Preparing tomorrow's doctors for the genomics era: A nationwide survey of UK medical students.

Introduction: Low confidence in genomics knowledge among clinicians is a major barrier to the integration of genomics into mainstream medicine. Here, we assessed the genomics confidence of UK medical students approaching graduation. Methods: We conducted a web-based nationwide survey of UK medical students in the final 2 years of study where participants rated their confidence in genomics concepts. Results: In total, 145 medical students across 19 medical schools participated. The amount of genomics teaching students reported receiving was positively associated with genomics confidence, with the amount of basic science teaching having the strongest influence. While confidence was high in core genomics principles, such as the difference between DNA, genes and chromosomes (95%), confidence dropped in clinical applications of genomics - only 50% reported a good understanding of the genetic contribution to disease and 28% reported good knowledge of clinically used genomic tests. Overall, 59% reported a poor understanding of variant interpretation; however, over half who reported receiving 'lots' of genomic medicine teaching reported a good understanding of this topic. Conclusion: Gaps in genomics knowledge and drivers in confidence have been identified herein, highlighting the need for improvements in undergraduate genomics education to prepare future doctors to confidently practise in the genomics era.

Multiresidue analysis of bat guano using GC-MS/MS.

Bats are the second largest mammalian order and are an endangered species group with a strong need for contamination monitoring. To facilitate non-invasive monitoring of the ecological burden in bat populations, a multiresidue method for the simultaneous quantification of 119 analytes including pesticides, persistent organic pollutants (POPs), active pharmaceutical ingredients (APIs), polycyclic aromatic hydrocarbons (PAHs), UV blockers, plasticizers, and other emerging pollutants in bat guano with gas chromatography tandem mass spectrometry (GC-MS/MS) was developed. Sample preparation and clean-up were performed with a modified QuEChERS approach based on DIN EN 15662. The method uses 1.00 g bat guano as sample with acetonitrile and water for liquid-liquid extraction. Phase separation is assisted by citrate-buffered salting out agent. For clean-up of the extract, primary secondary amine (PSA) was combined with graphitized carbon black (GCB). The lower limits of quantification (LLOQ) ranged between 2.5 and 250 µg kg-1. Linearity was shown in a concentration range from the respective LLOQs to 1250 µg kg-1. The median of the mean recovery was 102.4%. Precision was tested at three concentrations. Method and injection precision were adequate with a relative standard deviation (RSD) below 20%. Furthermore, the comparative analysis with LC-MS/MS demonstrated the reliability of the results and provided a valuable extension of the analytical scope. As proof of concept, three guano samples from a German nursery roost of Myotis myotis were analysed. The results show a time-dependent change in contaminant concentration, highlighting the strong need for non-invasive contamination monitoring of whole bat populations.

'Something that helped the whole picture': Experiences of parents offered rapid prenatal exome sequencing in routine clinical care in the English National Health Service.

OBJECTIVES: In October 2020, rapid prenatal exome sequencing (pES) was introduced into routine National Health Service (NHS) care in England. This study aimed to explore parent experiences and their information and support needs from the perspective of parents offered pES and of health professionals involved in its delivery. METHODS: In this qualitative study, semi-structured interviews were conducted with 42 women and 6 male partners and 63 fetal medicine and genetic health professionals. Interviews were transcribed verbatim and analysed using thematic analysis. RESULTS: Overall views about pES were positive and parents were grateful to be offered the test. Highlighted benefits of pES included the value of the additional information for pregnancy management and planning for future pregnancies. An anxious wait for results was common, often associated with the need to make decisions near to 24 weeks in pregnancy when there are legal restrictions for late termination. Descriptions of dealing with uncertainty were also common, even when results had been returned. Many parents described pES results as informing decision-making around whether or not to terminate pregnancy. Some professionals were concerned that a non-informative result could be overly reassuring and highlighted that careful counselling was needed to ensure parents have a good understanding of what the result means for their pregnancy. Emotional support from professionals was valued; however, some parents felt that post-test support was lacking. CONCLUSION: Parents and professionals welcomed the introduction of pES. Results inform parents' decision-making around the termination of pregnancy. When there are no diagnostic findings or uncertain findings from pES, personalised counselling that considers scans and other tests are crucial. Directing parents to reliable online sources of information and providing emotional support throughout could improve their experiences of care.

