Questions and Answers.docx

United States Department of Agriculture

Research, Education and Economics Agricultural Research Service

September 7, 2022

IN REPLY

REFER TO: Solicitation: 12305B22R0016 IDIQ Salmon Genotyping

Questions and Answers #1

1. What is the easiest way to present the proposal to you for multiple years? Typically, we would supply a quote so we could provide a quote for each year of the project based on the specifications in the PDF. Alternatively, I can put together one document that includes a breakdown by year. Do you have a preference for format that makes your life easier?

ANSWER: Provide a separate document with prices in a format that is listed in section B of the solicitation.

1. I want to make sure that I understand the way you would like to see everything presented. It appears as though there is a preference to quote the DNA extraction separate from the genotyping is that correct? From what I can understand, it looks like some of the DNA will be aliquoted and returned to the USDA (presumably for archival or some other analysis). For example, on page 3 of the PDF which outlines 2023-2024 requirements there are 4,129 DNA extractions in line item 1 associated with three studies-sea lice, color and harvest. In line item 2, some of that extracted DNA for 3,600 fish goes back to the USDA-please confirm whether it is harvest fish and sea lice fish (3,229 samples) or, harvest fish and color fish (3,600 samples). There are 3,6000 samples listed for line item 2 but those do not add up based on line item 1. I may also be mistaken in how I am interpreting the table. Finally, in line item 4, you would like to see the price for genotyping the samples extracted in line item 1?

ANSWER: Yes we would like to have five (5) separate quotes: 1) submission of tissue samples to be DNA extracted and then run on the indicated genotyping platform; 2) Extraction of DNA from submitted tissue sample with DNA returned to USDA; 3) Extraction of DNA from submitted tissue samples, aliquoting of the DNA into three lots, with two lots returned to the USDA and one lot used for genotyping on the indicated platform; 4) genotyping on the indicated platform from submitted DNA; 5) COO testing as indicated from submitted DNA. We will be mixing and matching how we submit samples any given year to fit what works best for us. We may submit some samples right away for extraction and genotyping while some samples we submit for just extraction and then we store the DNA for a year or more until submitting a subsample of the DNA for genotyping. All of the in the numbers of samples in the sheet are estimates as we don’t know how many fish will be sampled in any given year and include some front loading of samples in year one to clear some samples already collected. I think importantly for the vendors, samples will be submitted multiple times through out the year and not necessarily in lots of 356 samples (FYI: the chip we want them to run the samples on runs 356 samples at once, hence they are looking to run things in multiples of 356 to reduce their costs). We will try to submit things in several (probably 2 or 3) large lots throughout the year, it won’t a 100 or samples here and another 100 or so there. In short, they should not try to match samples numbers up of things extracted and what gets genotyped and so forth as not everything will add up nor will it meet these exact numbers.

1. Line item 3 is potential parents (5600 samples). Please confirm that in this line you would like to see one price for DNA extraction, aliquoting DNA into three lots, returning two lots to USDA and using one lot for genotyping. The other alternative is that this line item if for DNA extraction only and the genotyping of potential parents is actually 1400 samples on line item 4? In that case I am wondering if you are expecting 4 aliquots of DNA since 1400 does not divide equally into 5600.

ANSWER: Yes, I would like a single price for DNA extraction, aliquoting DNA into three lots, returning two lots to the USDA and using one lot for genotyping. As explained above the numbers will not add up as not all samples that are extracted will be genotyped.

1. Line item 5 is COO analysis including DNA extraction, correct?

ANSWER: No, COO analysis does not include DNA extraction. We will submit extracted DNA in a 96 well plate for COO testing.

1. Each period of performance appears to be 2 years rather than 1 year, is that correct? Will the samples be submitted in two lots, one in the first year of the period and one in the second?

ANSWER: Each period of performance is 1 year, January – December.

1. I noticed your salmon genotyping solicitation request on SAM.gov. I did you specifically call out arrays in your request, but was wondering if targeted GBS was also an option in this case?

ANSWER: No, we are not interested in GBS at this time.

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