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United Kingdom-London: Research laboratory services
Voluntary ex ante transparency notice
Section I: Contracting authority/entity
Section II: Object
Whole Genome Sequencing (WGS) Services
Our genome is comprised of 3 300 000 000 letters that make up the blueprint for who we are including the susceptibility to various diseases. The genome can be read using whole genome sequencing technologies, which can be broadly divided into short read and long read approaches.
This Whole Genome Sequencing (WGS) Service is to provide 300 000 GE WGS of the 500 000 announced by the Secretary of State for Health in October 2018 with the possibility of the remaining volumes being procured following further market assessment and due diligence during this contract period.
The WGS Service will cover short read sequencing technology services only.
Genomics England (‘the Contracting Authority’) was established in 2013 to make the UK the world leader in the application of genomics in healthcare through the 100 000 Genomes Project undertaken in partnership with NHS England. In October 2018 the Secretary of State for Health announced a commitment to undertake 500 000 whole genome sequences in clinical practice over the next 5 years in rare diseases and cancer delivered through the NHS Genomic Medicine Service.
Genomics England had a contractual relationship with Illumina Cambridge Ltd for Whole Genome Sequencing (‘WGS’) Services for the 100 000 genomes project and is about to embark on supporting the operation of a clinical WGS service in the NHS.
In doing so, the Contracting Authority has determined through considerable due diligence and assessment of the options available, the most appropriate course of action is to issue a transparency notice in the Official Journal (OJEU), for a WGS Service contract with Illumina Cambridge Ltd for reasons of technical skills required being limited to one supplier. Further explanation is provided at Annex D1 of this notice.
2) Scope of the procurement/requirements
In order to deliver WGS at scale for the NHS Genomic Medicine Services (GMS) there are key requirements for the service provider to meet to deliver the service successfully. These are:
(a) the service provider would need to be able to sequence over 60 000 samples per annum;
(b) the service provider would need a ISO accredited pipeline, meeting clinical standards;
(c) the service provider would need to deliver fast clinically meaningful turn around times (TAT) — rare disease working towards 28 days and cancer 21 days subsequently working towards 10 days.
Subsequently, the Contracting Authority has negotiated a contract with Illumina Cambridge Ltd to include the following requirement characteristics that delivers a clinically meaningful service for the NHS GMS.
(a) the contract will be non-exclusive over 5 years;
(b) there is no extension of term options;
(c) the contract provides for 300 000 GE to be sequenced over the life of the 5-year contract, with the first year commencing 1.4.2020. Additional minimal volumes could be required from the contract signature date to the service commencement date of 1.4.2020 in supporting the development of the service for go-live;
(d) to enable scaling of lab operations in line with requirements, all parties will meet on a monthly basis to provide a rolling sample forecast split between cancers and rare disease for planning purposes;
(e) in the absence of guaranteed volume, in order to scale lab operations at the level required to achieve volume requirements, the agreement sets out a tiered price for volumes that fall below an agreed volume per annum calculated on a transparent basis to reflect the cost of low volumes;
(f) the Contracting Authority will have the opportunity to terminate the contract at the end of year 3. The Contracting Authority will have the option to receive, upon termination, all laboratory capital equipment, or have it assigned to an agreed third-party provider;
(g) for all rare disease samples, the turnaround time will be 28 days. This is to be achieved within a transition period of 18 months from an initial turnaround time of 42 days;
(h) all cancer samples will be sequenced in 21 days to be achieved following a transition period of 12 months, from an initial 28 days. All parties will work together to drive turnaround times to 10 days within 36 months.
Continued at VI.3) Additional information.
Section IV: Procedure
The Contracting Authority:
(i) has a legal personality;
(ii) is mainly funded by the Department of Health and Social Care; and
(iii) has been established for the specific purpose of meeting needs in the general interest and does not have an industrial or commercial character and therefore meets the definition of a ‘body governed by public law’ under the Public Contracts Regulations 2015 (‘PCR’). The PCR covers ‘public contracts’ which means contracts for pecuniary interest which have as their object the execution or works, the supply of products or the provision of services. The contract is a services contract under PCR, therefore, caught by the PCR and therefore bound to follow public procurement rules.
