"Closed books": restrictions to primary healthcare access in Aotearoa New Zealand-reporting results from a survey across general practices.

AIM: In Aotearoa New Zealand, primary care is organised by enrolling patients with a primary care provider. However, the benefits of this arrangement are frustrated when providers "close their books" due to insufficient capacity for new patients. We investigated the extent, evolution and impact of this situation on health access and equity in access to primary healthcare. METHOD: We distributed a survey for general practice personnel in 2022, yielding 227 valid responses. We examined responses across respondents' practice characteristics, including practice size, rural-urban setting, average co-payments, region and ethnic composition of the catchment population. RESULTS: Most general practices are selectively enrolling their patients. In 2022, only 28% of respondents freely enrolled new people. Since 2019, most respondents (79%) had "closed books" or limited enrolments at some point. The situation worsened between 2019 and 2022, compromising equal opportunity and access in healthcare. CONCLUSION: Restricted enrolment poses a widespread barrier to health access and equity, and it worsened since the beginning of the COVID-19 pandemic. Addressing closed books and limited enrolments in general practice could significantly improve health services' access and equity. The study aims to inform ongoing health reforms.

Role of CAMK2D in neurodevelopment and associated conditions.

The calcium/calmodulin-dependent protein kinase type 2 (CAMK2) family consists of four different isozymes, encoded by four different genes-CAMK2A, CAMK2B, CAMK2G, and CAMK2D-of which the first three have been associated recently with neurodevelopmental disorders. CAMK2D is one of the major CAMK2 proteins expressed in the heart and has been associated with cardiac anomalies. Although this CAMK2 isoform is also known to be one of the major CAMK2 subtypes expressed during early brain development, it has never been linked with neurodevelopmental disorders until now. Here we show that CAMK2D plays an important role in neurodevelopment not only in mice but also in humans. We identified eight individuals harboring heterozygous variants in CAMK2D who display symptoms of intellectual disability, delayed speech, behavioral problems, and dilated cardiomyopathy. The majority of the variants tested lead to a gain of function (GoF), which appears to cause both neurological problems and dilated cardiomyopathy. In contrast, loss-of-function (LoF) variants appear to induce only neurological symptoms. Together, we describe a cohort of individuals with neurodevelopmental disorders and cardiac anomalies, harboring pathogenic variants in CAMK2D, confirming an important role for the CAMK2D isozyme in both heart and brain function.

Financial barriers to primary health care in Aotearoa New Zealand.

BACKGROUND: In Aotearoa New Zealand, co-payments to see a general practitioner (GP, family doctor) or collect a prescription are payable by virtually all adults. OBJECTIVE: To examine the extent to which these user co-payments are a barrier to accessing health care, focussing on inequities for indigenous Maori. METHODS: Pooled data from sequential waves (years) of the New Zealand Health Survey, 2011/12 to 2018/19 were analysed. Outcomes were self-reported cost barriers to seeing a GP or collecting a prescription in the previous year. Logistic regression was used to estimate odds ratios (ORs) of barriers to care for Maori compared with non-Maori, sequentially adjusting for additional explanatory variables. RESULTS: Pooled data included 107,231 people, 22,292 (21%) were Maori. Across all years, 22% of Maori (13% non-Maori) experienced a cost barrier to seeing a GP, and 14% of Maori (5% non-Maori) reported a cost barrier to collecting a prescription. The age- and wave-adjusted OR comparing Maori/non-Maori was 1.71 (95% confidence interval [CI]: 1.61, 1.81) for the cost barrier to primary care and 2.97 (95% CI: 2.75, 3.20) for the cost barrier to collecting prescriptions. Sociodemographics accounted for about half the inequity for both outcomes; in a fully adjusted model, age, sex, low income, and poorer underlying health were determinants of both outcomes, and deprivation was additionally associated with the cost barrier to collecting a prescription but not to seeing a GP. CONCLUSIONS: Maori experience considerable inequity in access to primary health care; evidence supports an urgent need for change to system funding to eliminate financial barriers to care.

Cohort profile: Nga Kawekawe o Mate Korona | Impacts of COVID-19 in Aotearoa - a prospective, national cohort study of people with COVID-19 in New Zealand.

