Optimising Exome Prenatal Sequencing Services (EXPRESS): a study protocol to evaluate rapid prenatal exome sequencing in the NHS Genomic Medicine Service

Background Prenatal exome sequencing (ES) for the diagnosis of fetal anomalies was implemented nationally in England in October 2020 by the NHS Genomic Medicine Service (GMS). is the GMS is based around seven regional Genomic Laboratory Hubs (GLHs). Prenatal ES has the potential to significantly improve NHS prenatal diagnostic services by increasing genetic diagnoses and informing prenatal decision-making. Prenatal ES has not previously been offered routinely in a national healthcare system and there are gaps in knowledge and guidance. Methods Our mixed-methods evaluation commenced in October 2020, aligning with the start date of the NHS prenatal ES service . Study design draws on a framework developed in previous studies of major system innovation. There are five interrelated workstreams. Workstream-1 will use interviews and surveys with professionals, non-participant observations and documentary analysis to produce in-depth case studies across all GLHs. Data collection at multiple time points will track changes over time. In Workstream-2 qualitative interviews with parents offered prenatal ES will explore experiences and establish information and support needs. Workstream-3 will analyse data from all prenatal ES tests for nine-months to establish service outcomes (e.g. diagnostic yield, referral rates, referral sources). Comparisons between GLHs will identify factors (individual or service-related) associated with any variation in outcomes. Workstream-4 will identify and analyse practical ethical problems. Requirements for an effective ethics framework for an optimal and equitable service will be determined. Workstream-5 will assess costs and cost-effectiveness of prenatal ES versus standard tests and evaluate costs of implementing an optimal prenatal ES care pathway. Integration of findings will determine key features of an optimal care pathway from a service delivery, parent and professional perspective. Discussion The proposed formative and summative evaluation will inform the evolving prenatal ES service to ensure equity of access, high standards of care and benefits for parents across England.


Background
Prenatal exome sequencing (ES) for the diagnosis of fetal anomalies was implemented nationally in England in October 2020 by the NHS Genomic Medicine Service (GMS). is the GMS is based around seven regional Genomic Laboratory Hubs (GLHs).Prenatal ES has the potential to significantly improve NHS prenatal diagnostic services by increasing genetic diagnoses and informing prenatal decision-making.Prenatal ES has not previously been offered routinely in a national healthcare system and there are gaps in knowledge and guidance.

Methods
Our mixed-methods evaluation commenced in October 2020, aligning with the start date of the NHS prenatal ES service .Study design draws on a framework developed in previous studies of major system innovation.There are five interrelated workstreams.Workstream-1 will use interviews and surveys with professionals, non-participant observations and documentary analysis to produce in-depth case studies across all GLHs.Data collection at multiple time points will track changes over time.In Workstream-2 qualitative interviews with parents offered prenatal ES will explore experiences and establish information and support needs.Workstream-3 will analyse data from all prenatal ES tests for nine-months to establish service outcomes (e.g.diagnostic yield, referral rates, referral sources).Comparisons between GLHs will identify factors (individual or service-related) associated with any variation in outcomes.Workstream-4 will identify and analyse practical ethical problems.Requirements for an effective ethics framework for an optimal and equitable service will be determined.Workstream-5 will assess costs and cost-effectiveness of prenatal ES versus standard tests and evaluate costs of implementing an optimal prenatal ES care pathway.Integration of findings will determine key features of an optimal care pathway from a service delivery, parent and professional perspective.

Discussion
The proposed formative and summative evaluation will inform the evolving prenatal ES service to ensure equity of access, high standards of care and benefits for parents across England.

Plain English summary
Background: Prenatal exome sequencing is a new test that is offered through the NHS Genomic Medicine Service.Prenatal exome sequencing is offered to pregnant women when ultrasound scans suggest that their baby may have a genetic condition that cannot be diagnosed using standard tests.If a genetic condition is diagnosed this can give parents important information about the outlook for their baby.It can also help with their decisions about whether to continue or end the pregnancy, pregnancy management, post-birth care and future pregnancies.
Study methods: The aim of this study is to evaluate the prenatal exome sequencing service.
To do this we will; 1. Study how prenatal exome sequencing is delivered across England using surveys and interviews with professionals.
2. Interview parents to ask what they think of prenatal exome sequencing and how support and information could be improved 3. Look at how many parents have prenatal exome sequencing and the test results.We will look carefully at who has access to the test and whether any particular groups are less likely to be offered testing.
4. Conduct workshops with health professionals and parents to identify any practical or ethical problems that arise when prenatal exome sequencing is offered.
5. Look at the cost of prenatal exome sequencing and compare it to the cost of other tests that are offered to diagnose genetic conditions in pregnancy.
6. Gather our findings together to make recommendations for best practice.
Patient and Public Involvement: A patient and public Involvement, engagement and participation (PPIEP) advisory group will work closely with the research team to design the study and develop study materials.They will also help us understand our findings to make sure the information and recommendations that come out of our research will be helpful to parents and the NHS.

Plain English summary
Background Prenatal exome sequencing is a new test that is offered through the NHS Genomic Medicine Service.Prenatal exome sequencing is offered to pregnant women when ultrasound scans suggest that their baby may have a genetic condition that cannot be diagnosed using standard tests.If a genetic condition is diagnosed this can give parents important information about the outlook for their baby.It can also help with their decisions about whether to continue or end the pregnancy, pregnancy management, post-birth care and future pregnancies.

Study methods
The aim of this study is to evaluate the prenatal exome sequencing service.
To do this we will; 1. Study how prenatal exome sequencing is delivered across England using surveys and interviews with professionals.
2. Interview parents to ask what they think of prenatal exome sequencing and how support and information could be improved 3. Look at how many parents have prenatal exome sequencing and the test results.We will look carefully at who has access to the test and whether any particular groups are less likely to be offered testing. 4. Conduct workshops with health professionals and parents to identify any practical or ethical problems that arise when prenatal exome sequencing is offered.

