INVITATION TO TENDER STAGE ONE: PRE-QUALIFICATION NHS GENOMIC MEDICINE CENTRE SELECTION

Transcription

1 INVITATION TO TENDER STAGE ONE: PRE-QUALIFICATION NHS GENOMIC MEDICINE CENTRE SELECTION

2 NHS England INFORMATION READER BOX Directorate Medical Operations Patients and Information Nursing Policy Commissioning Development Finance Human Resources Publications Gateway Reference: Document Purpose Document Name Author Publication Date Target Audience Resources NHS Genomic Medicine Centres - ITT Stage 1 Document NHS England 28 July 2014 Foundation Trust CEs, Medical Directors, Directors of Nursing, NHS Trust Board Chairs, NHS Trust CEs Additional Circulation List Description Cross Reference #VALUE! The procurement process for the procurement of NHS Genomic Medicine Centres is split into two stages. The first stage, is a prequalification exercise. This is designed to allow NHS England to assess each applicant's previous experience which is relevant to the project with the intention of selecting a number of applicants to take part in the second stage of this procurement process NHS Genomic Medicine Centres' Prospectus - Gateway Ref: Superseded Docs (if applicable) Action Required Timing / Deadlines (if applicable) Contact Details for further information 0 To note the content of the ITT Stage 1 document and consider applying for NHS Genomic Medicine Centre status. By 00 January Genomics Central Coordinating Team/Medical Directorate Quarry House Quarry Hill LS2 7UE Document Status 0 This is a controlled document. Whilst this document may be printed, the electronic version posted on the intranet is the controlled copy. Any printed copies of this document are not controlled. As a controlled document, this document should not be saved onto local or network drives but should always be accessed from the intranet 2

3 NHS England - Invitation to Tender Stage One: Pre-Qualification - NHS Genomic Medicine Centre Selection Version number: 1 First published: 28 July 2014 Updated: (only if this is applicable) Prepared by: NHS England 3

4 Contents Contents Introduction Definitions Scope of work Waves This Procurement process for Wave Interested parties Procurement Process Nature of process Timetable Pre-qualification Evaluation Criteria Overview of Pre-qualification Criteria Pre-Qualification Criteria Categories Table A - Scoring Criteria Requirements and Commercial Arrangements Overview Of Requirements Submission of Applications Format and content of Applications Receipt, Clarification and Validity of Application General Right to reject or disqualify an applicant and right to cancel or vary the Procurement Consortia and partnerships Conflicts of Interest Freedom of Information Security, Confidentiality and Permitted Disclosure General Jurisdiction and Governing Law Annex 1: Diseases relevant for the Project Disease selection Cancers Rare Inherited Diseases Annex 2: Glossary The following definitions shall apply in this Stage One ITT: Annex 3: Response Template

5 1 Introduction 1.1 Definitions In this Stage One ITT, terms shall have the same meaning given to them in the Prospectus. Other terms are defined in the Glossary in Annex Scope of work This Stage One ITT relates to the 100,000 Genomes Project ("the Project"), which has been established to deliver on the Government's commitment to sequencing 100,000 whole human genomes by the end of In the context of the Project, NHS England is selecting applicants to participate in the Project as NHS Genomic Medicine Centres, by way of this Procurement. Each successful applicant will enter into an agreement with NHS England to manage the delivery of the Project. 1.3 Waves NHS England's requirement to appoint NHS Genomic Medicine Centres is split into separate Waves - i.e. there will be a phased appointment of NHS Genomic Medicine Centres over the coming months. During Wave 1 it is NHS England's intention to select a minimum of five applicants to operate as the first Wave of NHS Genomic Medicine Centres, and further details will be provided in the second stage of the Procurement One of the key criteria in the selection of Wave 1 NHS Genomic Medicine Centres (and considered in the second stage of the Procurement process) will be in relation to the applicant's capacity and capability to commence delivering the services by 1 January Applicants should give due consideration to whether they are fully capable of commencing the delivery of the services by this time. Future Waves will allow applicants to commence services at later dates. NHS England intends to continue to engage with the market and keep all interested applicants appraised of progress on the Project and the process and timescales for future Waves Non-application or non-selection for Wave 1 does not preclude organisations from applying to become NHS Genomic Medicine Centres in future Waves. If an Applicant applies but is not selected for Wave 1, NHS England will provide the reasons for the non-selection of the Applicant's Application for Wave 1, subject to NHS England receiving a request for the same via the address england.genomics@nhs.net with the subject "NON-SELECTION REASONS" within 10 days of notification Where an organisation has applied for Wave 1, passes the Wave 1 qualification but is not selected to have a contract awarded to it, this will not preclude that organisation from applying in future Waves, provided that the organisation meets all of the relevant qualification criteria for that future Wave, including by: 5

