Neuromuscular disease genetics in under-represented populations: increasing data diversity

Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses 'solved' or 'possibly solved' ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% 'solved' and ∼13% 'possibly solved' outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally.

Characterizing phonemic fluency by transfer learning with deep language models

Though phonemic fluency tasks are traditionally indexed by the number of correct responses, the underlying disorder may shape the specific choice of words-both correct and erroneous. We report the first comprehensive qualitative analysis of incorrect and correct words generated on the phonemic ('S') fluency test, in a large sample of patients (n = 239) with focal, unilateral frontal or posterior lesions and healthy controls (n = 136). We conducted detailed qualitative analyses of the single words generated in the phonemic fluency task using categorical descriptions for different types of errors, low-frequency words and clustering/switching. We further analysed patients' and healthy controls' entire sequences of words by employing stochastic block modelling of Generative Pretrained Transformer 3-based deep language representations. We conducted predictive modelling to investigate whether deep language representations of word sequences improved the accuracy of detecting the presence of frontal lesions using the phonemic fluency test. Our qualitative analyses of the single words generated revealed several novel findings. For the different types of errors analysed, we found a non-lateralized frontal effect for profanities, left frontal effects for proper nouns and permutations and a left posterior effect for perseverations. For correct words, we found a left frontal effect for low-frequency words. Our novel large language model-based approach found five distinct communities whose varied word selection patterns reflected characteristic demographic and clinical features. Predictive modelling showed that a model based on Generative Pretrained Transformer 3-derived word sequence representations predicted the presence of frontal lesions with greater fidelity than models of native features. Our study reveals a characteristic pattern of phonemic fluency responses produced by patients with frontal lesions. These findings demonstrate the significant inferential and diagnostic value of characterizing qualitative features of phonemic fluency performance with large language models and stochastic block modelling.

E-Consent-a guide to maintain recruitment in clinical trials during the COVID-19 pandemic

BACKGROUND

The COVID-19 pandemic has posed daunting challenges when conducting clinical research. Adopting new technologies such as remote electronic consent (e-Consent) can help overcome them. However, guidelines for e-Consent implementation in ongoing clinical trials are currently lacking. The NeuroSAFE PROOF trial is a randomized clinical trial evaluating the role of frozen section analysis during RARP for prostate cancer. In response to the COVID-19 crisis, recruitment was halted, and a remote e-Consent solution was designed. The aim of this paper is to describe the process of implementation, impact on recruitment rate, and patients' experience using e-Consent.

METHODS

A substantial amendment of the protocol granted the creation of a remote e-Consent framework based on the REDCap environment, following the structure and content of the already approved paper consent form. Although e-Consent obviated the need for in-person meeting, there was nonetheless counselling sessions performed interactively online. This new pathway offered continuous support to patients through remote consultations. The whole process was judged to be compliant with regulatory requirements before implementation.

RESULTS

Before the first recruitment suspension, NeuroSAFE PROOF was recruiting an average of 9 patients per month. After e-Consent implementation, 63 new patients (4/month) have been enrolled despite a second lockdown, none of whom would have been recruited using the old methods given restrictions on face-to-face consultations. Patients have given positive feedback on the use of the platform. Limited troubleshooting has been required after implementation.

CONCLUSION

Remote e-Consent-based recruitment was critical for the continuation of the NeuroSAFE PROOF trial during the COVID-19 pandemic. The described pathway complies with ethical and regulatory guidelines for informed consent, while minimizing face-to-face interactions that increase the risk of COVID-19 transmission. This guide will help researchers integrate e-Consent to ongoing or planned clinical trials while uncertainty about the course of the pandemic continues.

TRIAL REGISTRATION

NeuroSAFE PROOF trial NCT03317990 . Registered on 23 October 2017. Regional Ethics Committee reference 17/LO/1978.

