Questions and Answers.docx

QUESTIONS AND ANSWERS - Solicitation 12639526Q0245 - Sequencing Services for Prnp Genotyping

1. Schedule of Items quantity. CLINs 0001, 0002 and 0003 each show an estimated quantity of one, with a unit of issue of each. No sample count is stated anywhere in the solicitation. Please provide the estimated annual number of samples for each period so that offerors can price the requirement accurately.

Answer: We estimate approximately 3,000 samples annually, for 3 years.

2. Sequencing mix. Please provide the estimated split between Sanger sequencing and next generation or Nanopore sequencing for each period.

Answer: 95% Sanger, 5% Nanopore

3. Pricing basis. Should the unit price be a per sample rate, or a single annual amount for each period? If a per sample rate is preferred, may offerors include volume price breaks?

Answer: Typically, this is a per-sample rate, with the option of volume discounts.

4. Order size definition. The Statement of Work requires overnight turnaround on tube orders and two to three days on large orders. Please define the sample count that separates a tube order from a large order.

Answer: Tube orders refer to less than 24 samples submitted, while large orders are generally more than 24, or in a 96-well format.

5. Service Contract Labor Standards. The solicitation states that the place of performance is currently unknown and that a wage determination for one possible place of performance is included as an attachment. We do not see a wage determination attached. Please confirm whether a wage determination applies, and whether the Service Contract Labor Standards apply when all sequencing is performed at a contractor owned commercial laboratory.

Answer: We are paying for a commercial service that the vendor charges based on a per-sample basis and does not add operating costs or similar.

6. Evaluation criteria. The Evaluation and Basis for Award section contains placeholder language, including a reference to the Schedule of Items on page X and a list of sample evaluation criteria file names. Please confirm the final evaluation criteria that will be applied to quotations.

On the user end (there may be additional requirements under the new Contracting process), these are the following requirements for this procurement:

Answer:

1. Provide high volume Sanger sequencing services and Next-Generation Sequencing (NGS) services including Nanopore sequencing services.

1. The contractor must demonstrate a 99% accuracy and a minimum of a 97% success rate across Sanger applications.

1. Provide a turn-around time of overnight on tube orders or 2-3 days on large orders.

1. Results should be returned as full ab1 files and quality scores should be provided for every sample (not just single codon results).

1. Must have the capacity to use custom-designed oligos that are provided with the samples.

7. Statement of Equivalent Rates for Federal Hires. FAR 52.222-42 lists an employee class of Aircraft Mechanic with a placeholder rate. Please confirm whether this clause applies to this requirement.

This does not appear to apply to this requirement.

8. Sample shipping. Please confirm whether the government or the contractor is responsible for the cost of shipping samples to the contractor laboratory.

Answer: The government will cover cost of shipping.

9. What is the source species for the DNA samples?

Answer: Primarily Mule deer, White-tailed Deer, and Elk.

10. What is the expected batching schedule and average number of samples per batch?

Answer: Batches of PCR amplicons are typically sent in 96 well-plates as batches of 96 samples about every 3-4 weeks. We request two reactions per sample.

11. What is the anticipated total annual sample number?

Answer: We estimate approximately 3,000 samples annually, for 3 years.

12. How much DNA will be provided per sample (volume/concentration)?

Answer: Samples are typically sent as 12ul aliquots with varying concentrations generally >10ng/ul.

13. The SOW mentions Nanopore (long-read) sequencing, but all data quality requirements and deliverables specifically reference Sanger sequencing. Is Nanopore sequencing required for this project? If so, please let us know your required data output per sample and deliverables (e.g. POD5 files).

Answer: We anticipate our sequencing needs to be 95% Sanger, 5% Nanopore. For Nanopore sequencing, we are looking for the raw-read sequences (.fastq) with coverage plots, per-base data/confidence files, and ideally a summary report of the run.

14. The fast turnaround times (TAT) may not always be possible. Are the stated TATs of overnight and 2-3 calendar days hard requirements?

Answer: A fast turnaround time of 2-3 calendar days is highly desirable. Ideally smaller batches of samples (i.e. <24) could be turned around within a couple days while larger batches (i.e. 2x 96 well plates) would be reliably completed within a week of shipment.