6 recertifying that the content of its application for Wave 1 remains correct and valid; notifying NHS England of any changes which have occurred in the organisation or its application; and the organisation completing any additional or amended criteria for that Wave. 1.4 This Procurement process for Wave The process for the Procurement of Wave 1 of the NHS Genomic Medicine Centres is split into two stages. The first stage, which this document relates to, is a pre-qualification exercise. This is designed to allow NHS England to assess each Applicant's previous experience that is relevant to the Project with the intention of selecting all those eligible to take part in the second stage of this Procurement process In the second stage, Applicants will be asked to respond to a draft contract and detailed specification in addition to other relevant information. Based on the results of the second stage of this Procurement process, NHS England intends to award contracts for Wave 1 to a minimum of five applicants, but further details of this will be set out in the second stage of this Procurement process. 1.5 Interested parties NHS England is acting as the contracting authority for this Procurement of NHS Genomic Medicine Centres In addition, NHS England is working alongside other partners to deliver the Project, including, without limitation, Genomics England, the Department of Health, Health Education England, Public Health England, the National Institute for Health Research and partners within academia At this time, the scope of the NHS Genomic Medicine Centres being procured by NHS England relates to those patients under the care of the NHS in England. Discussions are ongoing as to whether other territories in the UK may join the wider Project. 6

7 2 Procurement Process 2.1 Nature of process The Procurement will be conducted in accordance with the EU treaty principles of transparency, non-discrimination, equal treatment, mutual recognition and proportionality The Procurement will be conducted in accordance with the Public Contracts Regulations 2006 for a Part B service. As a result, NHS England will be conducting a competitive process in the form set out in this Stage One ITT, which will then be as more fully described in the second stage of the Procurement process. The qualification methodology is set out in paragraph 3 of this document. The ITT for stage two of the Procurement process will set out the award criteria, along with the specification and commercial approach NHS England's intention is to select all those eligible to participate in stage two of this Procurement process. Following this, it is NHS England's intention to award contracts to a minimum of five applicants. However, nothing will oblige NHS England to award any contracts as a result of this Procurement process. 2.2 Timetable The Prospectus set out an outline of the timetable for this Procurement. The anticipated timetable is now set out below: Date Stage 28 July 2014 Stage One ITT issued 17:00 GMT, 29 August 2014 Deadline for submitting Stage One ITT Applications W/c September Potential Provider Information Day 2 - for applicants to understand the next stages in the Procurement W/c October Results for Stage One ITT released W/c October Stage Two ITT issued October Site visits October/November Contractual and requirements discussions Mid/Late November Deadline for submitting Stage Two ITT Application December Results for Stage Two ITT released December Final clarifications December Contract award 1 January 2015 Contract begins - samples to be provided for analysis from this date Applicants should note that the submission deadline for any Applications in relation to this Stage One ITT is 17:00 GMT, 29 August

8 2.2.2 NHS England will first consider the experience of the Applicants - paragraph 3 of this document sets out the minimum standards NHS England sets for successful Applicants for this Stage One ITT NHS England reserves the rights: (i) not to consider any Application which is received later than the submission deadline stated in paragraph or after any extension has expired, if granted, and/or (ii) to amend the timetable of the Procurement process NHS England will publish a Contract Award Notice at the end of the Procurement, no later than forty eight (48) days after the contracts have been awarded. 8

9 3 Pre-qualification Evaluation Criteria 3.1 Overview of Pre-qualification Criteria Governance of the Procurement is overseen by the NHS England Genomics Programme Board and reporting within the NHS England Board Assurance Framework. For the purposes of oversight of the Procurement of NHS Genomic Medicine Centres an NHS England Genomics Procurement Board will be established. The NHS Genomic Medicine Centres Evaluation Team will comprise of representatives of the 100,000 Genomes Project Delivery Partners, including but not exclusive to NHS England, Genomics England and the Department of Health. The Evaluation Team will make recommendations to the NHS England Procurement Board in accordance with process set out in paragraph of this document The Evaluation Criteria for this Stage One ITT is set out in this paragraph. This is principally concerned with each Applicant's relevant previous experience and other evidence to demonstrate that they can meet the high level delivery requirements An explanation of the categories, as listed in Table A below, in relation to the pre-qualification criteria, is further described in paragraph Once Applications are received and opened following the deadline specified in paragraph 2.2, they shall be assessed according to this paragraph. If an Application is successful under the pre-qualification Evaluation Criteria in this paragraph, the Applicant will then be considered for stage two of the Procurement process For the pre-qualification Evaluation Criteria under this paragraph, evaluators will undertake the following process Once individual evaluators have completed their evaluations, the groups of evaluators responsible for this paragraph shall meet and moderate their scoring. This may be undertaken either in person or by audio conference or video conference). Once the groups of evaluators have reached consensus, they shall record their moderated score for each criteria along with their reasons. If they are unable to reach consensus, an average of each evaluator's score shall be the moderated score. This moderated score shall be the score presented to the NHS England Genomics Procurement Board. The NHS England Genomics Programme Board shall also be provided with a report of all Concerns, and the Programme Board may exercise NHS England's rights in this Stage One ITT in respect of those Concerns, and record how they are dealt with Once all evaluators have completed their evaluations of the Applications and scores have been moderated in accordance with this paragraph, the Procurement Board will assess the overall evaluation results, query the evaluation teams on the details of their Evaluation Criteria and confirm which Applicants shall be taken forward to the second stage of this 9

