Feasibility and ethics of using data from the Scottish newborn blood spot archive for research.

Background: Newborn heel prick blood spots are routinely used to screen for inborn errors of metabolism and life-limiting inherited disorders. The potential value of secondary data from newborn blood spot archives merits ethical consideration and assessment of feasibility for public benefit. Early life exposures and behaviours set health trajectories in childhood and later life. The newborn blood spot is potentially well placed to create an unbiased and cost-effective population-level retrospective birth cohort study. Scotland has retained newborn blood spots for all children born since 1965, around 3 million in total. However, a moratorium on research access is currently in place, pending public consultation.
Methods: We conducted a Citizens' Jury as a first step to explore whether research use of newborn blood spots was in the public interest. We also assessed the feasibility and value of extracting research data from dried blood spots for predictive medicine.
Results: Jurors delivered an agreed verdict that conditional research access to the newborn blood spots was in the public interest. The Chief Medical Officer for Scotland authorised restricted lifting of the current research moratorium to allow a feasibility study. Newborn blood spots from consented Generation Scotland volunteers were retrieved and their potential for both epidemiological and biological research demonstrated. Conclusions: Through the Citizens' Jury, we have begun to identify under what conditions, if any, should researchers in Scotland be granted access to the archive. Through the feasibility study, we have demonstrated the potential value of research access for health data science and predictive medicine.

Introduction

Longitudinal population health studies with extensive record linkage and deep genomic annotation have the potential to realise the objectives of preventative and predictive medicine. Ideally, these studies should cover the full life course. Epidemiological and biological analyses of newborn blood spots have the potential to anchor longitudinal studies at birth. The Danish Newborn Screening Biobank (DNSB) has shown that nucleic acid, metabolic and protein assays are feasible on archived newborn dried blood spots[1]. Denmark is currently the only country in the world where nation-level linkage of such secondary data to health records is approved[1]. However, issues of consent and sensitivity over genetic studies first need careful consideration. A Scottish Government commissioned review had previously considered the ethical, legal and social implications of research access to the Guthrie Card archive[2]. In Scotland, the Guthrie card archive (henceforth referred to as the Scottish newborn blood spot archive) is considered part of the medical record and subject to the provisions of the Data Protection Act 1998. The report recommended that the archive should be treated as both tissue and data in legal governance. The report also recommended wider public engagement on the issues. There are many ongoing research studies in Scotland that have obtained consent from study participants for NHS health record linkage. Others have explicit consent to use participants’ newborn blood spots. Nevertheless, a research study moratorium remains in place. The purpose of this study was to provide supporting evidence for a planned Scottish Government commissioned public consultation.

Here we report the verdict of a Citizens Jury that conditional research access to the newborn blood spots was in the public interest. We show that newborn blood spots from consented Generation Scotland volunteers that have been stored for over 30 years can be retrieved from the archive. We demonstrate that DNA can be reliably extracted from these blood spots for genetic and epigenetic analysis.

Methods

Citizens’ Jury

In June 2017, we brought together a small, diverse group of citizens to address the question: “Would research access to the Guthrie Card heel prick blood tests be in the public interest, and, if so, under what conditions?” A Citizens’ Jury is a well-established method to enable public participation in policy making, allowing informed deliberation on an issue and the provision of recommendations. Our Citizens’ Jury followed best practice for such deliberative public engagement[3]. First, we convened a steering group to provide oversight of the materials prepared for the Jurors and to identify a range of expert witnesses to give evidence. Next, we consulted a Patient Participatory Involvement and Engagement (PPIE) panel to review these materials. The academic researchers did not involve themselves directly in the Jury process, other than to provide evidence or observe. The recruitment, facilitation and analysis were conducted by Ipsos MORI, Scotland, to preserve neutrality. Jurors met together for two day-long sittings to hear evidence (neutral, for and against), deliberate and reach conclusions.