Introduction
Fetal anomalies occur in approximately 2-5% of pregnancies and cause around 20% of perinatal deaths 1,2 .When fetal structural anomalies are detected by ultrasound, routine prenatal testing options can include karyotyping, chromosomal microarray or gene-specific panels, which will diagnose around 40% of cases.Prenatal exome sequencing (ES), which can interrogate multiple genes at high resolution in a single test, has been shown to improve diagnostic yields by 8-10% in unselected pregnancies where there is a structural abnormality and normal karyotype and chromosomal microarray 3,4 .Factors such as the rigour of eligibility criteria, testing platforms, trio (parents and fetus) versus singleton (fetus only) sequencing and, in particular, whether there has been selection following genetic review all impact on diagnostic yield 5 .A growing number of studies have demonstrated the clinical utility of prenatal ES [6][7][8] and recent guidelines from professional bodies have considered the evidence for the use of this test [9][10][11] .Accurate genetic diagnosis allows tailored parental counselling about prognosis; informs decision-making about pregnancy management; and aids planning for delivery and perinatal management.It also circumvents the pre-and postnatal 'diagnostic odyssey' and allows accurate counselling about recurrence risk for future pregnancies.
The NHS in England is the first national healthcare system to systematically embed genome and exome sequencing in routine clinical care.To do this, genetic services across England have been reconfigured to establish a national NHS Genomic Medicine Service (GMS) which consolidates all genomic testing into a unified service that is delivered through seven regional NHS Genomic Laboratory Hubs (GLHs) and NHS Genomic Medicine Service Alliances (GMSAs) with a National Genomic Test Directory which dictates which genomic tests are

Amendments from Version 1
Two new authors have been added who contributed to the further development of the study methodology and manuscript editing.
We have clarified that the start date of EXPRESS aligns with the start date of the prenatal exome sequencing service.
We have corrected the discrepancy in the wording between Figure 1 and the text.
We have added additional information in the text about the framework for major systems innovation and how it will be applied in our analysis.
We have added additional detail about how each phase of data collection in workstream-1 will be analysed.
We have simplified our conceptual framework and analysis will focus on the framework for major systems innovation and the MRC guidance for process evaluations.
We have added a reference to the linked workstream(s) for each of the study objectives.
We have clarified the types of professionals we will interview in our national and local level interviews in workstream-1.
We have clarified the recruitment procedures for workstream-2 to address concerns around risk of selection bias in the parent interviews and we have added selection bias as a potential limitation of the study in the discussion.
We have revised the section describing workstream-3, adding a sub-section titled "Data collection and analysis" that includes further information about data quality and delineates the covariates and outcomes.
We have added further detail around the planned workshops in workstream-4, explaining that there will be separate parent and professional workshops to discuss ethical issues.
We have expanded the description of the integration of findings to clarify that data from all workstreams will be drawn together with the aim of addressing each of our study objectives and to explain who will be invited and the content of the planned workshops.
Any further responses from the reviewers can be found at the end of the article available through this service 12 .The NHS GMS aims to deliver high throughput and high-quality genomic testing with equity of access for patients across the NHS 13 .Prenatal ES was implemented nationally in the NHS GMS in October 2020 and is offered to parents across England when anomalies identified on fetal ultrasound are considered likely to have a genetic aetiology, as determined by a multidisciplinary team that includes a clinical geneticist.Prenatal ES is listed as R21 in the National Genomic Test Directory 12 .
Professional bodies have highlighted the many practical considerations to implementing a service that delivers prenatal ES [9][10][11] .As prenatal ES is being implemented nationally in England, there is the potential for wide variation in referrals, uptake and diagnostic rates.Research studies considering parent or professional views on prenatal ES largely support offering prenatal sequencing but raise concerns over the potential for increased parental anxiety, informed consent, management of parent expectations, cost, which results to report and when to reinterpret results [14][15][16][17][18][19] .The need for health professional education and new approaches to genetic counselling that support informed choice during a distressing and time-pressured period have also been highlighted 15,18 .Another key challenge will be counselling parents around the range of findings and possible uncertainties 20 .As a result, it is crucial that the prenatal ES service is evaluated and guidelines developed to support high quality care for parents and facilitate delivery of an equitable and efficient national service.
Here we provide an outline of the optimising EXome PREnatal Sequencing Services (EXPRESS) study; a three-year prospective evaluation of prenatal ES in the NHS GMS.The EXPRESS study commenced in October 2020 to align with the start of the prenatal ES service.We are analysing the national implementation of prenatal ES in order to determine an optimal care pathway that maximises benefits for parents while optimising use of NHS resources.This research will capture the perceptions of parents and professionals, identify ethical and practical issues and highlight any unintended consequences of the new care pathways.As our research started in the first year of the prenatal ES service, we proposed a formative evaluation that will deliver lessons for the developing service within the timeframe of the study.

Protocol
Study design EXPRESS is a multi-site, mixed-methods study that will evaluate how prenatal ES is offered in the NHS GMS.We will combine qualitative analyses of the service, stakeholder perspectives and ethical considerations with quantitative analyses of clinical outcomes and cost effectiveness.The research design draws on a framework developed in previous studies of major system innovation (Figure 1) 21,22 .The framework addresses the "how and why" of system innovation by considering key processes in implementing a new service: the decision to change (drivers to change, governance and leadership of decision making), decisions on care pathways (development and selection of care pathways), implementation approaches (consideration of context and approaches to facilitation) and implementation outcomes (adoption, spread and fidelity) 21,22 .The framework addresses "what works and at what cost" by linking these processes to service outcomes: evidence-based care, clinical outcomes, parent experiences and costs and consequences.As a result of applying the framework, our evaluation of the outcomes of the prenatal ES service (what works and at what cost) will be grounded in an understanding of the planning and implementation of the service (how and why) (Figure 1).

Study oversight
A Steering Committee with academic, professional and patient and public involvement, engagement and participation (PPIEP) members and a PPIEP Advisory Group will oversee the evaluation, providing guidance and feedback through regular interactions with the research team throughout the study.

Critical distance
Our research team includes several clinicians and laboratory scientists with a professional role in the NHS GMS, whose expertise will be crucial throughout the study.NJF and SM are independent of the NHS GMS and have extensive experience in the evaluation and appraisal of healthcare services and they will be responsible for ensuring that a "critical distance" is maintained throughout our evaluation.