10 Procurement process. This will be on the basis of all applicants who meet the minimum requirements set out below being taken forward. Applicants who meet these minimum requirements but are not subsequently selected to be awarded a contract will be entitled to a streamlined process for future Waves as set out in paragraph Applications submitted for this Stage One ITT will be evaluated in accordance with the methodology for this paragraph set out in table A below Each criteria within this paragraph is given a scoring method and a weighting. When scoring an Application, evaluators will give a score using the applicable scoring method but not apply the weighting for that criteria at that stage - weightings shall be applied later once the score is finalised. The criteria, scoring methods and weightings are set out in Table A below The scores shall be allocated to reflect the quality of the Application provided and the evidence which is provided with it. Individual evaluators will provide reasons for their decision-making, taking into account all of the elements within that criteria. Evaluators should also log any concerns they have regarding the risk profile of the Application, potential delays in implementing the NHS Genomic Medicine Centres and/or any material areas of concern and/or non-compliance ("Concerns") NHS England reserves the right to exclude Applicants for the following reasons: the discretionary exclusion criteria in Form C of Annex 3; an Applicant scoring 0 in any criteria in Form E of Annex 3 and/or less than 50% overall in Form E (in which case feedback shall be provided in a debrief session to assist Applicants in competing for future Waves); Applicants making one or more material amendments to key principles; Applicants effecting a material change in the risk profile of NHS England or its partners, an Applicant's application being incomplete or not capable of evaluation; the grounds set out in paragraphs and/or 6.1.2; an Applicant failing to notify NHS England of changes in accordance with paragraph 6.6.4; and in accordance with paragraph Pre-Qualification Criteria Categories NHS England sets out here additional background detail which should assist applicants in providing their responses to this Stage One ITT. 10

11 3.2.2 Diseases and capacity: This category relates to the Applicant's experience in delivering services in rare inherited disease and cancer, described in more detail in Annex 1 of this Stage One ITT. Capability in delivering services to those with rare inherited disease, and cancer and both acting on and incorporating genomic information in their clinical care, is a key requirement for an NHS Genomic Medicine Centre Please describe: Clinical services provided for patients with cancers and rare inherited diseases; Genetic and genomic services provided and/or accessed for patients with cancers and rare inherited diseases; A detailed assessment of capabilities and anticipated recruitment numbers in disease groupings and specific disorders provided in Annex 1. Please state the modelling, assumptions and calculations made to reach these figures and provide any supporting evidence to demonstrate previous recruitment of these patient groups ( e.g. from previous studies) as well as any ongoing recruitment to other studies in the diseases/conditions listed; A similar detailed assessment of any additional capacity and capability should also be provided for other conditions within the disease areas of cancer and rare inherited conditions to those specifically listed in Annex 1; and Any nationally recognised specialist skills or expertise relating to any of the diseases and conditions listed in Annex 1 or any additional specific diseases and conditions not listed The ability of the Genomic Medicine Centres to supply samples and the associated clinical information phenotypic data is critical to the success of the Programme. Collected samples from recruited patients will only progress to sequencing when the full phenotypic dataset is supplied. Applicants will need to provide information about the source of the data and the integrated informatics that demonstrates that they have the capacity and capability to deliver against the diseases and/or conditions Previous experience of clinical studies and trials: The structure of the Project is most directly comparable with major studies and/or trials. Therefore proven capability in coordinating and participating in multi-centre studies and/or trials, particularly those relatable to genomics, is relevant Please describe: Experience of delivering genomic and other clinical studies and trials; The infrastructure and capabilities for participating in relevant major studies and/or trials in place at present or previously; and 11