Using a quota sample, a representative pool of the adult public was recruited in terms of sex, age, working status and social grade. Additional quotas were set to ensure sufficient representation of people with children under the age of five, and people with a family history of a medical condition. An attitudinal quota was set to ensure inclusion of people with varied levels of trust in public, private and third sector organisations, as previous research has found this to be a significant factor underpinning views of data sharing and use[4]. A total of 20 were recruited of whom 19 participated on day one, and 18 returned for the second day a week later. Jurors were given monetary recompense for taking part in each sitting.

Day One started with a warmup session sharing their views on health research and health-relevant information, followed by evidence from various experts to stimulate discussion of issues around research use of the newborn blood spots. Day Two included further expert witnesses but more time for Jurors own deliberations and to arrive at a conclusion on the key question. Facilitation tools, such as speed dating techniques, meant that all Jurors could express and reflect on their own views as well as those of others, building up to group and plenary deliberations. The first day focused on more general discussion and information sharing; the second day involved detailed deliberation of the key question and delivering of the verdict. Both days were audio recorded and transcribed for subsequent analysis. A short questionnaire was administered at the end of each day to gauge individual level views and thinking.

Background information was provided by authors SCB and DJP during the morning of Day One. Over the 2 days, six witnesses were called to give evidence and answer Jurors’ questions. These comprised health care professionals and scientists, a Caldicott Guardian (a person responsible for protecting the confidentiality of people’s health and care information and making sure it is used properly) and a Genewatch spokesperson (representing not-for-profit groups that monitor developments in DNA technologies). Jurors also had access to a short video and other written information about comparative deliberations and policy in California and Denmark. Having heard on Day One some of the health research opportunities uniquely possible if access were granted, an introduction to some of the social, ethical and legal issues, and how the NHS protects privacy, Jurors heard more opposing and critical views on Day Two, with one witness cautioning against allowing research access and another the importance of not compromising the newborn screening programme itself.

Newborn blood spot documentation and sampling

Epidemiological feasibility

The Scottish newborn blood spots archive is stored in around 900 boxes each containing circa 3000 cards in a single secure location under the authority of the Director of the Scottish Newborn Screening laboratory and custodianship of the NHS Research Scotland Greater Glasgow and Clyde Biorepository. A unified digital record is in place from 2000 onwards, but the content and consistency of information available from older cards was not known at the outset. The design and information content of the newborn blood spots was known to have varied over time, but not documented. We were aware that some cards had suffered water damage prior to assembling the nation-wide archive. We also know that for a period of time some cards had been autoclaved before storage. For the vast majority, the newborn blood spots have simply been stored at room temperature. The unified newborn blood spot archive management database has limited, high-level summary information on the contents of each box.

We obtained permission from the Caldicott Guardians of NHS Research Scotland Greater Glasgow and Clyde and of Tayside to retrieve representative boxes from the NHS Research Scotland secure archive. Permission was given for (a) examination and documentation of a sub-sample from each box to provide a snap-shot of the information attached that might be required from the purposes of linkage to other routine health records and (b) sampling of cards corresponding to consented members of Generation Scotland.

Thirty boxes representing each decade from 1965 to 1999 were retrieved and examined by NHS Scotland staff at the NHS Research Scotland Greater Glasgow and Clyde Biorepository. Only summary information was shared with the rest of the study team.

The organisation and information content by box varied over time (Supplementary Fig. 1). In some boxes there were unlabelled bundles of cards (Supplementary Fig. 1D), but most had 4 labelled foolscap sub-boxes (Supplementary Fig. 1B) with multiple, date-labelled bundles of cards (Supplementary Fig. 1C).

We drew up a list of potential information that the newborn blood spots might carry from which to judge the feasibility of conducting epidemiological studies by linkage to NHS Scotland routine medical record and potentially additional consented data from research subjects.

For each box, we collected the following information: Box ID; Area Health board; Hospital; Type of card; Date of test; Child forename; Child surname; presence or absence of Community Health Index identifier. No personal information was recorded. Each box took 2 members of staff working in tandem ~2 h to document.