Patient and public involvement, engagement and participation
We are embedding PPIEP in all aspects of our study.Patient advocates are co-applicants on the grant and a PPIEP Advisory Group has been formed that includes representatives of rare condition charities and members who can advise on including the views of ethnic minority groups.The PPIEP Advisory Group have inputted into the design of the study and the development of study materials for parents.They have reviewed and revised parent-facing documents such as participant information sheets and topic guides and advised on plans for the recruitment of parents for qualitative interviews.Research findings will be shared with the PPIEP Advisory Group throughout the study and they will support the development of recommendations and information resources that will be helpful to parents, families and the NHS.Another key element of our PPIEP strategy is to have a qualitative researcher embedded within the parent support group Antenatal Results and Choices (ARC) who will have a broad appreciation of the information and support needs of parents who have experienced anomalies in pregnancy.

Study aims and objectives
The aim of EXPRESS is to provide a formative and summative mixed-methods evaluation of the new prenatal ES service, to ensure national delivery of an equitable, acceptable, ethical, robust and cost-effective care pathway that improves the quality of care for parents undergoing prenatal diagnosis in fetuses with anomalies likely to have a genetic aetiology.

Specific objectives:
A. Determine the clinical care pathways for prenatal ES in each of the seven GLHs (Workstream-1).
B. Establish whether prenatal ES is understandable and acceptable to key stakeholders, including parents (Workstream-2) and professionals (Workstream-1).
C. Identify the education and information needs and how they are best addressed for parents (Workstream-2) and health professionals (Workstream-1).
D. Establish the outcomes (diagnostic yield, referral rates, final diagnoses) of the prenatal ES programme (Workstream-3), compare these between regions, and identify any factors (individual or service-related) associated with variation in outcomes (All Workstreams -Integration of findings).
E. Identify any new ethical issues arising from offering the prenatal ES programme in the NHS and explore how health professionals can best be supported in addressing them (Workstream-4).
F. Formally evaluate the cost and cost-effectiveness of implementing the optimal prenatal ES pathway (Workstream-5).
G. Determine the key features that constitute the optimal prenatal ES pathway from a service delivery, patient and professional perspective (All Workstreams -Integration of findings).

Study setting
This is a nationwide study that will look at provision of prenatal ES across England through the NHS GMS.Prenatal ES testing is performed at two of the seven GLHs (NHS North Thames GLH and NHS Central and South GLH).Parents are referred through fetal medicine units (FMUs) by clinical geneticists from all GLHs.As such, the setting for our research are the seven GLHs and their linked clinical genetic services and FMUs.The seven GLHs are; NHS Central and South GLH, NHS East GLH, NHS North West GLH, NHS North Thames GLH, NHS South East GLH, NHS South West GLH and NHS North East and Yorkshire GLH.

Workstream overview
Our mixed-methods evaluation of the new prenatal ES service comprises five interrelated workstreams.

Workstream-1: Defining clinical care pathways Phase 1: Understand the goals and challenges for the current service
In the first 6 months of EXPRESS we will use three approaches to gain an understanding of the anticipated goals and early challenges for the prenatal ES service. 1) To identify key challenges for service delivery we will conduct a mixed-methods systematic literature review on the use of prenatal ES in both research and clinical settings worldwide.The review will be conducted according to PRISMA guidelines 23 .
2) To explore the drivers of implementation and examine the overarching ambitions and potential challenges for the service we will conduct 8-10 interviews at a national level with the key staff who were involved in decisions to establish the prenatal ES service or who were central in developing the national guidance for service delivery.We will also undertake a documentary analysis and collect any available business case and policy documents relating to the national implementation of prenatal ES.
3) To gather the views of professionals involved in delivering the prenatal ES service at a local level across England, we will conduct qualitative interviews with 2-3 professionals from each GLH; including clinical geneticists, fetal medicine specialists and clinical scientists.The interviews will explore professionals' expectations, perceptions of current challenges for delivery, foreseen ethical problems, training and education needs and plans for developing the service.

Phase 2: Establish emergent care pathways and produce an overview description of services
In months 6-18 of the study, we will produce a taxonomy of the care pathways emerging in practice for all seven GLHs.This work will document early indications of consensus and variation in service delivery, organisation and design, and will form the foundation for understanding why the different networks vary in service provision (if they do).To do this, we will conduct a cross-sectional survey with ~100 clinical staff across England to determine how eligibility criteria are applied, consider information available to clinicians (such as high-quality ultrasound scans for phenotyping), and explore training and education needs and overall views on prenatal ES and how it is delivered.We will also examine referral pathways and patient flow from general maternity units to FMUs to genetics services.A sub-set of survey participants from a range of backgrounds and geographies will be contacted to take part in a follow-up interview that will probe their responses to the survey in more depth.In addition, to examine how processes then change over time we will monitor service delivery through 6 monthly calls with a key contacts to ask a standardised list of questions.

Phase 3: In-depth case studies
We will produce in-depth case studies of prenatal ES services across each of the seven GLHs.A case study approach to data collection will be used [24][25][26] .We will refer to MRC guidance 27 on the conduct of process evaluations for studying the implementation of complex health interventions and apply the study design framework (Figure 1) to explain how the new prenatal ES services have developed over time, and across different contexts.As the prenatal ES service is entirely new to the NHS there is no baseline, so case studies will address how the service is being delivered against service objectives, aspirations and adaptations, and the plans identified by professionals in Phase 1 and 2. Data analysis will draw on quantitative data from the survey with health professionals and qualitative data from semi-structured interviews with staff from a range of backgrounds, key documents and non-participant observations of relevant team meetings in each GLH.

Recruitment of professionals
To recruit participants to semi-structured interviews, professionals from relevant backgrounds will be identified by the research team with the help of key contacts at each GLH.We will purposively sample health professionals from a range of backgrounds including clinical geneticists, genetic counsellors, fetal medicine consultants, midwives, clinical scientists and hospital chaplains.An invitation email along with a participant information sheet describing the purpose of the study will be emailed to potential participants.The professionals will be asked to contact the research team via telephone or email if they are interested in participating in an interview.To recruit participants to take part in the survey, the service leads from each regional genetics service in England will be asked to nominate 15-20 professionals from relevant clinical backgrounds to take part in the survey (clinical geneticists, genetic counsellors, fetal medicine consultants and midwives).An invitation email along with a participant information sheet describing the purpose of the survey will be emailed to potential participants.For non-participant observations we will notify the attendees in advance of the meeting of our intention to observe the meeting and obtain consent at the time of the meeting.