Heterologous infection and vaccination shapes immunity against SARS-CoV-2 variants

The impact of the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infecting strain on downstream immunity to heterologous variants of concern (VOCs) is unknown. Studying a longitudinal healthcare worker cohort, we found that after three antigen exposures (infection plus two vaccine doses), S1 antibody, memory B cells, and heterologous neutralization of B.1.351, P.1, and B.1.617.2 plateaued, whereas B.1.1.7 neutralization and spike T cell responses increased. Serology using the Wuhan Hu-1 spike receptor binding domain poorly predicted neutralizing immunity against VOCs. Neutralization potency against VOCs changed with heterologous virus encounter and number of antigen exposures. Neutralization potency fell differentially depending on targeted VOCs over the 5 months from the second vaccine dose. Heterologous combinations of spike encountered during infection and vaccination shape subsequent cross-protection against VOC, with implications for future-proof next-generation vaccines.

Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose

SARS-CoV-2 vaccine rollout has coincided with the spread of variants of concern. We investigated if single dose vaccination, with or without prior infection, confers cross protective immunity to variants. We analyzed T and B cell responses after first dose vaccination with the Pfizer/BioNTech mRNA vaccine BNT162b2 in healthcare workers (HCW) followed longitudinally, with or without prior Wuhan-Hu-1 SARS-CoV-2 infection. After one dose, individuals with prior infection showed enhanced T cell immunity, antibody secreting memory B cell response to spike and neutralizing antibodies effective against B.1.1.7 and B.1.351. By comparison, HCW receiving one vaccine dose without prior infection showed reduced immunity against variants. B.1.1.7 and B.1.351 spike mutations resulted in increased, abrogated or unchanged T cell responses depending on human leukocyte antigen (HLA) polymorphisms. Single dose vaccination with BNT162b2 in the context of prior infection with a heterologous variant substantially enhances neutralizing antibody responses against variants.

Treatment Updates for Neuromuscular Channelopathies

PURPOSE OF REVIEW

This article aims to review the current and upcoming treatment options of primary muscle channelopathies including the non-dystrophic myotonias and periodic paralyses.

RECENT FINDINGS

The efficacy of mexiletine in the treatment of myotonia is now supported by two randomised placebo-controlled trials, one of which utilised a novel aggregated n-of-1 design. This has resulted in licencing of the drug via orphan drug status. There is also good evidence that mexiletine is well tolerated and safe in this patient group without the need for intensive monitoring. A range of alternative antimyotonic treatment options include lamotrigine, carbamazepine and ranolazine exist with variable evidence base. In vitro studies have shown insight into reasons for treatment failure of some medications with certain genotypes opening the era of mutation-specific therapy such as use of flecainide. In the periodic paralyses, the ability of MRI to distinguish between reversible oedema and irreversible fatty replacement makes it an increasingly useful tool to guide and assess pharmacological treatment. Unfortunately, the striking efficacy of bumetanide in hypokalaemic periodic paralysis animal models was not replicated in a recent pilot study in humans.

SUMMARY

The treatment of skeletal muscle channelopathies combines dietary and lifestyle advice together with pharmacological interventions. The rarity of these conditions remains a barrier for clinical studies but the example of the aggregated n-of-1 trial of mexiletine shows that innovative trial design can overcome these hurdles. Further research is required to test efficacy of drugs shown to have promising characteristics in preclinical experiments such as safinamide, riluzule and magnesium for myotonia or bumetanide for hypokalaemic periodic paralysis.

Long-term implicit memory for sequential auditory patterns in humans

Memory, on multiple timescales, is critical to our ability to discover the structure of our surroundings, and efficiently interact with the environment. We combined behavioural manipulation and modelling to investigate the dynamics of memory formation for rarely reoccurring acoustic patterns. In a series of experiments, participants detected the emergence of regularly repeating patterns within rapid tone-pip sequences. Unbeknownst to them, a few patterns reoccurred every ~3 min. All sequences consisted of the same 20 frequencies and were distinguishable only by the order of tone-pips. Despite this, reoccurring patterns were associated with a rapidly growing detection-time advantage over novel patterns. This effect was implicit, robust to interference, and persisted for 7 weeks. The results implicate an interplay between short (a few seconds) and long-term (over many minutes) integration in memory formation and demonstrate the remarkable sensitivity of the human auditory system to sporadically reoccurring structure within the acoustic environment.