PURPOSE: The COVID-19 pandemic has had significant health, social and economic impacts around the world. We established a national, population-based longitudinal cohort to investigate the immediate and longer-term physical, psychological and economic impacts of COVID-19 on affected people in Aotearoa New Zealand (Aotearoa), with the resulting evidence to assist in designing appropriate health and well-being services for people with COVID-19. PARTICIPANTS: All people residing in Aotearoa aged 16 years or over, who had a confirmed or probable diagnosis of COVID-19 prior to December 2021, were invited to participate. Those living in dementia units were excluded. Participation involved taking part in one or more of four online surveys and/or in-depth interviews. The first wave of data collection took place from February to June 2022. FINDINGS TO DATE: By 30 November 2021, of 8735 people in Aotearoa aged 16+ who had COVID-19, 8712 were eligible for the study and 8012 had valid addresses so were able to be contacted to take part. A total of 990 people, including 161 Tangata Whenua (Maori, Indigenous peoples of Aotearoa) completed one or more surveys; in addition, 62 took part in in-depth interviews. Two hundred and seventeen people (20%) reported symptoms consistent with long COVID. Key areas of adverse impacts were experiences of stigma, mental distress, poor experiences of health services and barriers to healthcare, each being significantly more pronounced among disabled people and/or those with long COVID. FUTURE PLANS: Further data collection is planned to follow-up cohort participants. This cohort will be supplemented by the inclusion of a cohort of people with long COVID following Omicron infection. Future follow-ups will assess longitudinal changes to health and well-being impacts, including mental health, social, workplace/education and economic impacts of COVID-19.

Al-Gazali Skeletal Dysplasia Constitutes the Lethal End of ADAMTSL2-Related Disorders.

Lethal short-limb skeletal dysplasia Al-Gazali type (OMIM %601356), also called dysplastic cortical hyperostosis, Al-Gazali type, is an ultra-rare disorder previously reported in only three unrelated individuals. The genetic etiology for Al-Gazali skeletal dysplasia has up until now been unknown. Through international collaborative efforts involving seven clinical centers worldwide, a cohort of nine patients with clinical and radiographic features consistent with short-limb skeletal dysplasia Al-Gazali type was collected. The affected individuals presented with moderate intrauterine growth restriction, relative macrocephaly, hypertrichosis, large anterior fontanelle, short neck, short and stiff limbs with small hands and feet, severe brachydactyly, and generalized bone sclerosis with mild platyspondyly. Biallelic disease-causing variants in ADAMTSL2 were detected using massively parallel sequencing (MPS) and Sanger sequencing techniques. Six individuals were compound heterozygous and one individual was homozygous for pathogenic variants in ADAMTSL2. In one of the families, pathogenic variants were detected in parental samples only. Overall, this study sheds light on the genetic cause of Al-Gazali skeletal dysplasia and identifies it as a semi-lethal part of the spectrum of ADAMTSL2-related disorders. Furthermore, we highlight the importance of meticulous analysis of the pseudogene region of ADAMTSL2 where disease-causing variants might be located. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death.

Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in 105 families. Our cohort provides evidence of severe atypical in utero presentations of known genetic disorders and identifies novel phenotypes and disease genes. Inheritance of 42% of definitive diagnoses were either autosomal recessive (30.8%), X-linked recessive (3.8%) or autosomal dominant (excluding de novos, 7.7%), with risk of recurrence in future pregnancies. We report that at least ten families (5%) used their diagnosis for preimplantation (5) or prenatal diagnosis (5) of 12 pregnancies. We emphasize the clinical importance of genomic investigations of pregnancy loss and perinatal death, with short turnaround times for diagnostic reporting and followed by systematic research follow-up investigations. This approach has the potential to enable accurate counseling for future pregnancies.

Australian guidelines for the management of children with achondroplasia.

Achondroplasia is the most common form of skeletal dysplasia. In addition to altered growth, children and young people with achondroplasia may experience medical complications, develop and function differently to others and require psychosocial support. International, European and American consensus guidelines have been developed for the management of achondroplasia. The Australian focused guidelines presented here are designed to complement those existing guidelines. They aim to provide core care recommendations for families and clinicians, consolidate key resources for the management of children with achondroplasia, facilitate communication between specialist, local teams and families and support delivery of high-quality care regardless of setting and geographical location. The guidelines include a series of consensus statements, developed using a modified Delphi process. These statements are supported by the best available evidence assessed using the National Health and Medicine Research Council's criteria for Level of Evidence and their Grading of Recommendations Assessment, Development and Evaluation (GRADE). Additionally, age specific guides are presented that focus on the key domains of growth, medical, development, psychosocial and community. The guidelines are intended for use by health professionals and children and young people with achondroplasia and their families living in Australia.

Studying Disease-Associated UBE3A Missense Variants Using Enhanced Sampling Molecular Simulations.