Data collection and analysis
Interviews will be carried out by phone, video call or face-toface.Interviews will be digitally recorded and professionally transcribed verbatim.All qualitative data (interviews, observations, fieldwork notes, survey responses (open-ended questions and comments) and documents) will be anonymised and then analysed using the principles of codebook thematic analysis 28,29 .Data analysis will combine inductive and deductive approaches 30 .Data will be coded into meaningful units of text and then grouped into broader thematic categories that will be progressively reviewed and redefined.Qualitative data will be managed using NVivo version 12 (QSR International, Pty Ltd).To ensure the validity and rigour of the qualitative analysis two experienced qualitative researchers will conduct the analysis, following recommended protocols 31 .To strengthen the credibility of the findings and include the perspectives of parents and clinicians from a range of backgrounds, themes will be reviewed and discussed with the wider research team and the PPIEP Advisory Group.Descriptive statistics will be used to summarise findings from the quantitative survey data.
To understand the goals and challenges for the current service (Phase 1), we will draw on our findings from the literature review, interviews with key national staff, documentary analysis of national guidance and interviews with professionals from the seven GLHs and their associated clinical services.We will use thematic analysis to explore goals of the service, the context of the service and contextual factors shaping the service and the decision to change.
To establish emergent care pathways and produce an overview description of the services (Phase 2), we will draw on the cross-sectional survey and follow-up interviews with professionals from genetic and fetal medicine services across the seven GLHs.We will use descriptive statistics to analyse survey questions relating to care pathways and descriptions of the service.We will use inductive thematic analysis to code and extract data relating to local care pathways.We will triangulate this data to produce typologies of the care pathways emerging in practice across all seven GLHs, allowing us to compare and contrast different services within and between GLHs.
To understand implementation of prenatal ES services, we will conduct in-depth case studies (Phase 3), informed by Fulop et al.'s 21,22 conceptual framework of major system change (Figure 1) and MRC guidance on process evaluation 27 .The case studies will draw on interview data, survey data and documentary analysis.We will input summary data from these sources into case study templates and triangulate findings to explore implementation and barriers and facilitators to implementation.The use of case study templates will support the mapping of service components and care pathways into typologies that will allow comparison within and between GLHs.
To analyse the qualitative data for the case studies, a coding frame will be developed that incorporates the elements of major system change (i.e.decision to change, decisions on care pathways, implementation approaches, implementation outcomes and service outcomes) 21,22 and considers factors emphasised in the MRC guidance on process evaluation (i.e.context, implementation and mechanisms of impact) 24 .We will apply this coding frame to the data set and develop themes and sub-themes relating to our research questions, our study objectives, the literature and the empirical data.

Workstream-2: Parental views and experiences of prenatal ES.
Parent views and experiences of prenatal ES will be gathered through qualitative interviews with approximately 40 parents offered prenatal ES who either accepted or declined testing (recruited through FMUs and through parent support groups).FMUs from across England will be included as recruitment sites, with consideration given to maximising opportunities to reach parents with diverse socio-demographic backgrounds.Participants will be purposefully sampled to promote maximum variation in terms of clinical experiences and socio-demographic factors such as ethnicity and socio-economic background.
Using a semi-structured topic guide (developed with the feedback from the PPIEP Advisory Group), we will explore parents' views of prenatal ES and their thoughts on the information and support needs of parents.For parents offered ES, we will also ask about their experiences of the service, including what genetic counselling they received, their decision-making, motivations for having or declining testing, and costs incurred.

Recruitment of parents through FMUs
Invitations to parents to take part in an interview will only be given after the parents have been offered ES and have made their decision to accept or decline testing and, as such, this research will not impact on their decision-making about this test.The clinical team at FMUs that have offered prenatal ES will identify parents that accepted or declined prenatal ES.A letter explaining the interview study and the Participant Information Sheet will be sent to potential participants.The letter will include an invitation to participate in an interview and they will be asked to contact the research team via telephone or email if they are interested in participating.After two weeks, if the potential participant has not responded a member of the local clinical care team will call the potential participant to ask if they received the study invitation and whether they have any questions about taking part.If they are interested in taking part, the potential participant can give verbal consent for the research team to contact them directly about taking part in the study.As this will be a stressful and emotional time for parents, the researcher conducting the interviews will be guided by the clinical team as to the best time to send the initial invitation letter to the parents.

Recruitment of parents through parent support groups
We will recruit parents (with and without experience of prenatal ES) through registered parent support groups such as ARC.Parent support group members will be invited to participate through an advertisement on the parent group website or through social media (Facebook/Twitter).Parents will be asked to contact the research team if they are interested in participating.Parents will be sent the participant information sheet and invited to ask questions about the study and make a time for the interview

Data collection and analysis
Interviews will be carried out by phone, video call or faceto-face at a location convenient to the participant, such as their home or an office at the recruiting hospital.Interviews will be digitally recorded, professionally transcribed, anonymised and analysed using the principles of codebook thematic analysis 28,29 .Our recruitment target of approximately 40 interviews is guided by our previous research focused on new approaches to prenatal testing and should be sufficient to include parents with a range of clinical experiences and socio-demographic factors 32,33 .

Workstream-3: Factors associated with variation in outcomes across the GLHs.
In this workstream we will establish the outcomes (diagnostic yield, referral rates, final diagnoses) of the national prenatal ES service over a nine month period (01/09/2021 -31/05/2022).These outcomes will then be compared across regions to identify any factors (individual or service-related, including the clinical sources of referral) associated with variation in outcomes between GLHs.At the point of being consented for prenatal ES, parents will be asked to allow their data to be used for research purposes.