12 The consent and recruitment profile to these studies and/or trials, and historical performance in these matters Other relevant experience the Applicant has in delivering genomic services or clinical studies and/or trial should be described Data and Informatics: This Project will involve obtaining and updating detailed phenotypic, clinical, and administrative data in an appropriate digital form, together with longitudinal follow up of patients and, handling and tracking samples and consent. Although some of this data could be obtained from submissions to other datasets, e.g. in the Cancer Outcomes and Services Dataset (COSD) or Systemic Anti-Cancer Therapy Dataset (SACT) for cancer, it is envisioned that NHS Genomic Medicine Centres will develop streamlined processes for collection and linking of data from both cancer and rare inherited diseases to enable acquisition of a rich clinical data set by Genomics England to accompany the whole genome sequence (and these other datasets are in development at present between NHS England and GeL). No samples will enter the sequencing pipeline until this comprehensive information is received by Genomics England Applicants should provide information on whether the source data is currently stored in paper records or electronic systems. Applicants should also identify what would be required to improve the quality of this clinical data and its storage and linkage. It is important that the Applicant has the ability to provide phenotypic and clinical data (i) to the level required at initial recruitment, as evidenced by involvement in other studies and/or usual practice, and (ii) to provide this information on an ongoing basis for longitudinal data analysis and in response to potential evolution of clinical datasets Detailed data and information governance requirements will be provided in the second stage of the ITT process Please describe: Where is relevant data stored in all organisations that are part of the proposed NHS Genomic Medicine Centre, are these paper records or integrated electronic systems? How these, or similar, data have been linked in previous studies or in clinical practice Whether you already use SNOMED CT, and if not what are your plans to implement it? Systems in place for managing patient recruitment and tracking completion of phenotypic datasets, consent and sample collection and processing; 12

13 Systems in place for entering comprehensive data within a defined time period e.g. as evidenced by successfully meeting clinical trial requirements; The evidence of completion and of quality assessment from routine NHS clinical data sets, clinical audits and any other registries. What would be required to improve the quality of these systems for this Project and optimising submission to national audits and clinical datasets; and Existing systems for information governance Sample Collection, processing and DNA extraction: Tissue and blood samples will be collected for both DNA extraction and to enable other omic investigations to be performed such as transcriptomics and proteomics and full information will be provided in part 2 of this Procurement process. An understanding of the Applicant's experience to coordinate, collect, process and store a range of samples, for this purpose will need to be provided including from distributed sites and/or institutions if a partnership approach is proposed. DNA extraction will be undertaken in a hybrid model, both within NHS Genomic Medicine Centres when desired and quality criteria have been shown to be met, otherwise being performed in a central biorepository. As DNA extraction is a key component of the Project, it is important for NHS England to understand specifically what experience the Applicant has of extracting DNA from blood and tissue (FFPE and/or fresh frozen), including the final outcomes in terms of quantity and quality of this and whether this has been subject to assessment in any form by an external organisation Central Biorepository: All patient samples, including some parts of the tissue block, will need to be transported to a central Biorepository and all locally extracted DNA will be subject to a quality assurance process before sequencing. The logistical arrangements for achieving this will be detailed in part two of this Procurement process. However, NHS Genomic Medicine Centres will be responsible for: (i) obtaining all specimens within their footprint and storing a locally retained aliquot for further investigations and validation; and (ii) sending these to a central Biorepository. Any similar previous experience is therefore relevant and should be presented by Applicants Post annotation and validation of data: Raw data, variant call files and annotated genomic information will be accessible by NHS Genomic Medicine Centres within the Genomics England data infrastructure. All NHS Genomic Medicine Centres will be responsible for the validation of any identified genetic variants and for any further testing and investigations as part of usual clinical care. It is expected that all NHS Genomic Medicine Centres would actively participate in the Genomics England Clinical Interpretation Partnership (GeCIP) and would share further validation findings and refresh clinical management information as new data becomes available. Any experience which the Applicant has of sharing and reviewing genetic data is therefore relevant, along with proposals as to 13

