Service for European whitefish SNP panel development and genotyping

Natural Resources Institute Finland (hereafter referred to as "Luke") requests your tender for Service for European whitefish SNP panel development and genotyping with this Call for Tenders and its annexes. Luke is looking for a service provider to develop a SNP panel and to genotype European whitefish individuals with a minimum of 5 000 SNP markers (single nucleotide polymorphism markers). Luke will combine the genotype data of individuals with their phenotypes to study, for example, the genomic inheritance of the fish traits, to determine genetic sex, and to perform genomic evaluations in the Finnish national selective breeding programme. The subject of the procurement is described in more detail in Appendix 1-4 and other procurement documents. On supplier shall be chosen for the procurement.

The subject of the procurement is Service for European whitefish SNP panel development and genotyping The subject of the procurement is described in more detail in Appendix 1-4 and other procurement documents. Luke is looking for a service provider to develop a SNP panel and to genotype European whitefish individuals with a minimum of 5 000 SNP markers (single nucleotide polymorphism markers). Luke will combine the genotype data of individuals with their phenotypes to study, for example, the genomic inheritance of the fish traits, to determine genetic sex, and to perform genomic evaluations in the Finnish national selective breeding programme. a) Creation of SNP panel The service provider will develop a SNP panel with a minimum of 5 000 SNPs for European whitefish Coregonus lavaretus L. Luke will give the service provider information about the candidate SNP details. These information are: 1) Raw, unfiltered VCF output from the ddRAD SNP caller, and 2) a subset of ddRAD BAM files (~3-10, to be agreed), all of which originate from an analysis of over 2000 individuals of the breeding programme. The way in which DNA variants have been previously identified from these data sets, see, Fischer et al., BioRxiv https://biorxiv.org/cgi/content/short/2023.10.03.560633v1, and Calboli et al. 2023, https://doi.org/10.1093/jas/skad333. 3) The reference genome based on a female individual from the breeding programme. 4) In addition, Luke will provide a list of small set (<100) of pre-determined SNPs (variant and flanking sequence) that have passed earlier quality control filters. Luke will send the service provider around 384 fin clip samples which will be used by the service provider to design, produce, and validate the SNP panel. The data generated will be returned to Luke, and a report on the characteristics and functioning of the SNP panel will be sent to Luke by the service provider. Luke remains the owner of the information and tissue samples provided by the Luke, and the information derived from them by the Supplier to create the SNP panel for European whitefish. The service provider does not own this information, and this information cannot be used by the service provider for any other client or party, without a written permission from Luke. See further information in the agreement section X. After completing the SNP panel, Supplier shall deliver in a 1 week a report to Luke detailing the used lab protocols, the SNP panel characteristics, SNP genome locations, allele frequencies, quality control measures, validation results (including but not limited to call rate and reproducibility), and individual genotyping data that can be mapped on the genome. b) Genotyping of individuals -Genotyping of individuals using the developed SNP panel with a minimum of 5 000 SNP markers will be done for a total of 3 456 individuals during 2 years from the completion of the SNP panel. Luke will send fin tissue samples of individuals to the service provider in QR and bar-coded tubes. The samples will be sent in batches of around 1000 fish, and Luke covers the shipment costs. The samples sent to the service provider can be potentially used again by Luke in some future laboratory analysis, and hence they remain valuable for Luke even after the service providers has completed their analysis. The service provider will: -Extract DNA from the individual fin clips, -Generate SNP information on each fish, -Return the remaining tissue of each sample in the form of homogenate or the tissue itself in the individual QR coded tubes, -Cover the shipment costs of returning the samples, -Return all genotype data to Luke in a digital form. In the data, each sample has an individual code of the tube to which the individual's SNP data will be connected. Luke remains the owner of the data, and the service provider does not own the data.

The Natural Resources Institute Finland uses the Finnish government's common electronic order and invoice processing system, the Handi service. Purchases are allocated through the system to valid contracts and ordered through the electronic system. The Natural Resources Institute Finland only approves, processes and archives invoices in electronic form that are compliant with the European Standard. Invoices are requested to be sent as an electronic invoice through OpusCapita Solutions Oy, which acts as the Finnish government's e-invoice operator. We will return the received paper invoices to the biller. We require that the invoice include an order number or contract number so that our invoice processing system can automatically assign an invoice to the associated order.