Missense variants in UBE3A underlie neurodevelopmental conditions such as Angelman Syndrome and Autism Spectrum Disorder, but the underlying molecular pathological consequences on protein folding and function are poorly understood. Here, we report a novel, maternally inherited, likely pathogenic missense variant in UBE3A (NM_000462.4(UBE3A_v001):(c.1841T>C) (p.(Leu614Pro))) in a child that presented with myoclonic epilepsy from 14 months, subsequent developmental regression from 16 months, and additional features consistent with Angelman Syndrome. To understand the impact of p.(Leu614Pro) on UBE3A, we used adiabatic biased molecular dynamics and metadynamics simulations to investigate conformational differences from wildtype proteins. Our results suggest that Leu614Pro substitution leads to less efficient binding and substrate processing compared to wildtype. Our results support the use of enhanced sampling molecular simulations to investigate the impact of missense UBE3A variants on protein function that underlies neurodevelopment and human disorders.

A Standard Set of Value-Based Patient-Centered Outcomes and Measures of Overall Health in Adults.

BACKGROUND: The definition of population-specific outcomes is an essential precondition for the implementation of value-based health care. We developed a minimum standard outcome set for overall adult health (OAH) to facilitate the implementation of value-based health care in tracking, comparing, and improving overall health care outcomes of adults across multiple conditions, which would be of particular relevance for primary care and public health populations. METHODS: The International Consortium for Health Outcomes Measurement (ICHOM) convened an international panel (patients, clinicians, and topic experts). Following the development of a conceptual framework, a modified Delphi method (supported by public consultations) was implemented to identify, in sequence, the relevant domains, the best instruments for measuring them, the timing of measurement, and the relevant adjustment variables. FINDINGS: Outcomes were identified in relation to overall health status and the domains of physical, mental, and social health. Three instruments covering these domains were identified: PROMIS Scale v1.2-Global Health (10 items), WHO Wellbeing Index (5 items), and the WHO Disability Assessment Schedule 2.0 (12 items). Case-mix variables included a range of sociodemographic and biometric measures. Yearly measurement was proposed for all outcomes and most case-mix variables. INTERPRETATION: The ICHOM OAH Standard Set has been developed through consensus-based methods based on predefined criteria following high standards for the identification and selection of high-quality measures The involvements of a wide range of stakeholders supports the acceptability of the set, which is readily available for use and feasibility testing in clinical settings.

Severe congenital cutis laxa: Identification of novel homozygous LOX gene variants in two families.

We report three babies from two families with a severe lethal form of congenital cutis laxa. All three had redundant and doughy-textured skin and two siblings from one family had facial dysmorphism. Echocardiograms showed thickened and poorly contractile hearts, arterial dilatation and tortuosity. Post-mortem examination in two of the babies further revealed widespread ectasia and tortuosity of medium and large sized arteries, myocardial hypertrophy, rib and skull fractures. The presence of fractures initially suggested a diagnosis of osteogenesis imperfecta. Under light microscopy bony matrices were abnormal and arterial wall architecture was grossly abnormal showing fragmented elastic fibres. Molecular analysis of known cutis laxa genes did not yield any pathogenic defects. Whole exome sequencing of DNA following informed consent identified two separate homozygous variants in the LOX (Lysyl Oxidase) gene. LOX belongs to the 5-lysyl oxidase gene family involved in initiation of cross-linking of elastin and collagen. A mouse model of a different variant in this gene recapitulates the phenotype seen in the three babies. Our findings suggest that the LOX gene is a novel cause of severe congenital cutis laxa with arterial tortuosity, bone fragility and respiratory failure.

Healthy snacks in hospitals: Testing the potential effects of changes in availability.

BACKGROUND: Hospitals offer snacks for sale to patients, staff and visitors. AIM: As food choice is heavily influenced by the options available, the present study (a) audited snack availability and purchase in NHS hospital sites across a large UK city; and (b) tested the potential effects of changes to this availability in an online choice experiment. METHODS: In Study 1 (audit), single-serve snacks (n=376) available in 76 hospital food retail units were audited. Purchasing data were obtained from six food retail units over four weeks (27,989 sales). In Study 2 (online experiment), participants (n=159) chose snacks from pictured ranges containing 25% (minority), 50% (equivalent) or 75% (majority) healthy options. RESULTS: Available single-serve snacks varied markedly in calorie (18-641 kcals), fat (0-39 g), sugar (0.1-76 g) and salt (0-2.9 g). Only 30% of available snacks were healthy options and only 25% of the most commonly purchased snacks were healthy options. In Study 2, snack choice was significantly associated with the availability of healthy options in the choice array (X2 (2)= 59.71, p<.01). More participants made healthy choices when product ranges contained 75% healthy options compared to 50% (p<.01) and 50% healthy options compared with 25% (p<.01). CONCLUSIONS: Healthy snacks are readily available in NHS sites but there is a greater relative variety of unhealthy snack products. Many consumers continue to purchase unhealthy items. Further increasing the availability and variety of healthy options may support consumers to make healthier choices.