14 how these findings will be managed alongside current provision including outcomes from other genomic investigations. Applicants will need to provide evidence of access to bioinformatics, genetics and molecular pathology capability to inform and undertake the necessary validation, further investigation and interpretation steps and to liaise with the responsible clinical team. Please describe experience and capabilities in validating genomic findings, particularly in terms of laboratory testing but also detailing bioinformatics support available and proposals as to how these findings will be managed Reporting of findings for whole genome sequencing: A report will be issued that provides information on any pertinent mutations to the disease with a high likelihood of clinical relevance. This report will be dynamic, such that updated reports will be provided as improvements in annotation and understanding occur through the course of the programme. In addition clinically relevant pathogenic mutations in a small number of stated genes will also be provided in this report, unless patients opt out of receiving this information 1. The turnaround of this report would initially be expected to take approximately six months from when the samples have been supplied. However, the Project is aiming to reduce this turnaround time over the lifetime of the programme to 30 days Applicants must describe the process they would use for feeding back this information to patients as part of clinical care and also to related family members in the case of rare inherited diseases. A significant qualification aspect however is each Applicant's ability to engage with all relevant stakeholders, including any clinicians and patients/carers and family members, in order to make decisions on this kind of report Clinical care: All patients whose samples are supplied will need to follow their usual evidenced based care and management pathway inclusive of all diagnostics (which may involve routine or complex genetic/molecular analysis), other investigations and treatment. NHS Genomic Medicine Centres will need to be linked to all the institutions providing clinical care for the patients recruited and demonstrate the capabilities to appropriately feedback the genomic findings to patients and to family members (for rare inherited disease) as well as to undertake further validation testing as appropriate Ethics and consent: Patient consent will need to be obtained locally by the NHS Genomic Medicine Centres using the approved NHS Genomic Medicine consent for the Project. Demonstration of achieving local approval for multi-centre programmes in a short timescale and an infrastructure and experience for consenting appropriately as part of such programmes should be detailed Organisational governance and programme management and partnerships: It is expected that the Project will require the involvement of 1 This is currently under consideration by the Genomics England Ethics Advisory Committee and is subject to appropriate formal ethical approval of the Project 14

15 the board and CEO of each Applicant at a high level, and that this will be facilitated by regular reporting at board level. Each Applicant will need to demonstrate the capability to put in place robust programme management arrangements specifically for the Project, and be capable of complying with governance structures as required (including the governance as between entities working as partnerships/consortia). Evidence of previous programme management, and working across proposed partnerships, should be described in detail Partnerships and governance: Where NHS Genomic Centres are partnerships across multiple NHS organisations evidence of previous successful partnerships should be provided. It is important to describe an appropriate programme and project management structure and the proposed support from each relevant partner should be presented. If this is the case for your Application, please describe: Evidence of previous working and research relationships across organisations within the proposed NHS Genomic Medicine Centre; The planned programme and project management structure to manage the Project across the partners; and Whether partners fall under other established partnership structures, e.g. AHSNs or other clinical networks NHS transformation: As the Project is a major NHS transformation programme with some novel facets, many parts of the Project will be continually evolving as more information becomes available. It is therefore important to understand the Applicant's flexibility when working on previous projects which had an evolving scope and plans for engaging with the broad clinical team both within and outside of their institution with clinical care responsibilities for the patients and family members involved in the Project. 15

16 3.3 Table A - Scoring Criteria Form A - the details in Form A of Annex 3 are not evaluated, other than the financial criteria as set out in that section. Form B - the details in Form B of Annex 3 are mandatory exclusion criteria - if an Applicant indicates that it has breached one of the requirements then the Applicant will be excluded. Form C - the details in Form C of Annex 3 are discretionary exclusion criteria - these will be presented to the Procurement Board as Concerns for the Procurement Board's consideration. Form D - The items in Form D of Annex 3 are for information purposes only and are not evaluated, though they are likely to be evaluated in the second stage of the Procurement process. Form E - the items in Form E of Annex 3 are grouped, scored and weighted as follows: Group 1 - Diseases and capacity (17%) plus previous experience of clinical studies and trials (8%) = 25%; Group 2 - Data and informatics = 25%; Group 3 - Sample collection, processing and DNA extraction (8%), central biorepository (4%), post annotation and validation of data (8%) and reporting of findings for whole genome sequencing (5%) = 25%; and Group 4 - Clinical care (5%), Ethics and consent (5%), organisation and partnerships (10%) plus NHS transformation (5%) = 25%. The scoring applied to each category in Form E is as follows: 5 - a comprehensive answer with excellent detail and strong supporting evidence provided 3 - a good answer with some detail and an acceptable level of evidence provided 1 - a weak answer with little detail and little evidence provided

17 0 - little or no answer provided, with little detail and/or no evidence provided Form E Category Criteria Weighting (out of 100%) Diseases and capacity What is the Applicant's relevant experience of managing patients with the diseases listed in Annex 1? The Applicant is required to detail: 17% which, if not all, of the listed diseases the Applicant has any relevant experience with; whether this experience only relates to cancers or other diseases, or both; and evidence related to such experience, including the volumes and prevalence for each. The Applicant is also required to detail: appropriate assessment of cohort and recruitment size for disease areas; what estimates, modelling and calculations have taken place for rare inherited diseases and/or cancers and the evidence to support this; evidence of recruitment profile of these patient groups to clinical studies and/or trials (both previous and current); evidence of sufficient scale to act as an NHS Genomic Medicine Centre; details of other genomic studies and trials for the diseases listed in Annex 1 that are in a current recruitment phase and will remain so by 1st January 2015; and any national recognised specialist skills or expertise in any of the diseases listed in Annex 1 or additional diseases not listed. 17