Data collection and analysis
Cases will be identified from testing GLHs and data extracted for nine months.Pregnancy-level information on sociodemographics (age, socioeconomic status (Index of Multiple Deprivation, IMD) determined from postcodes, ethnicity), gestation at referral for testing, the hospital or clinic making the referral, and results of ES will be collected from testing GLHs.Pregnancy outcomes will be collected through NHS Digital in collaboration with the National Congenital Anomaly and Rare Disease Registration Service (NCARDRS).Data will be obtained from two sources.Data on congenital anomalies will be obtained from NCARDRS and on other pregnancy outcomes from NHS Maternity Hospital Episode Statistics (HES).All livebirths, fetal deaths with gestational age greater than or equal to 20 weeks and pregnancy terminations for fetal anomaly at any gestational age) with at last one registered anomaly delivered in England are included in NCARDRS, which follows the European Surveillance of Congenital Anomalies (EUROCAT) data quality guidance 34 .NHS Maternity Hospital Episode Statistics (HES) include data on all admissions to give birth in England and have high levels of completeness 35 .Information at the pregnancy level from Maternity HES on all women giving birth in England will be linked with NHS Digital on the basis of women's NHS number to the data from GLHs and NCARDRS before analysis of an anonymised dataset.Multi-level models will then be built examining the influence on outcomes of individual and GLH level factors (based on network pathways identified in Workstream-1).
Descriptive analyses: The following information will be described for each GLH: • Number of women giving birth in the GLH area annually (mapped on the basis of births in referring units and their associated home births).
• Characteristics of women giving birth in each GLH area: Age (mean, SD), IMD score (% in each quintile), ethnicity (grouped according to UK census classification).
• Number of women referred for prenatal ES annually and the sources of referrals.
• Characteristics of women referred for prenatal ES in each GLH area: Age (mean, SD), IMD score (% in each quintile), ethnicity (grouped according to UK census classification).
Other characteristics of each GLH will have been described as part of Workstream-1 and are likely to include categorical factors such as case selection; links between FMUs, clinical genetics and laboratories; laboratory pipelines; turn-around times; and interpretation and reporting of results.
Overall referral rates with 95% confidence intervals in each GLH will be calculated, and referral rates within population subgroups (IMD quintiles, ethnic groups) calculated to assess equity across the system and ensure the needs of ethnic minority and seldom heard populations are being appropriately considered.Factors associated with variations across GLHs in referral rates (population characteristics, GLH factors) will be examined using regression analysis.Similarly, in each GLH diagnostic yield will be calculated (proportion of women with a clear final diagnosis on the basis of prenatal ES) as well as outcomes of prenatal ES (proportion of women undergoing ES opting for termination, live birth rate, stillbirth rate and proportion of births with a confirmed anomaly) and factors associated with variation examined.

Workstream-4: Ethical analysis.
To inform and promote the achievement of high ethical standards in the NHS GMS, we will analyse ethical issues arising in the delivery of prenatal ES, through an ethical analysis of stakeholder workshops, interviews with professionals (Workstream-1), interviews with parents (Workstream-2), and engagement with the PPIEP Advisory Group.Ethical issues to address are likely to include, but will not be limited to, the following: • Enabling adequate levels of informed consent for this complex testing • Equity of access • Decisions about reporting results to parents in the context of increased uncertainty and complex probabilities • Questions relating to the sharing of data: for clinical and/or research purposes • Clarification of the nature and scope of the duties of care of health professionals and laboratory staff when offering this complex testing to pregnant women A systematic scoping review of the relevant literature, professional guidelines and reports of advisory bodies on the prenatal uses of genomics and genetics will provide an initial mapping of the likely ethical issues and themes for further investigation.Themes will be discussed with the PPIEP and incorporated into semi-structured topic guides used in the interviews with professionals (Workstream-1) and parents (Workstream-2).
Results will be combined to inform a comprehensive analysis of core ethical concepts and considerations to aid development of a draft ethics framework, which will be revisited and revised in light of findings from other arms of the study and three-four ethics workshops.There will be separate workshops for professionals and parents.Parents will be invited through patient groups (e.g. from ARC, UNIQUE and Genetic Alliance UK) and through NHS maternity services.The workshops with parents will explore views on potential ethical problems associated with offering prenatal ES in the NHS.The workshops with professionals will bring together clinical and laboratory staff from across the seven GLHs and associated clinical services.The professionals will be encouraged to discuss clinical cases and issues arising from delivering the prenatal ES service.Invitations to the workshops will be advertised through professional email lists and it is possible that individual professionals could attend more than one workshop.The workshops with professionals will gather evidence about ethical problems arising in practice and explore perspectives on the nature and scope of professional responsibilities in the provision of prenatal ES.The workshops with parents and professionals will allow us to gather a rich account of the ethical aspects of implementation in practice and identify possible solutions and/or forms of effective ethical advice.We will map key issues, explore themes in-depth and seek views on requirements for an effective ethics framework.

Workstream-5: Health economic evaluation Phase 1: Cost of prenatal ES versus standard testing
We will undertake a detailed micro-costing exercise to evaluate the unit costs of prenatal ES and other tests at each GLH.This will provide evidence on the likely affordability of prenatal ES for use in routine care.Micro-costing is a highly detailed costing approach that identifies all the underlying resources required for an intervention/activity, such as equipment, consumables, and staff time, and then calculates costs for these resources.We will follow a previously used approach to costing genetic tests 36 .The standard operating procedures for each test will be used to develop costing questionnaires to collect the resource use information.The questionnaires will cover each stage in the experimental protocol from sample preparation to data interpretation and reporting.Resource use information on staff time, consumables, and equipment will be derived from the questionnaires.The analysis will account for the expected cost of any errors or failures during the testing processes.For capital equipment items, the cost will be spread over the item's predicted lifetime and depreciated using equivalent annual costing.The cost of staff and consumables will be taken from market prices.The cost per test will be based on the measured annual throughput of the sequencing platforms.For standard testing we will adopt a two-stage approach.As these tests are currently established in routine care we will ascertain if each GLH has carried out their own micro-costing analysis for reimbursement purposes -in previous similar studies we have found this to be the case.If so, we will use these costs for our analysis, ensuring that the cost components included are commensurate across GLHs.If this is not the case, then we will undertake our own micro-costing exercise at each GLH where costs of standard tests are not available, utilising the same approach as described above for ES.Due to the sensitivity of these data the results for each individual GLH will remain anonymous and we will present mean and (anonymised) ranges only.