Factors affecting overall care experience for people living with rare conditions in the UK: exploratory analysis of a quantitative patient experience survey.

BACKGROUND: Although individually rare, collectively, rare conditions are common and affect a large number of people and are often chronic, life threatening and affect multiple body systems; the majority of them have no effective treatment. The literature has identified many specific challenges for those living with rare conditions, however, we do not know which of these in combination are most likely to impact how someone rates their overall experience of care. The aim of this study is to do further exploratory analysis of the Genetic Alliance UK 2020 Rare Experience survey data to identify which variables are most strongly associated with respondents' overall care experience. RESULTS: There were strong associations between most of the selected survey variables and the overall rated experience of care variable. In the multiple linear regression only nine variables remained in the best fit model: 'Trust and confidence in hospital staff involved in ongoing care'; 'Satisfaction with information provided by healthcare professionals-following diagnosis'; 'The professionals providing care work as a team'; 'Feel care is coordinated effectively'; 'The timing and frequency of appointments are convenient for the patient/carer/family'; 'Whether or not there is a specific healthcare professional to ask questions of about the rare/undiagnosed condition'; 'Experience of searching for a diagnosis'; 'Knowledge of whether there is a specialist centre for the condition'; and 'Number of different clinics attend for the condition'. CONCLUSIONS: Our findings indicate the challenges that play the largest part in explaining the varied experiences with rare disease healthcare in the UK for our survey respondents. These challenges should be further investigated with a broader sample of people affected by rare conditions, ideally through the implementation of a comprehensive national rare condition patient registry. Our findings highlight an important potential gap in the Framework, 'trust and confidence in healthcare professionals'; further research is required to fully understand the foundations of trust and confidence.

The disequilibrium of hope: A grounded theory analysis of parents' experiences of receiving a "no primary finding" result from genome sequencing.

Genome sequencing (GS) has the potential to reduce the "diagnostic odyssey" that many parents of children with rare undiagnosed conditions experience. While much research has considered the impact of receiving a diagnostic result, research has rarely focused solely on the impact of receiving a "no primary finding" (NPF) result. This study aimed to investigate the experience of parents of children with rare and undiagnosed conditions following an NPF result from GS. Nine parents whose child had an NPF result from GS were recruited through the social media platform of the charity SWAN (Syndromes Without A Name) UK. Semi-structured telephone interviews were conducted, transcribed verbatim, and analyzed using grounded theory. Analysis led to the emergence of two main themes. The first theme "Striving to Solve the Unsolved Puzzle" concerned the experience of striving to end the "diagnostic odyssey." The second theme "Navigating Hope, Lost then Found" plots the trajectory of hope raised by the promise of a new technology, dashed by the NPF, and the eventual return of small and distant hope for the future. Taken together, these themes allowed for a proposed theory: "The Disequilibrium of Hope," which highlights the dynamic and modifiable experience of hope participants experience in their GS journey. These results suggest GS can be an emotional rollercoaster for parents. While hope plays an important role in coping with the day-to-day life of living with a rare disease, careful management of expectations from GS is important during pre-test counseling, and continued follow-up and support are needed beyond result disclosure. An understanding of the disappointment and distress caused by an NPF result is valuable for healthcare professionals in this field to ensure counseling can be tailored. Further research should consider how to support parents after an NPF result.

Knowledge, attitudes and decision regret: a longitudinal survey study of participants offered genome sequencing in the 100,000 Genomes Project.

