CEFAS24-116 Request for Quotation for genotype-by-sequencing approach for estimating familial relations among pollack

Cefas is currently undertaking genetics based Close-Kin Mark-Recapture (CKMR) research on pollack populations. Cefas is seeking a supplier to sequence samples using a Genotype-by-Sequencing (GBS) approach. Samples have been collected from pollack originating from multiple areas across the English Channel with generated Single Nucleotide Polymorphisms (SNPs) being used to identify Parent-Offspring Pairs (POPs) as well as more distant kinship relationships, such as Half Sibling Pairs (HSPs).

Cefas is aware that there is a multitude of GBS approaches, some using propriety technology and some not. Cefas are seeking applications which offer a GBS approach that maximises SNP identification and coverage, to allow Cefas to explore kinship levels amongst pollack.

To aid with the above project, Cefas require the supplier to carry out DNA extraction of muscle tissues, quality control steps (DNA Quality Control information (i.e. pass/fail based on DNA concentration and DNA quality) supplied to Cefas before genotype-by-sequencing commences) and genotype-by-sequencing of pollack samples. Therefore, suppliers are asked to provide a cost per sample based on the above.

As standard, muscle tissue samples are to be provided by Cefas in LVL genetic sampling tubes with analytical grade ethanol and stored in -20oC: https://www.lvl-technologies.com/en/sample-storage/safe-2d-tubes-engl/safe-96-tissue-collection-951.

Cefas requires suppliers to provide an estimate of how long it would take to provide results for both 3000 samples and their individual minimum run length to process per sequencing, based on the 'Deliverables' section described below.

Deliverables: • DNA extraction of all samples • DNA Quality Control information (i.e. pass/fail based on DNA concentration and DNA quality) supplied to Cefas before genotype-by-sequencing commences. • Genotype-by-sequencing providing SNPS with an average of >30x coverage. o ~3000* tissue samples provided in total (exact amount to be confirmed) • Samples can either be submitted to the supplier as they are received by Cefas OR submitted all at once based on suppliers' flexibility • Sequencing files to be provided in fastq format with a QC Report o Final sample submission date being end of February 2025. o All results, with a final QC report, must be received by 15th of March 2025.

*Please note sample number stated above is the current estimated number of samples collected, final sample number may vary

Location for services to be undertaken: At the supplier's premises - all steps of the process must take place within the United Kingdom to ensure deterioration of samples

Download the Bidder Pack at https://defra-family.force.com/s/Welcome and search for CEFAS24-116 under opportunities.