Phase 2. Costs and consequences of the optimal prenatal ES pathway
We will undertake cost and cost consequences analyses of the different delivery pathways at each of the seven GLHs, plus the identified optimal prenatal ES pathway.In previous research we have argued that quality-adjusted life years are not commonly used in economic evaluations of prenatal testing for fetal anomalies 37 , and therefore we will not use them here (nor undertake a cost-utility analysis).Costs will be estimated from the perspectives of both the NHS and families, with the time horizon being the duration of pregnancy.Using an approach we have used in similar studies 37,38 , the analysis will proceed in the following stages: 1) We will delineate the pathways for prenatal diagnosis of fetal anomalies using prenatal ES, from referral for testing until birth outcome.This will be done for each of the seven GLHs and the optimal pathway, and will be based on data collected during Workstream-1.
2) Using the linked FMU outcomes/National Congenital Anomaly and Rare Disease Registration Service data collected during Workstream-3 we will plot the movement of pregnant women through each of the pathways.We will extract information on the numbers of women undergoing different tests, the numbers and type of fetal anomalies identified, the number of follow-up contacts related to testing, and pregnancy outcomes.
3) We will identify the unit costs associated with the main cost components of the identified pathways.These will be obtained from the micro-costing, supplemented with other unit costs from the GLHs, and published and other routinely available sources.
4) We will calculate the NHS costs associated with each pathway, by applying the unit costs associated with each item in the pathway from stage 3 with the numbers of women incurring that cost based on the data at stage 2.
5) We will calculate the financial costs to parents and families from the different pathways using data from the parent interviews in Workstream-2.
6) We will undertake a cost consequences analysis comparing the NHS and family costs of each pathway against the consequences, as delineated in Workstream-3 (e.g., diagnostic yield, birth outcome).

7)
We will use our analysis to assess the expected budget impact to the NHS of introducing prenatal ES, based on the mean costs per woman tested and projections of the expected numbers of women tested by prenatal ES nationally.
8) We will identify the main sources of uncertainty in our analyses and undertake a sensitivity analysis to explore the impacts of this uncertainty.

Integration of findings
Using an approach of simultaneous triangulation 39 , we will draw together data collected in the quantitative and qualitative analyses of the service (Workstream-1), qualitative analysis of stakeholder perspectives (Workstream-1, Workstream-2 and Workstream-4), quantitative analyses of clinical outcomes (Workstream-3), ethical analysis (Workstream-4), and the economics analysis (Workstream-5).The integration of findings will focus on addressing our study objectives and be underpinned by the conceptual framework of major system change (Figure 1).In line with the "how and why" of the study design framework (Figure 1), data, including quantitative surveys with professionals (Workstream-1), qualitative semistructured interviews with professionals (Workstream-1) and parents (Workstream-2) and ethics workshops (Workstream 4), will be used to identify drivers for change (decision to change), how services were planned (decision to change), factors influencing the service models and care pathways (decisions on care pathways), how services were implemented (implementation approaches) and adoption and sustainability of the service (implementation outcomes).To explore "what works at what cost" we will draw on the clinical outcomes established in Workstream-3, the costs and consequences identified in Workstream-5 and our understanding of the parent experience (Workstream-2).
We will also conduct two stakeholder workshops to report our findings and gather feedback that will explore identified local variation in the prenatal ES service and refine the key features of an optimal care pathway from a service delivery, parent and professional perspective.Invited participants will include professionals from a range of backgrounds and all GLHs, policy makers and patient group representatives.During the workshops we will present our key research findings and the draft recommendations developed by the research team and the PPIEP Advisory Group.Discussion will focus on refining and prioritising the recommendations.
Through this process we will define current service provision, identify the facilitators and barriers to optimal service delivery and highlight key lessons to inform future models of service provision and will produce recommendations for best practice.Invitations to parents to take part in an interview or workshop will be sent after the parents have been offered ES and have made their decision to accept or decline testing so that the research does not impact on parents' decision-making about prenatal testing.For interviews with parents and professionals, the potential participants will be given a participant information sheet describing the study, what participation involves, confidentiality and plans for data protection and data storage and written or verbal (recorded) consent will be obtained.For the surveys, returning a completed survey will be taken as implied consent to participate.

Study status
The study commenced on October 1 st 2020.The study is currently open for recruitment.

Study registration
The EXPRESS study was prospectively registered with the Research Registry (researchregistry6138).

Dissemination plan
Dissemination will be both formative, as we will feed back findings as the study proceeds, and summative.Our strategy for engagement, formative feedback and dissemination includes: • Workshops with professionals from a range of backgrounds.
• Progress reports shared at a national level with the NHS Genomics Laboratory Hub Partnership Board and professional bodies, such as the Joint Committee on Genomics in Medicine and the British Maternal and Fetal Medicine Society.
• Presentations at national and international conferences.
• Plain language summaries of findings, written with the help of the PPIEP Advisory Group, will be disseminated to parent and patient networks via meetings, newsletters, social media and the EXPRESS study website.
• A policy report that will describe the facilitators and barriers to optimal service delivery and deliver recommendations for best practice.

