ultimately receiving results is necessary and will be used by a Molecular Laboratory technician to notify the facility that samples are being submitted. There must be an option to specify the location of different DNA templates in regards to the wells of a 96-well PCR plate as well as the specific primer to be used with the DNA template. Furthermore, it is necessary that the online submission form allows for ample character length for naming samples/DNA template-up to 24 characters-that accommodates the sample naming systems adopted at the Otis Molecular Laboratory.
The contractor will be responsible for the security of all data collected and communication to the USDA. Order forms and sequence results will be archived and maintained by the contractor on the secure web server. All contractor collected data is the sole property of the U.S. government.
In the event of DNA sequencing failure due to equipment failure, reagent failure, and/or human error, we require that samples be re-sequenced at no additional cost. The Otis Molecular Laboratory should be notified in such an instance, either via an online tracking system or direct correspondence (E-mail or telephone). If the samples in question still fail after the second attempt, the contractor should communicate with the Otis Molecular Laboratory for further solutions. The number of instrument-caused failed reactions should be less than 5% of the total submission.
6. Pre- Award Test Sample
Interested vendors are required to process 48 DNA sequencing reactions for evaluation purposes. Purified PCR product and sequencing primers will be supplied. Test sample results, including chromatogram, sequence text file, and base call quality files, shall be submitted at no expense to the Government. We require that 85% of submitted samples return a successful sequence.
We will evaluate success of a sequencing reaction as follows: 1) a clean chromatogram with minimum double peaks in base calling, and 2) upon exclusion of the first and last 40 base calls (primer binding and adjacent sites), the remaining sequence should have a Q score greater than 30 (Q30) for at least 90% of base calls, with 85% of the base calls having a score of Q40. If either of the two criteria are not met, the sequencing reaction is considered a failure. Please contact Dr. Yunke Wu. E-mail: Yunke.Wu@usda.gov. Telephone: (508)-563-0927 to request for samples to be sent. Results shall be returned to Dr. Yunke Wu before solicitation close date.
7. Pricing shall include shipping costs (fill out price schedule in Attachment 1 - Statement of Work)
Line Item | Description | Est. Quantity | Cost  ea| Total
0001 | Base Year: 7/19/19-7/18/20 Sanger DNA sequencing | 3000ea |____|___
0002 | Option Year 1: 7/19/20-7/18/21 Sanger DNA sequencing | 3000ea |___|___
0003 | Option Year 2: 7/19/21-7/18/22 Sanger DNA sequencing | 3000ea |___|___
0004 | Option Year 3: 7/19/22-7/18/23 Sanger DNA sequencing | 3000ea |___|___
0005 | Option Year 4: 7/19/23-7/18/24 Sanger DNA sequencing | 3000ea |___|___
8. The provision at 52.212-1, Instructions to Offerors -- Commercial, applies to this acquisition. Please see Attachment 1 - Statement of Work
9. The provision at 52.212-2, Evaluation -- Commercial Items applies to this acquisition. Please see Attachment 1 - Statement of Work
10. Quoters shall include a completed copy of the provision at 52.212-3, Offeror Representations and Certifications -- Commercial Items, with its quote.
11. The clause at 52.212-4, Contract Terms and Conditions -- Commercial Items, applies to this acquisition. Please see Attachment 1 - Statement of Work
12. The clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders -- Commercial Items, applies to this acquisition. Please see Attachment 1 - Statement of Work
13. Please see Attachment 1 - Statement of Work for other applicable terms and conditions.
52.217-8 -- Option to Extend Services (Nov 1999)
52.217-9 -- Option to Extend the Term of the Contract (Mar 2000)
52.222-49 --Service Contract Labor Standards -- Place of Performance Unknown (May 2014)
14. To be considered, interested vendor must submit the following:
- Filled Price Schedule (Attachment 1 - Statement of Work)
- A currently active Federal Contractors Registration at http://www.sam.gov. Contractors shall include a printed copy of the first page of the SAM listing, or a DUNS number if the SAM application is in progress.
- Technical Capabilities Statement. Statement should include evidence of capacity or capability in meeting and providing the services specified in the Statement of Work.
- Pre-Award Test Sample Results
- Past Performance References. Contractors shall submit at least 3 customer references for similar work from the last 12 months including contact information and/or previous contract numbers with the USDA.
- A copy of the completed provision 52.212-3, Offeror Representations and Certifications-Commercial Items. Contractors shall complete only paragraph (b) of this provision if the offeror has completed the annual representations and certifications electronically at http://www.sam.gov. If an offeror has not completed the annual representations and certifications electronically at the SAM website, the offeror shall include a copy of the completed provision with the quotation.
Contractors are advised to carefully review their submission requirements specified in this section and the provision 52.212‐2, Evaluation - Commercial Items. The Government may evaluate solely on the information provided in the submission and will not assume that any contractor possesses capabilities that are not specifically identified in their submission. Failure to comply with the requirements of the solicitation may result in a quote receiving no further consideration for award. It is the Contractors responsibility to ensure completeness of their submission. In order for a contractor to have a complete package, the following must be submitted to the Contracting Officer to be considered acceptable.
15. All questions must be submitted in writing directly to the contracting officer by email at Kimyen.n.tu@aphis.usda.gov by July 10th, 2019. All quotes should be submitted electronically by EMAIL ONLY to Kimyen.n.tu@aphis.usda.gov by July 12th, 2019 @ 12PM central time.

Opportunity closing date

12 July 2019

Value of contract

to be confirmed