RFQ_Supplemental.docx

RFQ-RML-D-1978596

Additional information: Questions & Answers

1) [Starting material]

· Will you be sending us extracted gDNA as a starting material for whole exome sequencing and whole genome sequencing; and total RNA for RNA-seq? Yes we will be sending gDNA. We included blood as a possibility in rare cases but will almost always be sending gDNA

· I’m asking this question as ‘Ability to accept DNA and blood samples’ are described under 3) COMTRACTOR REQUIREMENT; however, it is described as ‘NIAID will supply DNA (2ug) and RNA patient samples and microarray chips.’ Under 5) GOVERNMENT FURNISHED MATERIALS.

· Will you also be providing microarray chips for CGH microarray? If so, what are the chips you will be sending? Is it correctly understood that the service we provide will be running and analyzing? Yes, we will be providing microarray chips for CGH microarrays. Specifically, we will provide SurePrint G3 Custom CGH Array 4x180K 60-mer, 180K features, one 1 in x 3 in slide, four microarrays per slide from Agilent

[RNA-Seq application]

· Would you please confirm that you are looking for mRNA sequencing using library kit for poly-A selection? Yes we are looking for mRNA sequencing

[Clinical Whole Exome Sequencing- rapid exomes]

· Is this the requirement for rapid turnaround time under 6) REPORTING REQUIREMENTS AND DELIVERABLES and also listed on the price line?

“We also require the vendor to offer a “rapid” 3-week turnaround time (for WES and WGS) from the time the contractor receives the patient sample. This allows for timely return of data to inform patient care at the NIH.” Yes, this is what this item on the price line is referring to.

2) According to Section 6: Reporting. It states Reports on each sample for use by the NIAID Team. Are you requesting a standard clinical report for each WES/WGS?

We are not requesting a standard clinical report for each WES/WGS. We only need data generation and information about the quality of data for each sample – QC results and depth of coverage

3) Is this “data generation only” or if they/you want full clinical interpretation for each of the tests?

We only want data generation for WES/WGS. We don’t want full clinical interpretation for each of these tests. For the clinical CMAs, we do want clinical interpretation and a clinical report.

4) What is the period of performance for this SOW? The order will be valid for 1 year from the date of award

5) Can you please confirm the coverage requirement for both WGS and WES? Are they in fact the same: 95% at 20X coverage? Yes, they are the same.

6) For the CLIA NGS processing, do you require lab director signature? No

7) For WES the following is requested “Develop and validate probes for deep intronic and UTR variants”. Please clarify the scope: will a custom exome assay need to be validated? How large are the added regions of interest? Thus far we have several genes with deep intronic or UTR variants that contribute to the phenotypes in our patients. Preferably they are validated; however, this is not a requirement. These regions are individual SNVs of interest.

8) Can you confirm that the aCGH arrays are Agilent arrays? Yes

9) What is the mechanism and format to submit our response? Is there a template which we can use as a guide to submit? There is mention of emailing our offer to you directly. Is there an additional web-based submission which we will need to also submit?

The quote just needs to be sent to me via email. There is no other submission requirement.

As far as formatting, we will need a quote that is formatted per the line item description provided and then just enough supporting documentation to explain to my customer the details of how your sequencing services will meet the specifications as outlined in the statement of work and the delivery times.

You may also submit any other documents that summarize your capabilities / why you think your institution is a good fit to the requirement.