W81XWH22Q0067-0001 Question - Answers.pdf

AMENDMENT #0001

The Governments responses to Industry’s questions related to Solicitation W81XWH22Q0067.

1) Helpful but not necessary to have a general idea of what the samples are (e.g. soil, stool, filters, swabs, etc) for

DNA extractions?

Governments Response: The samples will primarily be stool samples collected as part of human subjects (most commonly) or rodent-model research (less commonly). There is a low likelihood of samples being derived from low biomass material or sources (e.g., swabs). The capability to extract DNA from low biomass material is preferred but not required as the primary and immediate reason for this contract is stool sample analysis (~100-250 mg stoo/sample).

2) What scale is required for the 16s sequencing (how many reads to target) e.g. 20k, 100k, 1 million / sample)?

Governments Response: To some extent this may depend on the project and available funding; however, 25-50k reads/sample will be sufficient for most projects. Ideally, the proposer could propose a tiered approach whereby pricing is scaled to sequencing depth.

3) What scale is required for metagenomes (e.g. 10 million reads, 50 million, 100 million)?

Governments Response: To some extent this may depend on the project and available funding; however, 5-10 Gb/sample will be sufficient for most projects. Ideally, the proposer could propose a tiered approach whereby pricing is scaled to sequencing depth.

4) The deliverables required for both 16s and metagenomes are not defined for the bioinformatics portion. Since there are so many types of analysis possible for either 16s or metagenomes 16s can range from a basic taxonomic analysis to full qiime2 analysis with advanced biostatistics, picrust, lefse, writing full or simple reports etc.

Governments Response: The analysis required will depend on the complexity of the project. At a minimum, rarefaction plots, taxonomy tables (i.e., read counts with assigned taxonomies at phyla, family, genus, and, if possible, species level-resolution) and alpha (observed ASVs, Shannon, Simpson) and beta (Bray-Curtis, weighted and unweighted UniFrac) diversity metrics are required as deliverables for 16S sequencing projects.

Those outcomes as well as genes, gene families, and gene pathways with associated read counts are required at minimum for metagenomics analyses. It is preferred that there be options for more complex bioinformatic analyses (e.g., metagenome assembled genomes) and for using statistical techniques that handle paired and/or longitudinal data, while accounting for the sparsity and compositional nature of the data based on best practice recommendations at the time of analysis.

5) Metagenomes can range from providing an annotation report to doing complex experimental group comparisons

The consulting and bioinformatics are open ended such that I could spend the next 10 years doing free analysis and consulting since no scope is defined to estimate labor unless labor is reported separately from the basic tasks for consulting and bioinformatics as I do see a labor reporting criteria.

Governments Response: The concern is justified, and our recommendation is to define a scope of work within the quote. For example, defining what “advanced bioinformatics and data analysis” means to the proposer and an acceptable rate for that item. Several tiers of analysis at progressively increasing levels of complexity could be quoted if each tier was defined by the suite of analytical tools/deliverables available within that tier. We do not expect the contractor to enter into a never-ending cycle of data analysis. What we would prefer, is the opportunity to discuss the analytical approach for each project and have the contractor identify the “tier” of pricing associated with that analytical approach. Alternately, the proposer can explicitly define the analytical approaches that they are willing to perform and associated costs. The scope of the analytical capability would then be considered in evaluating the proposals.

6) The main issue above is quoting for the amount of data that may be required, and quoting for consulting and bioinformatics without knowing the scale of time to allocate especially if the contract is fixed price.

Governments Response: Please see response to number 5. The proposer is encouraged to develop a means to account for the scale of time within the quote such that discussions between the Government and contractor prior to initiating each new task order on the contract can identify the appropriate time commitment and costs for a given project.

7) Is this is a brand-new contract OR if there is (was) an incumbent performing these services?

Governments Response: This is a brand-new requirement. Previously, these services have been performed within Department of Defense laboratories. We are seeking alternative options.

8) If not brand new, could you please provide the current / previous contract number?

Governments Response: NA