Discussion
The EXPRESS study will inform the evolution of a prenatal ES service that delivers equity of access and high standards of care across England with an associated improvement in prenatal diagnostic services and benefits for parents.Our findings will be shared with key stakeholders on a regular basis throughout the course of the study to facilitate improvements in service delivery, and identify future evaluation and research needs.This work will also be an exemplar for evaluating other aspects of the NHS GMS; for example, recommendations about how best to optimise communication between clinical genetics, laboratories and non-genetic specialists will be transferable, as well as recommendations around supporting equity of access and inclusion of diverse population groups.As the NHS is an early adopter of prenatal ES, findings may be useful to others internationally as they implement similar services.As our research will commence within the first year of the prenatal ES service, we anticipate generating lessons for the GLHs within the timeframe of the study.
A key strength of the research is our mixed-methods approach and engagement with stakeholders from a range of backgrounds.
The duration of the study means that we will be responding to themes arising in the case studies and will allow us to study developments within the service and strategic responses to issues in the service.As previously noted, PPIEP will be embedded throughout the study.There are, however, some potential limitations.The multi-site nature of the study and having several different workstreams will require GLHs to be highly engaged with the research.Participants in the health professional surveys and interviews (Workstream-1) and the parent interviews (Workstream-2) will be self-selected, introducing the risk of selection bias.In addition, as the study is focused on the implementation of prenatal ES within the NHS, a national healthcare service that is unique in many ways, some findings may not be directly generalisable to healthcare systems in other countries.However, we do anticipate that many challenges will be common across countries and lessons from the study will be transferable to other settings.Adapting to challenges created by the Covid-19 pandemic will impact our evaluation.In particular, approaches to data collection may be amended.Working remotely and offering interviews by phone or video call will be used if needed.This approach reflects how health services are adapting to Covid-19 with the use of virtual appointments, but we do recognise that virtual appointments can be a barrier for some people.Comparison of telephone and face-to-face interviews indicates data quality and richness is similar 40 and participants reportedly value the practical ease of being interviewed by telephone and some can feel more comfortable when discussing sensitive topics 41,42 .However, privacy needs and access to technology need consideration and may necessitate in person interviews in some cases.
1 New York Genome Center, New York, NY, USA 2 Columbia University Irving Medical Center, New York, NY, USA 3 New York Genome Center, New York, NY, USA 4 Columbia University Irving Medical Center, New York, NY, USA This is an important study the NHS has embarked to evaluate the prenatal exome sequencing service.The NHS in England is the first large national healthcare system to systematically embed genome and exome sequencing in routine clinical care.The overall study design will deliver high throughput and high-quality genomic testing with equity of access for patients across the NHS and collect potential data for variation in referrals, uptake, diagnostic rates, parent and provider expectations, costs, and technical considerations of genomic reporting in a prenatal setting.
The 3-year prospective evaluation of prenatal ES in the NHS GMS will analyze the national implementation of prenatal and determine an optimal pathway that maximizes benefits for parents while optimizing use of NHS resources.This research will identify ethical and practical issues and highlight any unintended consequences of the new testing modality.
The research study design is based on a framework developed in previous studies of major system innovation, which is well thought through.A Steering Committee with academic, professional, and patient and public involvement, will oversee the evaluation and provide guidance through regular interactions with the research team throughout the study.The study has 7 objectives clearly defined with the nationwide setting and will look at provisions of prenatal ES across England.The study team has identified Phases of the study, data collection and analysis for each phase is also described.The strengths and limitations are recognized by the study team.I am looking forward to seeing the results of this innovative study which will inform the implementation of prenatal ES nationally and some aspects may be informative internationally.
Is the rationale for, and objectives of, the study clearly described?Yes This important research is obviously well underway, but this was not clear to me until I got to page 10.I wrote the following before realising this: EXPRESS is described as a 3-year prospective evaluation of prenatal ES in the NHS GMS.This is confusing as on page 4 it says that prenatal ES was implemented nationally in the NHS GMS in Oct 2020, yet in other places the implication is that this has not begun, and the evaluation will be on the 1 st 6 months, 18 months etc. See 1 st para on page 5 -'research will commence in the first year of the prenatal ES service'.
○ Also, on page 7 under Phase 3, 'As the prenatal ES service is entirely new to the NHS, there is no baseline,.."

○
This needs clarification -how does EXPRESS fit into the existing service?Has it already begun?
When I reached page 10, I saw that the study began in Oct 2020, so this protocol is retrospective.Does the protocol need to reflect this somehow with use of past tense when appropriate?It refers to COVID-19 in the Discussion, so this is a contemporary issue.

Use of Figure 1:
The way this was referred to in the text could have been clearer; why were details relating to the 4 boxes on the LHS provided, but no other sections?Does the phrase 'developing and agreeing new service models' = 'decisions on care pathways'?This Figure is not referred to elsewhere.
Aligning of Objectives and Workstreams was not always done.For instance, where are the health professional education and information needs (part of Objective C) studied?
WS1: Phase 1, section 2): 'key staff' = 'professionals' ?What is the difference between 2) and 3) interviewees -those establishing the service versus those delivering the service?This should be made clearer and not left until a few paragraphs later where there is a rather vague description of recruitment of 'professionals', somewhat a repeat of phase 1, section 3).
How will the quantitative surveys mentioned in WS 1, phase 2, examine 'referral pathways and patient flow..' and then be summarised as frequencies (see last sentence of data analysis)?
WS2: Selection/recruitment bias? 1 st paragraph says 'participants will be purposefully sampled to ensure…'.The next paragraph says parents who have accepted or declined ES will be identified and a letter sent to potential participants (I presume this includes those who declined) who will then have to contact the research team themselves if they decide to participate.The same process is used for those offered ES and those with previous fetal anomaly.How will bias be recognised and dealt with?
WS3: Data quality.It seems imperative that outcome data quality is high, so a reference to the quality is needed.Is there complete ascertainment of outcomes of all types?
The dot points relating to the descriptive analysis are very simplistic, especially the 4 th where covariates and outcomes are mixed up.What is the 'source of referral' -is this the GLH?If not, is that to be something also collected under dot point 2?
WS4: Information will be used from WS1 interviews with 2-3 professionals per GLH.Then there will be 3-4 Workshops, also with people from the GLHs and clinical services.This all sounds rather vague, but maybe that's OK -could they be the same people?Will professionals and parents be in the same workshops?
WS5: This was clear and plenty of detail supplied.
The Integration of findings section (relating to Objective G, I presume) also has workshops, but who with etc? I'm not sure if such lack of detail is acceptable for a protocol paper like this, but I am left feeling that the evaluation is very open-ended.Maybe refer back to Figure 1 to help bring it all together.
Is the rationale for, and objectives of, the study clearly described?Yes

Are sufficient details of the methods provided to allow replication by others? Partly
Are the datasets clearly presented in a useable and accessible format?