Next, circa 1 in 100 cards from each box were examined in detail and the presence or absence of the following features documented: Child DOB; Additional comments on card; Number of blood spots; Size of spots; Mother’s CHI; Mother’s forename, surname and birth name; Mother’s date of birth; Address; Postcode; Whether the cards had been autoclaved prior to archiving; Any other comments.

Cards from 1965 had very little information on them and in many cases did not even record the sex of the baby. Information content increased progressively over time. By the 1990s, the sex of the child and home address were generally recorded.

Retrieval of cards from consented volunteers

Over 24,000 Generation Scotland (GS) volunteers were recruited as adults between 2006 and 2011[5]. All were born before 1993, before the digital recording of newborn blood spots began. Consent for linkage to medical records was optional but was given by 98% of volunteers. They were asked to give information about their place of birth (country and council area). A total of 8703 volunteers with linkage consent were born in Glasgow or Tayside area health boards between 1965 and 1992. The set of 30 boxes retrieved and documented for epidemiological purposes were selected on the basis that (a) Greater Glasgow and Tayside were the regions for which we had Caldicott Guardian approval and (b) they were expected to include bundles from Generation Scotland participants as the majority came for these regions. A list of names, birthplace and date of birth was extracted from the GS database and sent to the NHS Greater Glasgow and Clyde Biorepository to look for matching cards. Pseudonymous ids were added to the list so that any samples from matching cards could be labelled and linked back to the GS database after genotyping. Ninety-two matching cards were identified amongst newborn blood spots from Tayside. Of these, 58 were usable for punching having fulfilled the prerequisite of leaving one spot intact (Supplementary Fig. 2). Six to ten punches were taken from each card, placed in vials labelled with a pseudonymous ID for matching to the samples donated at baseline by each Generation Scotland volunteer, and couriered to the Edinburgh Clinical Research Laboratory Genetics Laboratory for DNA analysis.

Biological feasibility

Genetic analysis of de-identified cards

Unlike the Danish Newborn Screening Biobank (DNSB), the Scottish newborn blood spot archive comprises a variety of paper types and storage conditions, particularly for older cards. To establish the effect this might have on the recovery of analysable DNA, a pilot study in 2012–2014 was undertaken on a de-identified set of 136 newborn blood spots dated from 1965 to 2012 (Table 1). The study was mandated by the Scottish Chief Scientist Office, following a favourable opinion from the Scottish Legal Office and North of Scotland Research Ethics Committee. De-identified cards were provided by the Scottish National Dried blood spot collection, Biochemical Genetics Laboratory, Duncan Guthrie Institute, Greater Glasgow Health Authority, Yorkhill, Glasgow. DNA was extracted from 3 mm punches using the Sigma ENA kit. Yields varied from sample to sample, but there was no significant effect of date of birth and sufficient material was obtained for Sanger DNA or exome sequencing in 94% of samples (Table 1). Exome sequencing used the Ion AmpliSeq exome kit run on IonTorrent Proton sequencer. Data analysis and variant calling used the IonReporter IonExpress variant caller, 42–45 million mapped reads, 94.2–94.7% on target, mean depth 122–130 reads per sample. Thirty one of 32 runs met standard QC criteria for variant analysis.

Table 1

Newborn blood spots blood spot DNA extraction and Sanger sequencing.

Time period	Newborn blood spots sampled	Successfula DNA extractions	Extractions that failed DNA sequencing	Mean yield of DNA extracted (μg)	Net yield for analysis
1965–1974	17	15	0	16.7	88%
1975–1984	32	31	1	19.5	94%
1985–1994	17	16	1	17.3	88%
1995–2004	18	17	0	23.1	94%
2005–2019	16	16	1	22.9	94%
2010–2013	36	36	0	19.7	100%
Sum	136	131	3	19.9	94%

aIn 5/136 (3.8%) the extraction process failed to recover measurable quantities of DNA using the methods described.

