Request for Information for metagenome sequencing of the total nucleic acids (DNA, RNA)

Please note that this is a Request for Information only and not a Call for Tenders or an Invitation to Tender. The information provided in this request for information is preliminary and the subject of the procurement may change later. Finnish Institute for Health and Welfare (THL) is preparing a Call for Tenders for a framework contract entailing metagenome sequencing of the total nucleic acids (DNA, RNA) extracted from the samples (Lot1) and tentatively also on the use of probe-enrichment methods targeted to human pathogens for some of the samples prior metagenomic sequencing (Lot2). The sample material originates mainly from environmental and wastewater sources, but also other sample matrices are possible. This request is part of the market research process to identify the potential services and service providers available on the market. Participation in a request for information is not binding on either party. Those who respond to this request will not be compensated for responding to the request for information, nor for the cost of responding. Responding to this notification is not a prerequisite for participation in a subsequent Call for Tenders and does not affect the tenderer's position in it. Please send your answer before the time limit; 7/29/2024 3:00 PM (UTC +3). Regarding the sequencing service available for nucleic acid samples: Metagenomic sequencing (shotgun sequencing) 1. Which sequencing platforms do you use? 2. What methods/technologies you have available for shotgun metagenome sequencing (Lot1)? 3. Targeted metagenomics (Lot2): a. Do you offer targeted metagenome sequencing service? What kind of kits you use, can you provide lists of possible targets per each kit? Is it possible to modify the target lists based on the customer needs? b. What kind of additional library preparation options you can offer for total nucleic acids (DNA, RNA)? c. In case of use of probe-enrichment or amplicon-based protocols, does your metagenomic sequencing service include sequencing runs from pre-constructed libraries (by customer)? 4. Can you provide references or case studies where your metagenome sequencing services have been used with environmental DNA/cDNA samples? Sample handling 5. In case of RNA as a starting material, do you prefer receiving RNA or cDNA from the customer? 6. What quality control measures do you have in place for your sequencing processes? Is this information available for the customer? 7. Can samples be sent on individual tubes or in 96-well format? Does sample vessel affect the service price? 8. What are your sample submission quality and quantity requirements for DNA, RNA/cDNA and/or PCR-amplicons when ordering metagenome sequencing? Does the customer need to prove the sample quality/quantity and how are the exceptions handled? 9. Is it possible to include the sample shipment from the customer (THL) to your sequencing facilities (courier service or similar) into your sequencing service package? 10. Is the sample shipment location within the European Union? Data Delivery 11. In what format will you deliver the sequencing data? 12. What kind of actions you have in place to protect the data? 13. How long do you store the sequencing data? 14. What options are available for accessing and downloading the sequencing data? 15. Timeline: How many days after the service provider has received samples is it possible to receive the data? What are the factors that affect the delivery time? 16. Lead time: How early must the customer notify the service supplier about the incoming sample shipment if a specified delivery time is expected? Customer support, pricing, and billing 17. What level of technical support is available during the project? Can you provide qualifications of your staff responsible of the sequencing projects? 18. What is the cost structure for your sequencing services? 19. How does the number of samples in a sequencing batch affect the unit price of sequencing (i.e., is the sequencing cheaper per sample if there are more samples shipped to the sequencing at the same time, when the same sequencing depth is used for all samples)? 20. Is there a pricing difference between sequencing of total nucleic acids (DNA, RNA) and pre-made libraries? 21. How does the requirement for a specified timeline to deliver the data (e.g., within 21 days) affect the price of the service?