Published date: 12 September 2024

Last edited date: 12 September 2024

Closed opportunity - This means that the contract is currently closed. The buying department may be considering suppliers that have already applied, or no suitable offers were made.


Closing: 30 September 2024, 12pm

Contract summary

Industry

  • Analysis services - 71620000

Location of contract

Any region

Value of contract

£20,000 to £30,000

Procurement reference

CF-0364600D8d000003VQwdEAG

Published date

12 September 2024

Closing date

30 September 2024

Closing time

12pm

Contract start date

28 October 2024

Contract end date

28 February 2025

Contract type

Service contract

Procedure type

Open procedure (below threshold)

Any interested supplier may submit a tender in response to an opportunity notice.

This procedure can be used for procurements below the relevant contract value threshold.

Contract is suitable for SMEs?

Yes

Contract is suitable for VCSEs?

No

Description

Cefas is currently undertaking a population genetics assessment on colossal squid. Cefas is seeking a supplier to sequence rare samples using a genotype-by-sequencing (GBS) approach. Tissue samples (mainly tentacles) have been collected from various regions across the globe. The samples themselves are in two types of preservative, depending on the institutes which collected the samples; ethanol and formaldehyde.

Cefas is aware that there is a multitude of genotype-by-sequencing approaches, some using propriety technology and some not. We are seeking applications which offer a GBS approach that maximises SNP identification and coverage to allow Cefas explore population structure. Additionally, suppliers must have a comprehensive DNA extraction step to compensate for varying levels of sample preservation.

Due to the scarcity of these animals, we have 33 samples but we expect samples to be run in duplicate at an average coverage of x30 depth for each duplicated sample.

Requirement:
To aid with the above project, Cefas require DNA extraction of squid tissues in ethanol (31) and formaldehyde (2). Assessment of DNA quantity and quality (see 'Deliverables' sections) will need to be completed and discussed with Cefas before genotype-by-sequencing of squid samples begins. Cefas are seeking the highest sequencing coverage possible to compensate for minimum samples sizes. Therefore, suppliers are asked to provide a cost per individual sample (n=66, in total).

The colossal squid currently has no reference genome. For the benefit of potential suppliers considering which restriction enzymes to use, we supply the following genome information of two closely related species;

Estimate genome size = 3.2 Gb (2.74-3.67 Gb) (based on two species, Eupyrmna scolopes and Doryteuthis pleii) GoaT (genomehubs.org).

Due to the rarity of samples, we will require the supplier to duplicate extraction of DNA, testing of DNA quality/quantity and genotype-by-sequencing per sample. All samples have been obtained and are ready to be sent as soon as the Contract is finalised.

Deliverables:
• DNA Quality Control report (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 depth.
• Quality control report of genotype-by-sequencing to ensure desired coverage.
• Sequencing files to be provided in compressed fastq format.
• All results must be received by 1st December 2024.
; Download the Bidder Pack at https://defra-family.force.com/s/Welcome and search for CEFAS24-126 under opportunities.

More information

Previous notice about this procurement

CEFAS24-126 RFQ for Genotype-by-sequencing approach of Colossal Squid

  • Opportunity
  • Published 12 September 2024

About the buyer

Contact name

Laura Anderson

Address

Pakefield Road
Lowestoft
NR33 0HT
GB

Email

procure@cefas.gov.uk