Sampling of cards

Of the 92 newborn blood spots matched to GS volunteers, 58 (63%) had sufficient dried blood spot material remaining to take 3 mm diameter punch samples, while leaving at least one spot intact. These 58 were from Generation Scotland research volunteers born between 1983 and 1989 (i.e. 32–38 years between collection and profiling). DNA was extracted from between 6 to 8 blood spot punches using the QIAamp DNA Investigator Kit (Qiagen; cat. no. 56504), following the manufacturer’s instructions. The concentration of the DNA samples was measured using a Qubit 2.0 fluorometer and the Qubit dsDNA HS assay (Thermo Fisher; cat. no. Q32854). Total yield isolated was between 196 and 1177 ng of DNA. Up to 500 ng DNA (range 160–500 ng) underwent bisulfite conversion (Zymo EZ-96). DNA methylation was profiled using the Infinium HumanMethylationEPIC v1.0 BeadChip (Illumina Inc.; cat. no. WG-317-1001), according to the manufacturer’s protocol (in batches of 8 samples, 56 assayed of the 58 samples processed). Arrays were scanned on an iScan and analysed using GenomeStudio v2011.1.

DNA methylation analysis and statistical methods

DNA methylation quality control

DNAm profiles were obtained from the 56 individuals using the Illumina MethylationEPIC beadchip, measuring ~850,000 CpGs across the genome. Quality control measures were performed, removing probes with high detection p-values (>0.05) in >5% of samples (N = 52,375), or a beadcount <3 in more than 5% of samples (N = 5038). Three samples were removed for having >5% of sites with a detection p-value >0.05. In addition to these standard quality control measures, additional checks were performed to ensure newborn blood spots and baseline samples matched with regard to predicted sex and genotype (Supplementary Information Methods, Supplementary Figs. 3 and 4 and Supplementary Table 1). Quality control and analysis code have been deposited in a public repository[6]. To access Generation Scotland data, including the data derived in the feasibility study described here, please go to www.ed.ac.uk/generation-scotland/for-researchers/access.

Sample checks

Confirmatory analyses were performed using newborn blood spots DNA methylation data to ensure predicted sex (using X-chromosome data) and genotype (using “rs” control probes on the EPIC array) were consistent with peripheral blood-based genotyping and DNA methylation data on samples collected at baseline recruitment (2006–2011) (Supplementary Table 1). Detailed information on sample checks is presented in Supplementary Information Methods and Supplementary Figs. 3 and 4.

Smoking

An individual’s smoking status can be reliably predicted using composite DNA methylation-derived smoking scores, and effects have also been observed in the offspring of mothers who smoked during pregnancy[7]. Moreover, information from a single probe in the aryl-hydrocarbon receptor repressor gene (AHRR; cg05575921) can serve as a robust marker of smoking, with lower DNA methylation levels associating with current smoker status. Maternal smoking status at the time of sample collection was derived from smoking status at GS baseline, and the “years stopped” variable for former smokers, where both mother and baby are in GS. DNA methylation-based estimates of smoking status were obtained, using previously validated methods[8]. A composite score for smoking status (EpiSmokEr) was obtained using Guthrie sample DNAm data and, along with cg05575921 DNA methylation levels, was plotted against maternal smoking status at the time of sampling (Fig. 1). Consistent with previous literature, a higher overall value was observed for the EpiSmokEr score in the offspring of current smokers whereas a lower overall value was observed for the offspring of never smokers, supporting an association at the population level (Fig. 1a; ever smoker β = 0.78; sex-adjusted linear regression P = 0.026). DNA methylation levels at cg05575921 were also consistent with the literature, with lower overall levels in the offspring of current smokers relative to never smokers (Fig. 1b; ever smoker β = −0.72; sex-adjusted linear regression P = 0.05).

Fig. 1

EpiSmokEr score and AHRR DNAm plotted against maternal smoking status.

Methylation-derived smoking scores from newborn blood spot DNA (y-axis) plotted against maternal smoking status (current, former, never) at time of birth (NCurrentSmokers = 10; NFormerSmokers = 5; NNeverSmokers = 26). Results are shown for the EpiSmokEr score, a composite measure comprised of multiple CpG sites (a), and DNA methylation levels at a single CpG (cg05575921) in the AHRR gene (b). Upper and lower hinges correspond to the upper and lower quartiles, respectively. Whiskers extend to data points as far as 1.5 times the interquartile range. Outlying data points are defined as those beyond the whiskers. Thick horizontal lines represent the median.