We used cross-sectional surveys to compare the knowledge, attitudes, and decision regret of participants who had consented for genome sequencing (GS) for rare disease diagnosis in the 100,000 Genomes Project (100kGP) across two timepoints (at the time of consenting for GS (T1) and 12-18 months later (T2)). At T1, participants (n = 504) completed a survey that included measures of general knowledge of GS ("Knowledge of Genome Sequencing" (KOGS)), specific knowledge of GS and attitudes towards GS ("General attitudes" and "Specific attitudes"). At T2, participants (n = 296) completed these same assessments (apart from the specific knowledge scale) together with an assessment of decision regret towards GS ("Decisional Regret Scale"). At 12-18 months after consenting for GS, participants' basic knowledge of GS had remained stable. General knowledge of GS varied across topics; concepts underlying more general information about genetics were better understood than the technical details of genomic testing. Attitudes towards GS at T2 were generally positive, and feelings towards GS (both positive and negative) remained unchanged. However, those who were more positive about the test at the outset had greater specific knowledge (as opposed to general knowledge) of GS. Finally, although the majority of participants indicated feeling little regret towards undergoing GS, those with low positive attitude and high negative attitude about GS at T1 reported greater decision regret at T2. Careful assessment of patient knowledge about and attitudes towards GS at the time of offering testing is crucial for supporting informed decision making and mitigating later regret.

Learning to generalise but not segment an artificial language at 17 months predicts children's language skills 3 years later.

We investigated whether learning an artificial language at 17 months was predictive of children's natural language vocabulary and grammar skills at 54 months. Children at 17 months listened to an artificial language containing non-adjacent dependencies, and were then tested on their learning to segment and to generalise the structure of the language. At 54 months, children were then tested on a range of standardised natural language tasks that assessed receptive and expressive vocabulary and grammar. A structural equation model demonstrated that learning the artificial language generalisation at 17 months predicted language abilities - a composite of vocabulary and grammar skills - at 54 months, whereas artificial language segmentation at 17 months did not predict language abilities at this age. Artificial language learning tasks - especially those that probe grammar learning - provide a valuable tool for uncovering the mechanisms driving children's early language development.

ADAMS project: a genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis based in the UK.

PURPOSE: Genetic studies of multiple sclerosis (MS) susceptibility and severity have focused on populations of European ancestry. Studying MS genetics in other ancestral groups is necessary to determine the generalisability of these findings. The genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis (ADAMS) project aims to gather genetic and phenotypic data on a large cohort of ancestrally-diverse individuals with MS living in the UK. PARTICIPANTS: Adults with self-reported MS from diverse ancestral backgrounds. Recruitment is via clinical sites, online (https://app.mantal.co.uk/adams) or the UK MS Register. We are collecting demographic and phenotypic data using a baseline questionnaire and subsequent healthcare record linkage. We are collecting DNA from participants using saliva kits (Oragene-600) and genotyping using the Illumina Global Screening Array V.3. FINDINGS TO DATE: As of 3 January 2023, we have recruited 682 participants (n=446 online, n=55 via sites, n=181 via the UK MS Register). Of this initial cohort, 71.2% of participants are female, with a median age of 44.9 years at recruitment. Over 60% of the cohort are non-white British, with 23.5% identifying as Asian or Asian British, 16.2% as Black, African, Caribbean or Black British and 20.9% identifying as having mixed or other backgrounds. The median age at first symptom is 28 years, and median age at diagnosis is 32 years. 76.8% have relapsing-remitting MS, and 13.5% have secondary progressive MS. FUTURE PLANS: Recruitment will continue over the next 10 years. Genotyping and genetic data quality control are ongoing. Within the next 3 years, we aim to perform initial genetic analyses of susceptibility and severity with a view to replicating the findings from European-ancestry studies. In the long term, genetic data will be combined with other datasets to further cross-ancestry genetic discoveries.

How executive functioning, sentence processing, and vocabulary are related at 3 years of age.

There is a wealth of evidence demonstrating that executive function (EF) abilities are positively associated with language development during the preschool years, such that children with good executive functions also have larger vocabularies. However, why this is the case remains to be discovered. In this study, we focused on the hypothesis that sentence processing abilities mediate the association between EF skills and receptive vocabulary knowledge, in that the speed of language acquisition is at least partially dependent on a child's processing ability, which is itself dependent on executive control. We tested this hypothesis in longitudinal data from a cohort of 3- and 4-year-old children at three age points (37, 43, and 49 months). We found evidence, consistent with previous research, for a significant association between three EF skills (cognitive flexibility, working memory [as measured by the Backward Digit Span], and inhibition) and receptive vocabulary knowledge across this age range. However, only one of the tested sentence processing abilities (the ability to maintain multiple possible referents in mind) significantly mediated this relationship and only for one of the tested EFs (inhibition). The results suggest that children who are better able to inhibit incorrect responses are also better able to maintain multiple possible referents in mind while a sentence unfolds, a sophisticated sentence processing ability that may facilitate vocabulary learning from complex input.