Not applicable
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Epidemiology, prenatal genetics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.
Author Response 25 Jun 2022

Melissa Hill
Thank you for your thoughtful and constructive comments.We have revised the manuscript and hope that your comments have been addressed to your satisfaction.We agree that the start date of EXPRESS matching the start date of the prenatal ES service was not made clear until part way through the manuscript.We have added a sentence to the abstract and to the last paragraph of the introduction to make it clear upfront that EXPRESS started at the same time as the prenatal ES service.We have also changed the tense throughout when referring to the start of the service or the start of EXPRESS.Thank you for picking up the discrepancy in the wording between the figure and the text.

Use of
We have changed the text describing the key elements of the framework for major systems innovation to match the wording in the figure .We have also added further information in the text about the framework (including additional references to the figure) and how it will be applied in our analysis to the sections on Study Design, Workstream-1 -Data Collection and Analysis and Integration of Findings.
This feedback prompted us to add more detail about how the analysis of the three separate phases in worksteam-1 will be conducted.As we worked through this revision, we made the decision to remove Normalisation Process Theory from our planned analysis framework to focus on the framework for major systems innovation and the MRC guidance for process evaluations.As such we have removed the reference to Normalisation Process Theory throughout the manuscript.
Aligning of Objectives and Workstreams was not always done.For instance, where are the health professional education and information needs (part of Objective C) studied?
To address this point we have added the relevant workstream(s) to each of objectives listed in the Specific Objectives.Training and education needs of professionals will be addressed in workstream-1 through the interviews and surveys with professionals -we have added a reference to this in the description of workstream-1.
WS1: Phase 1, section 2): 'key staff' = 'professionals' ?What is the difference between 2) and 3) interviewees -those establishing the service versus those delivering the service?This should be made clearer and not left until a few paragraphs later where there is a rather vague description of recruitment of 'professionals', somewhat a repeat of phase 1, section 3).
We have added additional detail to distinguish between the types of professionals we will interview in our national level interviews -staff involved at a national level in deciding to implement the service and who developed the national guidance on service delivery (point 2) and in our local level interviews -the staff on the ground at each GLH who are delivering the service in their daily clinical practice (point 3).
How will the quantitative surveys mentioned in WS 1, phase 2, examine 'referral pathways and patient flow..' and then be summarised as frequencies (see last sentence of data analysis)?
We have changed the wording of the sentence referring to frequencies to be clear that descriptive statistics will be used to analyse the survey data.We have also included additional detail about the analysis plans for the three phases of data collection described in workstream-1.This includes a description of how the summarising of the qualitative and quantitative data into case study templates will allow service components and care pathways to be categorised into typologies for comparison within and between GLHs.
WS2: Selection/recruitment bias? 1 st paragraph says 'participants will be purposefully sampled to ensure…'.The next paragraph says parents who have accepted or declined ES will be identified and a letter sent to potential participants (I presume this includes those who declined) who will then have to contact the research team themselves if they decide to participate.The same process is used for those offered ES and those with previous fetal anomaly.How will bias be recognised and dealt with?
We agree that there is the potential for selection bias in the parent interviews and also in the professional interviews/survey where purposeful sampling will also be used.Letters of invitation to take part in an interview will be sent to parents who accepted prenatal ES testing and also to those who declined.We have added an additional step in our recruitment procedure to engage parents in the study, whereby the local clinical team will call the potential participants to discuss the study if they have not responded to the initial letter of invitation.To reduce the risks of selection bias for the professional survey and interviews we are approaching key contacts, such as the clinical geneticists who act as service leads for their region, so that we target the most appropriate people in each GLH with our study invitations.We have added a sentence to the discussion to acknowledge the risk of selection bias.The risk of selection bias will be acknowledged and discussed in the limitations section of any resulting publications.
WS3: Data quality.It seems imperative that outcome data quality is high, so a reference to the quality is needed.Is there complete ascertainment of outcomes of all types?
The dot points relating to the descriptive analysis are very simplistic, especially the 4 th where covariates and outcomes are mixed up.What is the 'source of referral' -is this the GLH?If not, is that to be something also collected under dot point 2?
We have revised the section describing workstream-3, adding further information about data quality, clarified the 'source of referral', and moved information related to data collection to a sub-section titled "Data collection and analysis".We have also delineated the covariates and outcomes by adding a separate bullet point for each one.
WS4: Information will be used from WS1 interviews with 2-3 professionals per GLH.Then there will be 3-4 Workshops, also with people from the GLHs and clinical services.This all sounds rather vague, but maybe that's OK -could they be the same people?Will professionals and parents be in the same workshops?
We have added additional detail about the planned workshops.Separate workshops for professionals and parents will be held.We hope that holding workshops specifically for parents will help to facilitate an open discussion that is focussed on the issues that are most important to parents.Parents will be invited through patient groups (e.g. from ARC, UNIQUE and Genetic Alliance UK) and through NHS maternity services.For the workshops with professionals it is possible that some professionals will attend more than one workshop as invitations will be advertised broadly and no restrictions on attendance will be applied.This potential for bias will be discussed in any publications that arise.
WS5: This was clear and plenty of detail supplied.

Thank you.
The Integration of findings section (relating to Objective G, I presume) also has workshops, but who with etc? I'm not sure if such lack of detail is acceptable for a protocol paper like this, but I am left feeling that the evaluation is very open-ended.Maybe refer back to Figure 1 to help bring it all together.
As suggested, we have added a paragraph to the section on Integration of findings to highlight that integration of the data from all workstreams will focus on addressing our study objectives and be underpinned by the conceptual framework of major system innovation which is described in Figure 1.
We have added more detail about who will be invited and the purpose and content of the proposed workshops.

Figure 1 .
Figure 1.Conceptual framework underpinning our evaluation of the prenatal ES service.Adapted from Fulop et al. 21,22 .

Figure 1 :
The way this was referred to in the text could have been clearer; why were details relating to the 4 boxes on the LHS provided, but no other sections?Does the phrase 'developing and agreeing new service models' = 'decisions on care pathways'?This Figure is not referred to elsewhere.
Our research is being conducted in accordance with the UK Policy Framework For Health and Social Care Research which sets out the principles of good practice in the management of research.Qualitative and quantitative data for this research will be collected in a range of settings, and participants will include parents, health professionals and policy makers.

the study design appropriate for the research question? Yes Are sufficient details of the methods provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.