Research ethics

The original Sanger DNA and exome sequencing study was mandated by the Scottish Chief Scientist Office, following a favourable opinion from the Scottish Legal Office and the North of Scotland Research Ethics Committee, REC ref. 11/ns.0014. A letter approving the inspection and documentation of newborn blood spots and selective sampling of GS cards for methylation analysis was provided by the Chief Medical Officer for Scotland on 4 September, 2019. The Caldicott Guardians of NHS Greater Glasgow and Clyde and NHS Tayside granted approval on 30 January 2020 and 3 March 2020, respectively. Volunteers for Generation Scotland gave informed consent at the time of recruitment for biological studies, including genetic studies, on their biological samples and for linkage to medical records. A substantial amendment to the Research Tissue Bank approval for Generation Scotland to cover the feasibility study was submitted to the East of Scotland Research Ethics Committee and approved on 13 March 2020.

The Citizens Jury followed INVOLVE guidelines and was conducted by the polling organisation, Ipsos MORI, on behalf of the University of Edinburgh research team. This work was carried out in accordance with the requirements of the international quality standard for Market Research, ISO 20252:2012, and with the Ipsos MORI Terms and Conditions which can be found at http://www.ipsos-mori.com/terms. Ipsos MORI conducted their own internal ethical review through their ethical review team. The Ipsos MORI Project Director (CM) was then responsible for ensuring that the research materials (recruitment screener, participant information sheets, discussion guides) were clear and met the ethics principles on informed consent, right to refuse, principles of anonymity and confidentiality. No sensitive information was collected. Materials were saved in a secure folder with access restricted to the Ipsos MORI team (CM, SD). After completion, all personal information (participant names, contacts details, recordings and transcripts) were securely destroyed using Ipsos MORI digital shredding software.

Table 2

Citizens Jury conditions and recommendations regarding research access.

Condition 1: The ultimate purpose of the research should be to advance medical research in ways that could potentially benefit public health.

Condition 2: Any organisation requesting access to the data should provide a clear rationale for their research, which should be approved by an ethics committee. Access should be granted solely for the use outlined in their research request.

Condition 3: There should be appropriate regulation and oversight of the process by an independent body—that includes an ethics committee—with the authority to issue sanctions for misuse.

Condition 4: Consent should be based on an opt-out system, with the option to opt-out within one year of the child being born, and again when the child turns sixteen.

Recommendation: Mechanisms should be put in place (in the form of a central website) that enable members of the public to check on the types of research being undertaken with Guthrie Card data and the outcomes.

Table 3

Newborn blood spot archive examination and sample selection for analysis.

Step 1	Information recorded (Boxes)
	Box ID; Area Health board; Hospital; Type of card; Date of test; Child forename; Child surname; presence or absence of Community Health Index identifier.
Step 2	Information recorded (Cards)
	Child DOB; Additional comments on card; Number of blood spots; Size of spots; Mother’s CHI; Mother’s forename, surname and birth name; Mother’s date of birth; Address; Postcode; Whether the cards had been autoclaved prior to archiving; Any other comments.
Step 3	Sample selection
	• Pseudonymised ID list of consented Generation Scotland (GS) participants provided to Greater Glasgow and Clyde Biorepository (GGCB) • GGCB staff look for matches between newborn blood spots and GS IDs • 92 matching cards identified and checked for usability • 6–10 punches of 3 mm diameter taken from 58 cards and couriered to the Edinburgh Clinical Research Facility for DNA analysis
Step 4	Sample analysis
	• DNA methylation data from newborn blood spots compared to DNAm in peripheral blood at time of recruitment (2006–2011) • DNA methylation data from newborn blood spots analysed for smoking signatures and correlated with recorded maternal smoking status