18 Form E Category Criteria Weighting (out of 100%) Previous experience of clinical studies and trials What experience does the Applicant have of delivering other relevant genomic trials (such as the Deciphering Developmental Disorders (DDD) project, the Genomics England Pilot Study, and phases one and two of the CRUK Stratified Medicine Programme)? 8% Describe the infrastructure and capabilities for participating in major studies and trials? Experience of performance in consent and recruitment to multi-centre trials relevant to genomics. Experience in providing comprehensive clinical phenotypic data in a timely manner for clinical studies and supporting evidence. Data and Informatics What other studies has the Applicant been involved with which demonstrate their capability to collect and provide information according to standards and timelines required by other projects? Please detail your existing data and health informatics systems that will enable high quality data to be provided by the Applicant. Please detail any plans for improving data infrastructure for this project and clinical care using any Capital Investment Funding allocated to this programme? Please detail systems in place for managing patient recruitment and tracking completion of phenotypic datasets, consent and sample collection and processing. Please detail systems in place for entering comprehensive data within a defined time period e.g. as evidenced by successfully meeting clinical trial requirements. Please detail whether you already use SNOMED CT and if not what plans there are to 25% 18

19 Form E Category Criteria Weighting (out of 100%) implement it. Applicants should also provide detail on: where relevant data is stored in all organisations that are part of the proposed Genomic Medicine Centre; Previous experience and evidence of linking and integrating relevant data within the institution; Previous experience and evidence of linking relevant data across a partnership and distributed institutions; Evidence of completion and quality assessment from routine clinical data sets, clinical audits and any registries; and Existing systems for information governance. Sample Collection, processing and DNA Extraction What experience does the Applicant have of, obtaining blood and/or tissue samples, processing and storing them for - clinical trials and studies; - other omic investigations including for RNA extraction. Please describe how sample collection and processing has been coordinated and quality controlled across multiple sites and/or institutions. What experience does the Applicant have of collecting and processing patient data and samples from a distributed supply model? 8% 19

20 Form E Category Criteria Weighting (out of 100%) What experience does the Applicant have of extracting DNA from blood and tissue (FFPE or fresh frozen)? Central Biorepository Post annotation and validation of data Reporting of findings for whole Please describe the quantity and quality of the DNA obtained from whole blood and tumour, as verified by objective methods or another organisation) and any success rates where whole genome sequencing has been performed on samples supplied? Where the Applicant has experience of successfully sending specimens to a central Biorepository, what arrangements did it establish to facilitate this process? Please detail any failures with sending samples to central biorepositories or processing laboratories and actions that were taken to mitigate these. Provide details of storage and local aliquot/tissue retention arrangements for samples. What is the Applicant's experience with handling and sharing data, particularly at the level of the whole genome from blood and/or tissue? What systems are in place and what experience and capability does the Applicant have of validating genetic variants, undertaking further investigations and interpretation? How will findings be managed alongside current provision including outcomes from genomic investigations? What is the Applicant's access to specialist expertise in bioinformatics, genetics and molecular pathology? What experience does the Applicant have in relation to engaging with key stakeholders, including any clinicians and patients/carers and family members, in order to make 4% 8% 5% 20

21 Form E Category Criteria Weighting (out of 100%) genome sequencing decisions on any reported genetic or genomic findings? What process would be used for feeding back this information to patients as part of clinical care and also to family members in the case of rare inherited diseases? Clinical care Please provide information on the Applicant's usual evidence based care pathway for patients with cancer and/or rare inherited diseases? 5% What is the Applicant's experience in providing complex genetic/genomic information to other clinical specialities (outside of clinical genetics) and to the whole clinical team responsible for the care of the patients and for feeding back information to patients and to family members in the case of rare inherited diseases? Ethics and consent Organisational governance and programme management How has the Applicant previously managed any procedures for obtaining consent for genetic/genomic studies? Does the applicant have experience of using an Ethics Committee to advise on handling informed consent for research on (a) patients; and (b) patients' family members? If so, please provide details. Previous experience of achieving local approval for multi-centre programmes in a short timescale? Infrastructure and resources for consenting appropriately as part of such programmes in place or suitable proposal provided? Please provide board level support for the Project from the Applicant's institution and all entities working as partnerships/consortia. Please describe how compliance with governance arrangements will be achieved including between entities working as partnerships/consortia and evidence of previous 5% 10% (evaluated together as one criterion with Partnerships and 21

