Questions_CEG_0003.pdf
PDF 40 KB Posted
- Attached to
- AMPLICON SEQUENCING SERVICES
- Solicitation number
- 140G0226Q0047
About this file
This document is a Questions and Answers (Q&A) file addressing contractor inquiries regarding a USGS genomic sequencing services solicitation.
The contracting agency requires a contractor capable of providing AVITI sequencing services as a minimum to ensure continuity of multi-year research projects already utilizing that platform. Illumina sequencing services, including MiSeq or NextSeq alternatives, may be considered for new projects if they meet specific project objectives. The agency will ship a minimum of 96 samples per shipment but frequently sends 384 samples at a time, with annual volumes ranging from 384 samples minimum to 1,600–3,100 samples likely. Contractors may provide detailed service descriptions beyond the solicitation's pricing schedule, provided they include summary statements clarifying whether services fulfill AVITI or other service requirements. The agency acknowledges that legacy MiSeq instruments reach end-of-life in December 2030 and has accepted the MiSeq i100 Plus as an acceptable replacement, provided appropriate overlap exists with Bacteria 16S rRNA V4 primers to ensure low sequencing error rates and that error rate data can be produced. The agency will not accept the Illumina NextSeq 2000 as a substitute for AVITI sequencing due to workflow constraints requiring a single sequencing platform throughout project analysis phases, despite comparable output specifications and base quality performance.
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Other files
| File | Type | Posted |
|---|---|---|
| Sol_140G0226Q0047_Amd_0003.pdf | ||
| Sol_140G0226Q0047_Amd_0002.pdf | ||
| Sol_140G0226Q0047_Amd_0001.pdf | ||
| Attachement_1_Questions_and_Answers_0001.pdf | ||
| B08_Attachment_A__Statement_of_Work.pdf | ||
| B08_Attachment_B_Pricing_Schedule.xlsx | XLSX spreadsheet | |
| Sol_140G0226Q0047.pdf |
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Does the contractor need to provide both Illumina and AVITI sequencing services or would Illumina sequencing suffice across all libraries?
We require a contractor that at minimum provides AVITI sequencing. We may opt to use Illumina MiSeq or other services if those are available.
How many samples will be shipped at a time? How many will be sent per year?
We will ship at minimum 96 samples but frequently will be shipping 384 samples at a time.
We will be sending a minimum of 384 samples per year but will more likely be providing somewhere between 1600 to 3100 samples per year.
Most of the items (services) listed in the pricing schedule have incomplete descriptions. When I have submitted responses to past USGS solicitations, I have provided a detailed list of the actual services that are offered by the MSU Genomics Core. Will it be acceptable to that for this solicitation? I can add comments next to my services to indicate which are related to the general service descriptions in the pricing schedule from this solicitation
Yes, this is acceptable. Please provide a summary statement whether services fulfill the requirements associated with AVITI or other services.
The 5-year term solicitation requires an Illumina MiSeq running a ver. 2 PE250 flow cell. However, these (legacy) MiSeqs were no longer sold after Sept. 2025, and end-of-life (no service support) is Dec. 2030- one year prior to this contract's end date.
We realize that the MiSeq platform an end-of-life in December 2030. This is one reason we are seeking a contractor that provides AVITI sequencing services in addition to other services.
We have decommissioned our three legacy MiSeqs and replaced them with a new MiSeq i100 Plus, an instrument that generates PE300 data and more of it at a lower cost than the legacy MiSeq. Is the MiSeq i100 an acceptable substitute?
We would consider the MiSeq i100 Plus as an acceptable replacement of the MiSeq. We would need to make sure there was appropriate overlap of the Bacteria 16S rRNA V4 primers with this sequencing chemistry to ensure low sequencing error rates. Can you all produce data on sequencing errors?
Please note, that we do require a sequencing contractor that offers AVITI sequencing services to allow sequencing continuity on research in progress. We may consider Illumina sequencing services for new projects if that meet project objectives.
Aviti and Illumina sequencers are both requested, and both generate essentially the same type of data. In the questions page, it states that an Aviti instrument is required; however, that requirement, based on its comparative output to the legacy MiSeq, would seem to be strictly output based, i.e., a 100M read output requirement for the Aviti run samples. We also operate an Illumina NextSeq 2000 that is capable of generating a 100M (and 400M) read output at PE300, 2 x 300bp, just like the Aviti and does so with an equivalent or higher base quality. Would this instrument not be a valid substitute for an Aviti?
We have some multi-year projects that have used and plan to continue to use AVITI sequencing. For project continuity, we require AVITI sequencing for those projects. We would consider comparable Illumina services for new projects, but are current workflows select a single sequencing platform for the entire project analysis.
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