RFQ Attachment 3 - QA.pdf

Genomics Sequencing Services for the NIAID Centralized Sequencing Program Notice ID: RFQ-NIAID-24-2224314

RFQ Attachment 3 – Questions & Answers

9/11/2024 – Amendment 1

Q1. What is the anticipated start date?

A1. Anticipated start date is immediately after award; estimated award date is 9/23/2024.

Q2. Is there anticipated numbers or past indicators of how many duos and trios can be expected?

A2. We expect about 15%-20% of samples to be trios and 10%-15% to be duos.

Q3. Is an encrypted, secure, password protected email link acceptable for data delivery?

A3. Email delivery with a link to secure download of the data files would be acceptable.

Q4. Are the deliverables for raw data post-analysis?

A4. Deliverables are for raw data in the form of CRAMs, along with some processed data such as unfiltered gVCFs and other data deliverables listed in the SOW.

Q5. What is the cadence of data delivery? i.e. Weekly? Monthly? Every 50? Etc.

A5. Data delivery should be provided once a batch designated and sent by the NIAID team has been completed. For example, if a batch of 50 are sent as “Batch 1”, then data delivery should take place once sequencing has been completed and CRAMs and other data deliverables are ready for delivery for all of the samples that passed QC in “Batch 1”.

Q6. Will the plate format tubes be micronic?

A6. We need 96-well deep well sample plates that are compatible with QIAgility robotic aliquoting.

No specific company is needed as long as compatibility with QIAgility is met.

Q7. Is DNA the only type of specimen that will be sent?

A7. Yes.

Q8. We do not utilize Fluidigm. We have an internal capability for assessment of contamination, sex, and relationship with other samples (duos/trios). Can you provide further clarification on the need for Fluidigm?

A8. Any comparable or better method for assessment of contamination, sex, and relationship with other samples is acceptable. If an alternative method is proposed, evidence of its comparability is required, including sensitivity and specificity.

Q9. What is the expected cadence of incoming batches?

A9. Batches of 50 samples each will be sent approximately every two weeks.

Q10. Do all samples need to be returned?

A10. No. Samples do not need to be returned. On rare occasions NIAID may request samples back, such as in cases when DNA has been depleted or a sample swap is suspected.

Q11. Would the manifest include volume and concentration?

A11. Yes.

Q12. What quantity and measurement does the NIAID use?

A12. NIAID uses Nanodrop. We require volume, concentration, DNA quality (ie. A260/A280 ratio), and quantity needed for sequencing as measured by Nanodrop.

Q13. Are subcontractors permitted to be used for any portion of the desired - not mandatory -deliverables or must all work be performed by the contractor?

A13. Yes, subcontractors can be used as long as the requested information regarding expertise and capability are demonstrated.

Q14. Are BAM files an acceptable substitute for CRAM raw data files?

A14. Yes.

Q15. We have found that identity check by Molecular Tracer is more accurate than using Fluidigm SNP tracer; therefore, is a combination of Molecular Tracer (for sample identity analysis) and bioinformatic analysis (for contamination assessment, sex and relationship assessment) acceptable?

A15. Any comparable or better method for assessment of contamination, sex, and relationship with other samples is acceptable. If an alternative method is proposed, evidence of its comparability is required, including sensitivity and specificity.

Q16. For what proportion of the samples will polygenic scores be expected?

A16. Polygenic scores are desirable, but not required. If they are provided, then we would expect polygenic scores to be part of deliverables for all samples.

Q17. Please provide additional requirements for the Polygenic risk scores. Will these scores be returned to patients or will the scores be "information use only"?

A17. These will be information use only initially with potential for future return to patients if they are clinically validated.

Q18. For what proportion of the samples will pharmacogenomic allele calling be expected?

A18. Pharmacogenomic allele calling is desired for all samples.

Q19. Please provide clarification on the "Pharmacogenomic allele calls" in the "Desired Deliverable" section of the SOW: Is allele calling the sole deliverable? Or is there are interpretation requirement? If an interpretation is required, please provide additional information on the required specifications.

A19. Pharmacogenomic allele calling is the sole deliverable desired. Interpretation is not required.

Q20. Please provide additional information on the requirements for the 96-well plates. Are there any specific requirements that must be met, such as the plate manufacturer?

A20. We need 96-well deep well sample plates that are compatible with QIAgility robotic aliquoting.

No specific company is needed as long as compatibility with QIAgility is met.