RFQ-Amendment1.pdf

RFQ 75N95024Q00297 Amendment 1

Request for Quotation No.: 75N95024Q00297.

Title: Neurodegenerative Disease Research – Whole Genome Sequencing

RFQ Response due Date: 5:00 PM Eastern Time on June 10, 2024 (unchanged)

Amendment No.: 1

Date of Issuance: 07/05/2024

Point of Contact: Iris Merscher, Contracting Officer - E-mail: iris.merscher@nih.gov

ISSUING OFFICE OF ACQUISITIONS

National Institute on Drug Abuse (NIDA) on behalf of the National Institute on Aging (NIA)

PURPOSE OF RFQ AMENDMENT No. 1

The purpose of this amendment is to:

1) Respond to Questions received regarding the RFQ.

2) Revise the Statement of Work – SOW (RFQ-Attachment 1)

NOTE: The SOW (page 1 – Specific requirements – 2nd sentence) is revised to read as follows:

“The contractor should target 30x samples; minimum 100Gb will be generated in case 30X coverage unmet from sample nature”.

GENERAL RFQ QUESTIONS/ANSWERS:

Question 1: Would the government be okay with using KAPA Hyper Prep PCR free instead of Truseq

DNA PCR-Free?

Response 1: No. Illumina’s TruSeq DNA PCR-Free Library preparation kit (350bp) is required for this project.

Question 2: Would the government be okay with using Equalbit 1x dsDNA HS Assay Kit (Vazyme

Biotech Co.) or Qubit 2.0 DNA HS Assay (ThermoFisher)?

Response 2: No. The project requires the QC process to be completed by quantification with picogreen method using Victor X2 fluorometry. Qualification with Agilent genomic DNA screentape, alternatives will not be acceptable.

Question 3: Would the government be okay with another data transfer method besides google cloud such as FTP or S3?

Response 3: No. Data transfer via Google cloud server is required.

mailto:iris.merscher@nih.gov

Question 4: The statement of work lists a specific Illumina library that is to be used but we use a customized, off-the-shelf kit from Illumina. We do use a flourmeter, but not the Victor-branded one, specifically. Can we use our customized kit, or does it have to be off-the-shelf?

Response 4: No. It is required that libraries be constructed using Illumina’s TruSeq DNA PCR-Free Library preparation kit (350bp).

Question 5: Can you clarify if the section on requirements at the top of page 2 states that only two of the certifications are required? We are not cGLP-certified, and we are not ISO 9001-certified. I am not clear if we need all 4 certifications (but only provide documentation for

2) or if having two is sufficient.

Response 5: Having 2 of these certifications is sufficient.

Question 6: Based on the SOW, sequencing using Illumina technology is requested. Would there be an opportunity for sequencing in a long-read system using PacBio and Nanopore technologies?

Response 6: Sequencing must be performed using Illumina NovaSeq6000 S4 (2x150bp). Alternatives are not acceptable for this requirement.

Question 7: Can sequencing be performed on Illumina Novaseq X Series?

Response 7: Sequencing must be performed using Illumina NovaSeq6000 S4 (2x150bp). Alternatives are not acceptable.

Question 8: Does sequencing need to be performed in CLIA/CAP certified lab?

Response 8: Vendor must provide at least two (2) of the certifications and/or accreditations: ISO 9001 certified based on quality management principles, cGLP certified which ensure current good laboratory practice regulations as defined by the FDA, CLIA certified which ensures Clinical Laboratory Improvement Amendments of 1988 are practiced, CAP laboratory accreditation to ensure precise testing results. CLIA is not required, but two of the above certifications must be met.

Question 9: Does the work need to be performed as a CLIA validated assay?

Response 9: No.

Question 10: What sample type will the DNA provided be sourced from (e.g. blood, FFPE, frozen biopsies etc.)?

Response 10: DNA will be sourced from either blood or frozen biopsies.

Question 11: Are alternative, equivalent options acceptable to the Victor X2 fluorometry reader?

Response 11: No. It is required that the QC process be completed by quantification with picogreen method using Victor X2 fluorometry. Qualification with Agilent genomic DNA screentape, alternatives will not be acceptable.

Question 12: For option years: if reagents or kits specified are discontinued or updated, will the NIH accept vendor-recommended alternative, equivalent kits or will the NIH be revising reagents/kit requirements as part of an amended SOW?

Response 12: In that situation, vendor recommended alternatives shall be submitted to the NIH for review/acceptance.

Question 13: For the following statement: "The contractor should target 30x samples; max 100Gb will be generated in case 30X coverage unmet from sample nature. " - Can you please confirm if this should read a minimum of 100Gb/sample generated or is max 100Gb correct?

Response 13: Yes. The SOW (page 1 – Specific requirements – 2nd sentence) shall read as follows: “The contractor should target 30x samples; minimum 100Gb will be generated in case 30X coverage unmet from sample nature”.

Question 14: The SOW states a minimum of 500ng of purified gDNA would be provided, but also notes that only samples with >1.0ug of DNA shall pass QC and move forward with the library process. Would samples >500ng, but not meeting the 1.0ug threshold be processed on a case-by-case basis?

Response 14: Yes, samples >500ng, but not meeting the 1.0ug threshold should be processed on a case-by-case basis.

Question 15: The specification requests the Illumina TruSeq DNA PCR-Free kit, and NovaSeq 6000 sequencing platform with S4 flow cell. Illumina now offers newer versions of both items that perform as well or better, and at a lower cost. Is it acceptable to offer the NovaSeq X- Plus sequencing platform with 25B flow cell, and/or the newer Illumina DNA PCR-Free kit?

Response 15: Illumina’s TruSeq DNA PCR-Free Library preparation kit (350bp) is required for this project along with NovaSeq 6000 sequencing platform with S4 flow cell. Alternatives will not be acceptable.

End of Amendment 1