Sequencing and Genotyping Services Framework

Sequencing and Genotyping Services Framework

The University of Edinburgh is intending to create a framework covering a wide range of sequencing and genotyping services.

United Kingdom-Edinburgh: Research laboratory services

2020/S 185-447966

Prior information notice

This notice is for prior information only

Services

Legal Basis:

Directive 2014/24/EU

Section I: Contracting authority

I.1)Name and addresses

Official name: University Of Edinburgh
Postal address: Charles Stewart House, 9-16 Chambers Street
Town: Edinburgh
NUTS code: UKM75 Edinburgh, City of
Postal code: EH1 1HT
Country: United Kingdom
E-mail: andrew.helmn@ed.ac.uk
Telephone: +44 1316502508
I.2)Information about joint procurement

I.3)Communication

Additional information can be obtained from the abovementioned address

I.4)Type of the contracting authority

Body governed by public law

I.5)Main activity

Education

Section II: Object

II.1)Scope of the procurement

II.1.1)Title:

EC0900 Sequencing and Genotyping Services Framework

 

Reference number: EC0900

II.1.2)Main CPV code

73111000 Research laboratory services

II.1.3)Type of contract

Services

II.1.4)Short description:

 

The University of Edinburgh (UoE) is intending to create a framework covering a wide range of sequencing and genotyping services.

The UoE have internally available resources and this framework is designed to support these resources. End-users will be encouraged to approach our internal resources first and foremost but if capability, capacity or cost isn’t suitable, then successful suppliers on the framework will be able to compete for this business.

It is intended that each lot will work on a ranked basis, with direct call-offs being used as a preferred mechanism for speedy purchases but in the case of larger value or more complex requirements, a mini-competition may be run instead which would invite all suppliers from the appropriate lot.

The estimated cost indicated in this notice is a rough calculation from spend across all lots. This is an estimate only at this time and does not provide any guarantee on potential spend levels.

Suppliers should note that Covid-19 and Brexit may result in significant reductions in spend from the indicated level.

Minimum standards will focus on suppliers capacity and capability, both from a technical and financial perspective.

Technical scored questions will focus on but not limited to:

1) service delivery e.g. turn-around time, available equipment, storage, order processes/procedures;

2) quality assurance e.g. project references, sample quality assurance, obtained accreditation;

3) logistics/process e.g. shipping arrangements, tracking ability, weekend storage, shipping formats

4) technical support/contract management e.g. continuous improvement, invoice procedures, poor/failed sample integrity;

5) sustainability/community benefits e.g. service elements promoting good sustainable practice;

6) added value e.g. suppliers will be asked to provide an example rebate system based on annual spend levels, early payment discounts, re-sequencing charge.

Suppliers are only to bid for the lots relevant to them but can apply for more than one.

Lots may be awarded on a staggered basis depending on the complexity of submissions and duration of evaluation.

Please note: this notice is by no means a firm indication of how the framework will operate. The University reserves the right to alter the content up to the point of tender publication.

Lot names, descriptions may change alongside intended call-off strategies.

In addition, the current and potential economic and pandemic orientated climate may result in the University pulling the tender before it’s publication or during the tender process.

Suppliers are encouraged to get in contact with andrew.helmn@ed.ac.uk for further information.

 

II.1.5)Estimated total value

Value excluding VAT: 1 500 000.00 GBP

II.1.6)Information about lots

This contract is divided into lots: yes
II.2)Description

II.2.1)Title:

Lot 1: Short Read Genomic Sequencing and Analysis

 

Lot No: 1

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Paired end library sequencing

Long mate pair library sequencing

Linked read sequencing

Genome Sequence imputation

Including data transfer

QC of sequence data — specific to the lot

Including Library Prep (and sample QC) — specific to the lot

Bioinformatic Services — Data Analysis, Interpretation and Reporting of sequencing services — specific to the lot.

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 2 – Long Read Genomic Sequencing & Analysis

 

Lot No: 2

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Pacific Biosciences (PacBio) Sequencing

Oxford Nanopore Technology (ONT/Nanopore) sequencing

VASA-Seq

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 3 – Transcriptome Sequencing & Analysis

 

Lot No: 3

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

RNA-Sequencing (mRNA and total RNA sequencing)

Full length transcript or cDNA sequencing

Small RNA Sequencing

Nanostring

Microarray services

Direct RNA sequencing (Oxford Nanopore)

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 4 – Targeted Sequencing & Analysis

 

Lot No: 4

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Exome Sequencing

Targeted / Gene Sequencing

Custom sequence capture

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 5 – Microbial Sequencing & Analysis

 

Lot No: 5

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Whole Genome PacBio Sequencing (for microbial)

Whole Genome Nanopore Sequencing (for microbial)

Whole Genome Short Read Sequencing (for microbial)

16s Microbial Sequencing

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 6 – Single Cell Sequencing & Analysis

 

Lot No: 6

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Single Cell Isolation and Sequencing

Single Nuclei Isolation and Sequencing

Single cell ATAC-Seq

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 7 – Other Genomic Methods & Analysis

 

Lot No: 7

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Methylation Sequencing (reduced representation or whole genome bisulphite sequencing)

ATAC-Seq Library Preparation

ChiP-Seq Library Preparation

HiC library preparation / sequencing

RIP-Seq

Ribo-Seq

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 8 – Optical Mapping

 

Lot No: 8

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Optical Mapping

Including data transfer

QC of sequence data – specific to the lot

Including Library Prep (and sample QC) – specific to the lot

Bioinformatic Services – Data Analysis, Interpretation & Reporting of sequencing services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 9 – Sanger Sequencing / Genotyping

 

Lot No: 9

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Sanger sequencing / genotyping

Plasmid DNA extraction

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 10 – Array-based genotyping

 

Lot No: 10

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Genotyping of Single Nucleotide Polymorphism (SNP)

Array-based genotyping

Include all-inclusive genotyping services – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 11 – Other Genotyping services

 

Lot No: 11

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Genotyping of simple sequence repeat (SSR)

Genotyping by Microsatellite

Genotyping of low number SNPs

Include all-inclusive genotyping services – specific to the lot – specific to the lot

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 12 – Genotyping of transgenic animals

 

Lot No: 12

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Genotyping of transgenic animals

Genetic background characterisation

1-7 genes per animal, with up to 6 different alleles detectable for each gene

A panel of genetic markers that can distinguish between the common lab strains of mouse and rat evenly spaced through the genome

 

II.2.14)Additional information
II.2)Description

II.2.1)Title:

Lot 13 – DNA/RNA Extraction

 

Lot No: 13

II.2.2)Additional CPV code(s)

73111000 Research laboratory services

II.2.3)Place of performance

NUTS code: UKM75 Edinburgh, City of

II.2.4)Description of the procurement:

 

Whole blood

Saliva

FTA paper

Buccal swabs

Mammalian cell lines/primary cells (cell pellets)

Plant and animal tissue

FFPE tissue

Bacteria

 

II.2.14)Additional information

II.3)Estimated date of publication of contract notice:

30/10/2020

Section IV: Procedure

IV.1)Description

IV.1.8)Information about the Government Procurement Agreement (GPA)

The procurement is covered by the Government Procurement Agreement: yes

Section VI: Complementary information

VI.3)Additional information:

 

Note: to register your interest in this notice and obtain any additional information please visit the Public Contracts Scotland website at https://www.publiccontractsscotland.gov.uk/Search/Search_Switch.aspx?ID=630912

(SC Ref:630912)

 

VI.5)Date of dispatch of this notice:

18/09/2020