22 Form E Category Criteria Weighting (out of 100%) successful implementation of governance structures for a major clinical project. Governance below) Demonstrate successful management of a major clinical programme and the structures you have put in place. Evidence of learning from and responding to previous problems with major projects demonstrated. Partnerships and governance NHS transformation Please detail your approach to troubleshooting and remedying poor performance especially when responsible for other sites and/or institutions. Established relationships between partner organisations with evidence of previous successful working and robust governance arrangements? Appropriate scale of proposed partnership to act as an NHS Genomic Centre? Credible proposed programme and project management structure to manage the Project including performance across the partners? Proposed partners linked through a relevant established network? Please provide examples illustrating the flexibility of the Applicant to evolve aspects of previous projects in a rapid and timely manner when their scope has changed. Please provide information on how it is envisaged that all clinical teams will be engaged in the findings and outcomes of this Project. 10% (evaluated together as one criterion with Organisational governance above) 5% 22

23 4 Requirements and Commercial Arrangements 4.1 Overview of Requirements The requirements of NHS England for the services to be performed by NHS Genomic Medicine Centres can be summarised as follows, based on the Prospectus: identification of cases; ethics and consent, enrolment and case registration; collection of samples and the associated data from clinical and laboratory records; provision of clinical phenotype data to a nationally agreed minimal dataset; integrated Information Governance and Research and Development frameworks; preparation and extraction of DNA from blood and FFPE tissue where quality criteria are met, and preparation of samples for other 'omic investigation; sample transport logistics and supply of samples to a central biorepository; the validation of sequence findings and further confirmatory testing; additional clinical and laboratory investigations to more precisely define the clinical phenotype; and delivery the effective and evidence-based clinical care treatment plan, where relevant informed by the results of the Whole Genome Sequencing.

24 5 Submission of Applications 5.1 Format and content of Applications All Applications must be submitted: In electronic copy only, in editable word processing format; Using the template set out in Annex 3, with a maximum of one page of A4 paper / 500 words per criteria; Without any marketing material - this will not be evaluated; By to the following address england.genomics@nhs.net with the subject "NHS GMC WAVE 1 APPLICATION" with a delivery receipt requested - if applicants do not receive a delivery receipt they should assume that their application has not been received and try again; without any assumptions, as potential Applicants who consider that items may need clarifying should do so in accordance with paragraph 5.2; where applicants are applying as consortia or partnerships, indicating which entities the relevant responses relate to; and including all of the items set out in Annex 3; and Applicants are required to include a single point of contact in their organisation for their Application. Applicants should ensure that their addresses are monitored in the absence of that single point of contact to ensure that communications are addressed in appropriate timescales. 5.2 Receipt, Clarification and Validity of Application The period in which potential Applicants can raise clarification questions commences on the day the Stage One ITT is issued. Applicants are urged to review the Prospectus, this ITT and any other documents issued by NHS England immediately upon receipt and identify and submit any clarification questions as soon as possible. Should an Applicant submit clarification questions, these must be sent via to england.genomics@nhs.net with the subject "ITT STAGE ONE CLARIFICATIONS". Clarification questions received by any other method may not receive a response. The deadline for submitting any clarification questions is five working days before the final date of submission of the Application, as outlined in paragraph As detailed further in paragraph below, NHS England reserves the right to provide an anonymised copy of any clarification questions, and the answers to those questions, to all Applicants.

25 5.2.3 NHS England may require that Applicants clarify specific elements of their Application in writing within 3 working days (including that of partners/consortium members/supply chain members) and/or provide additional information within that same timescale. Any such clarification received shall then be added to that Applicant's response for the purposes of the evaluation and, should that Applicant be successful, the basis of their appointment. Failure to respond within 3 working days or as required shall be dealt with in accordance with paragraph

26 6 General 6.1 Right to reject or disqualify an applicant and right to cancel or vary the Procurement NHS England reserves the right to reject or disqualify an Applicant and/or its supply chain members where: the Application (or any part thereof) is submitted late, is completed incorrectly, is incomplete or fails to meet NHS England's submission requirements which have been notified to Applicants in this Stage One ITT; the Applicant and/or its supply chain members is/are unable to satisfy the terms of Article 45 of Directive 2004/18/EC and/or Regulation 23 of The Public Contracts Regulations 2006 (as amended) at any stage during the Procurement; there is a material change in identity, control, financial standing or other factor impacting on the selection affecting the Applicant and/or its supply chain members; the Applicant and/or its supply chain members is/are guilty of serious misrepresentation in relation to its Application and/or the Procurement; any Applicant directly or indirectly canvasses or offers or agrees to offer any gift or consideration to any member, officer or agent of NHS England, Genomics England or the Department for Health (or anyone involved in this Procurement on their behalf) as an inducement to bribe or influence the award of any contract in relation to the Procurement (or any matter pertinent to it); or the Application is not properly completed, contains other conditions or non-required additions, deletions, significant mistakes, any changes to the scope or any calculating errors NHS England reserves the right to: cancel, clarify or vary the Procurement, including the terms of this Stage One ITT, at any period during this Procurement process, although NHS England shall not adjust the evaluation methodology once the Applications have begun to be opened; reject an Application where the Applicant does not comply with a clarification request as set out in paragraph 5.2.3; and/or as outlined in paragraph 2.2.3, amend the timetable of the Procurement process and not consider any Applications which are not submitted by the submission deadline or, if applicable, any extension.