Towards a global view of multiple sclerosis genetics.

Multiple sclerosis (MS) is a neuroimmunological disorder of the CNS with a strong heritable component. The genetic architecture of MS susceptibility is well understood in populations of European ancestry. However, the extent to which this architecture explains MS susceptibility in populations of non-European ancestry remains unclear. In this Perspective article, we outline the scientific arguments for studying MS genetics in ancestrally diverse populations. We argue that this approach is likely to yield insights that could benefit individuals with MS from all ancestral groups. We explore the logistical and theoretical challenges that have held back this field to date and conclude that, despite these challenges, inclusion of participants of non-European ancestry in MS genetics studies will ultimately be of value to all patients with MS worldwide.

Participant experiences of genome sequencing for rare diseases in the 100,000 Genomes Project: a mixed methods study.

In this mixed methods study, a survey and in-depth interviews were used to explore whether decision regret and the psychological impact of receiving genome sequencing (GS) results differed between parents and patients, and between those who received a genetic diagnosis and those who did not. Participants (n = 77) completed a survey that included the Decisional Regret Scale (DRS) and an adaptation of the Multidimensional Impact of Cancer Risk Assessment (MICRA) at least 12 months after consenting for GS for rare disease diagnosis in the 100,000 Genomes Project. Survey participants were invited to take part in an interview and 39 agreed; 12 with a diagnosis, 5 with variants of uncertain significance, and 19 with no pathogenic findings identified. Both survey and interview findings indicated that decision regret was low. DRS scores revealed no differences in levels of regret between parents and patients, or between those with a diagnosis and those without. Though MICRA scores indicated minimal evidence of negative psychological impacts of receiving GS results, subscale analysis revealed greater distress and uncertainty for parents compared to patients. Receiving a diagnosis was found not to influence MICRA scores, supporting interview findings of both positive and negative emotional and psychological impacts irrespective of a genetic diagnosis. Our findings have implications for policy and practice as GS is integrated into the UK and worldwide; notably, that expectation-setting is critical when offering GS, and that post-test counselling is important regardless of the GS result received, with parents perhaps needing additional emotional support.

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 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 improved3. 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.

What's out there for parents? A systematic review of online information about prenatal microarray and exome sequencing.

OBJECTIVE: To identify what online patient information (presented in English) is available to parents about prenatal microarray (CMA) and exome sequencing (ES), and evaluate its content, quality, and readability. METHOD: Systematic searches (Google and Bing) were conducted, and websites were categorised according to their purpose. Websites categorised as patient information were included if they were: in English, directed at patients, or were a text, video, or online version of an information leaflet. Author-developed content checklists, the DISCERN Genetics tool, and readability tests (the Flesch Reading Ease Score, the Gunning Fog Index, and the Simple Measure of Gobbledygook Index) were then used to assess those sources of patient information. RESULTS: Of the 665 websites screened, 18 met the criteria. A further 8 sources were found through a targeted search of professional organisations, resulting in 26 sources available for further evaluation. In general, this was found to be low in quality, omitted details recommended by national or international guidance, and was written at a level too advanced for average readers. CONCLUSION: Improvements should be made to the content, quality, and readability of online information so that it both reinforces and complements the discussions between parents and clinicians about testing options during pregnancy.

Decision-making, attitudes, and understanding among patients and relatives invited to undergo genome sequencing in the 100,000 Genomes Project: A multisite survey study.