Regulation 32(2)(b)(ii) PCR describes the single operator exclusion and is the premise for this award without prior publication. This specific exclusion relates to a demonstration that only Illumina Cambridge Ltd could deliver the services described for technical reasons, where the services cannot be obtained from any other economic operator. The scope of requirements in this notice are the basis for this assessment, which has been presented as the National Sequencing Strategy advisory document to the National Genomics Board.
As evidenced by the National Genomics Board advisory document, Illumina's short read sequencing technology is currently the only technology that can generate highly accurate and affordable whole genome sequencing (‘WGS’) within a high throughput, accredited environment. Furthermore, Illumina Cambridge Ltd is able to provide a complex combined sequencing and bioinformatics service. While there are other players in the WGS market, none can provide an ISO accredited and clinically acceptable service, at scale. In order to provide clinically acceptable sequencing samples at the scale required, Illumina Cambridge Ltd operate a laboratory that meets the required standards to be deemed suitable for results through the pipeline to be used in the care of patients.
For technical reasons, it has been determined that Illumina Cambridge Ltd are the only service provider able to meet the justified requirements set out. Furthermore, Illumina Cambridge Ltd are the only organisation able to deliver the requirement at the scale specified in the UK. Further details are provided within this notice and should be read in conjunction with this explanation.
The Contracting Authority will enter into a service contract with Illumina Cambridge Ltd following the conclusion of a minimum 10-day standstill period from the date of issue of this notice. The 10-day standstill period will end on 28.9.2019 at 11.59 p.m. BST, enabling a contract to be signed on 29.9.2019 or thereafter.
Section V: Award of contract/concession
Whole Genome Sequencing (WGS) Service
Section VI: Complementary information
3) Competition/Market Assessment
The National Genomics Board (NGB) commissioned the Contracting Authority to assemble a representative expert advisory group to provide a National Sequencing Strategy advisory document focused on whole genome sequencing, for consideration. The National Sequencing Strategy advisory document is available at https://genomicsengland.bravosolution.co.uk within project_683
Background: previous whole genome sequencing evaluations within Genomics England.
In 2013 Genomics England tested the whole genome sequencing market and 2 suppliers, Illumina Cambridge Ltd and complete genomics, took part in a tender, with Illumina Cambridge Ltd being successful based on technology readiness, ability to run a sequencing centre and willingness to co-invest. Complete genomics was then acquired by BGI, a Chinese company, and withdrew from the UK and European markets.
In August 2017 Genomics England undertook a re-assessment of available sequencing technologies. This concluded that Illumina Cambridge Ltd remained the only company that had sufficient capacity, quality, support and infrastructure to support sequencing for the 100 000 genomes project.
In 2019, the advent of the NHS Genomic Medicine Service (GMS) and an aspiration towards sequencing 5 000 000 genome analyses announced by the UK Secretary of State made it timely to re-evaluate the current whole genome sequencing market, examine how the technologies are likely to develop over the next 3-5 years, and how to secure best value and quality sequencing for the UK.
The conclusion of the National Sequencing Strategy is that Illumina Cambridge Ltd short read sequencing is currently the only technology that can generate highly accurate and affordable WGS within a high throughput, accredited service environment. This is unlikely to change over the next 2 years, unless BGI can more rapidly prove its technology and establish it in a ISO accredited, clinically acceptable sequencing service centre. BGI, which until relatively recently had been focused on the domestic Chinese market, are now looking to make inroads as a global supplier and potentially extend into wider markets including the UK and Europe. However, to be in a position to meet the requirements described in the scope, a significant investment is required. It is estimated, following engagement with the market, that it will likely take at least 2 years for competition to be in a ready state to compete for the services.
The strategy concludes with a commitment to review and engage with the market on a regular basis, over the period of this contract, to ensure value is at the center of all decisions. To that end, the Contracting Authority will take forward industry and stakeholder consultations to support a determination of at what point in the future will the competitive environment conditions be sufficiently developed to support competition, as part of a National Sequencing Strategy market management exercise.