27 6.2 Consortia and partnerships Where the applicant is successfully awarded a contract as part of a consortium or group of different entities, each entity in such consortium or group shall be jointly and severally liable for the performance under the applicable contract. 6.3 Conflicts of Interest NHS England is likely to regard a conflict of interest as arising where an Applicant and/or a member or members of its supply chain or advisers have been involved in advising NHS England on matters relating to the Procurement or in the preparation of documents or information relating to the Procurement A conflict may also arise where a staff member from an Applicant and/or member of its supply chain and/or their advisers is related to an employee of NHS England NHS England is keen to avoid conflicts of interest. NHS England reserves the right to disqualify Applicants and/or supply chain members where there is an actual or potential conflict of interest Each Applicant should review the prior or current involvement of itself and its supply chain members and their advisers with NHS England. In the event that an Applicant identifies an actual or potential conflict, it should contact the Procurement Board by ing england.genomics@nhs.net with the subject "WAVE 1 CONFLICT OF INTEREST" to discuss such conflict prior to submission of its Application, or if later, immediately on it arising. 6.4 Freedom of Information NHS England is required to comply with its legal responsibilities under FOIA Laws. As a result, Applicants should be aware of NHS England's obligations and responsibilities under the FOIA Laws to disclose, on request, recorded information held by NHS England If an Applicant considers that any of the information included in its Application is commercially sensitive, it should identify which it is and explain what harm may result from disclosure if a request is received, and the time period applicable to that sensitivity Applicants should be aware that, even where they have indicated that information is commercially sensitive, NHS England might in any event be required to disclose it under the FOIA Laws if a request is received Applicants should also note that the receipt of any material marked 'Confidential' or its equivalent by NHS England should not be taken to mean that NHS England accepts any duty of confidence by virtue of that marking and NHS England retains the right to disclose such information under the FOIA Laws. 27

28 6.5 Security, Confidentiality and Permitted Disclosure This Stage One ITT is issued on the basis that all matters referred to in it are strictly confidential. No matter relating to this document or its contents or the proposed Project and/or Procurement shall be disclosed to any person, company or other legal entity without the prior written consent of NHS England (except as strictly necessary by the Applicant in order to obtain quotations necessary for the preparation of its Application in relation to insurance or professional advice). The information may not be used for any other purpose Applicants should ensure that they take steps to maintain such standards of security as are required by the conditions of this Stage One ITT in order to prevent unauthorised disclosure of any confidential information Applicants acknowledge and agree that: NHS England may disclose detailed information relating to Applicants' responses to the Stage One ITT (or stage two of the Procurement process) to NHS England's members, directors, officers, employees, agents or advisers and they may make Applicants' written responses available for private inspection by NHS England's members, directors, officers, employees, agents or advisers; NHS England reserves the right to disseminate information that is materially relevant to all Applicants, even if the information has only been requested by one Applicant, subject to the duty to protect any Applicant's commercial confidence in its responses. Should Applicants wish to avoid such disclosure (for example, on the basis that the request or response contains commercially confidential information or may give another Applicant a commercial advantage) the request must be clearly marked "In confidence - not to be circulated to other Applicants" and the Applicant must set out the reason(s) for the request for non-disclosure to other Applicants. Subject to the provisions of this paragraph 6.5.3, NHS England will act reasonably as regards the protection of commercially sensitive information relating to the Applicant. 6.6 General Except as specifically prescribed by law, NHS England shall have no liability whatsoever to any Applicant in relation to the outcome of the application process under this Stage One ITT or the second stage of the Procurement process and, for the avoidance of doubt, NHS England shall not be liable for any loss of profit or other economic loss incurred by any Applicant No guarantee can be given, and no representation is made, as to the accuracy of information contained within this document (including all its appendices, attachments and schedules, and the Prospectus and any other documents issued in relation to this Procurement). Each Applicant is responsible for obtaining (at its own expense) all information which it deems necessary or desirable for the preparation of its Application. Neither NHS 28