The association between region of birth and sexually transmitted infections among people of black Caribbean ethnicity attending sexual health services in England, 2015

BACKGROUND/INTRODUCTION

In England, people of Black Caribbean (BC) ethnicity are disproportionately affected by sexually transmitted infections (STIs), but it is unclear whether this varies by their region of birth.

AIM(S)/OBJECTIVES

To examine differences in STI diagnoses among UK- and Caribbean-born BC people.

METHODS

Data on STI diagnoses in BC people attending specialist sexual health services (SHSs) during 2015 and living in England were obtained from the GUMCAD STI surveillance system, the national surveillance system for STIs in England. Associations between being UK- or Caribbean-born and each of several STI diagnoses were examined, using univariate and multivariable generalised estimated equations logistic regression models adjusted for sexual orientation, place of residence (London vs. non-London), HIV status, area-level deprivation, and STI diagnosis in the last year. All analyses were stratified by age (<25 vs. ≥25 years).

RESULTS

In 2015, 63,568 BC people made 108,881 attendances at specialist SHSs; 81.9% of these attendances were made by UK-born BCs. The median age (years) was 26 for UK-born and 35 for Caribbean-born people (p≤0.001). Chlamydia, gonorrhoea and non-specific genital infection (NSGI) were the most commonly diagnosed STIs among UK- (5.8%, 2.1% and 2.8%) and Caribbean-born people (4.5%, 1.7% and 3.5%) respectively. Among BCs aged under 25, no significant differences in STIs were found between UK- and Caribbean-born people. Among BCs aged ≥25, compared to Caribbean-born people, those who were UK-born were more likely to be diagnosed with chlamydia (AOR 1.15 [95%C.I. 1.04-1.27]); gonorrhoea (AOR 1.23 [95%C.I. 1.06-1.45]) and genital herpes (AOR 1.23 [95% C.I. 1.10-1.56]) and less likely to be diagnosed with NSGI (AOR 0.89 [95% C.I. 0.80-0.99]) and Trichomoniasis (AOR 0.84 [95% C.I. 0.71-0.99]).

DISCUSSION/CONCLUSION

STI diagnoses in BC people aged ≥25 attending specialist SHSs vary by region of birth. Country of birth may have an influence on social and sexual networks and therefore transmission of STIs.

Addressing the challenges of knowledge co-production in quality improvement: learning from the implementation of the researcher-in-residence model

The concept of knowledge co-production is used in health services research to describe partnerships (which can involve researchers, practitioners, managers, commissioners or service users) with the purpose of creating, sharing and negotiating different knowledge types used to make improvements in health services. Several knowledge co-production models have been proposed to date, some involving intermediary roles. This paper explores one such model, researchers-in-residence (also known as 'embedded researchers').In this model, researchers work inside healthcare organisations, operating as staff members while also maintaining an affiliation with academic institutions. As part of the local team, researchers negotiate the meaning and use of research-based knowledge to co-produce knowledge, which is sensitive to the local context. Even though this model is spreading and appears to have potential for using co-produced knowledge to make changes in practice, a number of challenges with its use are emerging. These include challenges experienced by the researchers in embedding themselves within the practice environment, preserving a clear focus within their host organisations and maintaining academic professional identity.In this paper, we provide an exploration of these challenges by examining three independent case studies implemented in the UK, each of which attempted to co-produce relevant research projects to improve the quality of care. We explore how these played out in practice and the strategies used by the researchers-in-residence to address them. In describing and analysing these strategies, we hope that participatory approaches to knowledge co-production can be used more effectively in the future.