PURPOSE: The purpose of this study was to assess decisions, attitudes, and understanding of participants (patients, parents, relatives) having genome sequencing for rare disease diagnosis. METHODS: This study involved a cross-sectional observational survey with participants in the 100,000 Genomes Project. RESULTS: Survey response rate was 51% (504/978). Most participants self-reported that they had decided to undergo genome sequencing (94%) and that this was an informed decision (84%) with low decisional conflict (95%). Most self-reported that they had chosen to receive additional findings (88%) and that this was an informed decision (89%) with low decisional conflict (95%). Participants were motivated more by the desire to help others via research than by the belief it would help them obtain a diagnosis (Z = 14.23, P = 5.75 × 10-46), although both motivations were high. Concerns were relatively few but, where expressed, were more about the potential psychological impact of results than data sharing/access (Z = 9.61, P = 7.65 × 10-22). Concerns were higher among male, Asian or Asian British, and more religious participants. General and context-specific understanding of genome sequencing were both moderately high (means 5.2/9.0 and 22.5/28.0, respectively). CONCLUSION: These findings are useful to inform consent guidelines and clinical implementation of genome sequencing.

Non-adjacent dependency learning in infancy, and its link to language development.

To acquire language, infants must learn how to identify words and linguistic structure in speech. Statistical learning has been suggested to assist both of these tasks. However, infants' capacity to use statistics to discover words and structure together remains unclear. Further, it is not yet known how infants'  statistical learning ability relates to their language development. We trained 17-month-old infants on an artificial language comprising non-adjacent dependencies, and examined their looking times on tasks assessing sensitivity to words and structure using an eye-tracked head-turn-preference paradigm. We measured infants' vocabulary size using a Communicative Development Inventory (CDI) concurrently and at 19, 21, 24, 25, 27, and 30 months to relate performance to language development. Infants could segment the words from speech, demonstrated by a significant difference in looking times to words versus part-words. Infants' segmentation performance was significantly related to their vocabulary size (receptive and expressive) both currently, and over time (receptive until 24 months, expressive until 30 months), but was not related to the rate of vocabulary growth. The data also suggest infants may have developed sensitivity to generalised structure, indicating similar statistical learning mechanisms may contribute to the discovery of words and structure in speech, but this was not related to vocabulary size.

Does speed of processing or vocabulary size predict later language growth in toddlers?

It is becoming increasingly clear that the way that children acquire cognitive representations depends critically on how their processing system is developing. In particular, recent studies suggest that individual differences in language processing speed play an important role in explaining the speed with which children acquire language. Inconsistencies across studies, however, mean that it is not clear whether this relationship is causal or correlational, whether it is present right across development, or whether it extends beyond word learning to affect other aspects of language learning, like syntax acquisition. To address these issues, the current study used the looking-while-listening paradigm devised by Fernald, Swingley, and Pinto (2001) to test the speed with which a large longitudinal cohort of children (the Language 0-5 Project) processed language at 19, 25, and 31 months of age, and took multiple measures of vocabulary (UK-CDI, Lincoln CDI, CDI-III) and syntax (Lincoln CDI) between 8 and 37 months of age. Processing speed correlated with vocabulary size - though this relationship changed over time, and was observed only when there was variation in how well the items used in the looking-while-listening task were known. Fast processing speed was a positive predictor of subsequent vocabulary growth, but only for children with smaller vocabularies. Faster processing speed did, however, predict faster syntactic growth across the whole sample, even when controlling for concurrent vocabulary. The results indicate a relatively direct relationship between processing speed and syntactic development, but point to a more complex interaction between processing speed, vocabulary size and subsequent vocabulary growth.

Aligning Developmental and Processing Accounts of Implicit and Statistical Learning.

A long-standing question in child language research concerns how children achieve mature syntactic knowledge in the face of a complex linguistic environment. A widely accepted view is that this process involves extracting distributional regularities from the environment in a manner that is incidental and happens, for the most part, without the learner's awareness. In this way, the debate speaks to two associated but separate literatures in language acquisition: statistical learning and implicit learning. Both fields have explored this issue in some depth but, at present, neither the results from the infant studies used by the statistical learning literature nor the artificial grammar learning tasks studies from the implicit learning literature can be used to fully explain how children's syntax becomes adult-like. In this work, we consider an alternative explanation-that children use error-based learning to become mature syntax users. We discuss this proposal in the light of the behavioral findings from structural priming studies and the computational findings from Chang, Dell, and Bock's (2006) dual-path model, which incorporates properties from both statistical and implicit learning, and offers an explanation for syntax learning and structural priming using a common error-based learning mechanism. We then turn our attention to future directions for the field, here suggesting how structural priming might inform the statistical learning and implicit learning literature on the nature of the learning mechanism.