Dissecting the journey to breast cancer diagnosis in sub-Saharan Africa: Findings from the multicountry ABC-DO cohort study.

Most breast cancer patients in sub-Saharan Africa are diagnosed at advanced stages after prolonged symptomatic periods. In the multicountry African Breast Cancer-Disparities in Outcomes cohort, we dissected the diagnostic journey to inform downstaging interventions. At hospital presentation for breast cancer, women recalled their diagnostic journey, including dates of first noticing symptoms and health-care provider (HCP) visits. Negative binomial regression models were used to identify correlates of the length of the diagnostic journey. Among 1429 women, the median (inter-quartile range) length (months) of the diagnostic journey ranged from 11.3 (5.7-21.2) in Ugandan, 8.2 (3.4-16.4) in Zambian, 6.5 (2.4-15.7) in Namibian-black to 5.6 (2.3-13.1) in Nigerian and 2.4 (0.6-5.5) in Namibian-non-black women. Time from first HCP contact to diagnosis represented, on average, 58% to 79% of the diagnostic journey in each setting except Nigeria where most women presented directly to the diagnostic hospital with advanced disease. The median number of HCPs visited was 1 to 4 per woman, but time intervals between visits were long. Women who attributed their initial symptoms to cancer had a 4.1 months (absolute) reduced diagnostic journey than those who did not, while less-educated (none/primary) women had a 3.6 months longer journey than more educated women. In most settings the long journey to breast cancer diagnosis was not primarily due to late first presentation but to prolonged delays after first presentation to diagnosis. Promotion of breast cancer awareness and implementation of accelerated referral pathways for women with suspicious symptoms are vital to downstaging the disease in the region.

Geospatial barriers to healthcare access for breast cancer diagnosis in sub-Saharan African settings: The African Breast Cancer-Disparities in Outcomes Cohort Study.

We examined the geospatial dimension of delays to diagnosis of breast cancer in a prospective study of 1541 women newly diagnosed in the African Breast Cancer-Disparities in Outcomes (ABC-DO) Study. Women were recruited at cancer treatment facilities in Namibia, Nigeria, Uganda and Zambia. The baseline interview included information used to generate the geospatial features: urban/rural residence, travel mode to treatment facility and straight-line distances from home to first-care provider and to diagnostic/treatment facility, categorized into country/ethnicity (population)-specific quartiles. These factors were investigated in relation to delay in diagnosis (≥3 months since first symptom) and late stage at diagnosis (TNM: III, IV) using logistic regression, adjusted for population group and sociodemographic characteristics. The median (interquartile range) distances to first provider and diagnostic and treatment facilities were 5 (1-37), 17 (3-105) and 62 (5-289) km, respectively. The majority had a delay in diagnosis (74%) and diagnosis at late stage (64%). Distance to first provider was not associated with delay in diagnosis or late stage at diagnosis. Rural residence was associated with delay, but the association did not persist after adjustment for sociodemographic characteristics. Distance to the diagnostic/treatment facility was associated with delay (highest vs lowest quartile: odds ratio (OR) = 1.56, 95% confidence interval (CI) = 1.08-2.27) and late stage (overall: OR = 1.47, CI = 1.05-2.06; without Nigerian hospitals where mostly local residents were treated: OR = 1.73, CI = 1.18-2.54). These findings underscore the need for measures addressing the geospatial barriers to early diagnosis in sub-Saharan African settings, including providing transport or travel allowance and decentralizing diagnostic services.

A flexible computational pipeline for research analyses of unsolved clinical exome cases.

Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial diagnostic rates of ~25-30%. Here we develop a robust computational pipeline to rank variants for reassessment of unsolved rare disease patients. A comprehensive web-based patient report is generated in which all deleterious variants can be filtered by gene, variant characteristics, OMIM disease and Phenolyzer scores, and all are annotated with an ACMG classification and links to ClinVar. The pipeline ranked 21/34 previously diagnosed variants as top, with 26 in total ranked ≤7th, 3 ranked ≥13th; 5 failed the pipeline filters. Pathogenic/likely pathogenic variants by ACMG criteria were identified for 22/145 unsolved cases, and a previously undefined candidate disease variant for 27/145. This open access pipeline supports the partnership between clinical and research laboratories to improve the diagnosis of unsolved exomes. It provides a flexible framework for iterative developments to further improve diagnosis.

RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features.

Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.

Breast cancer survival and survival gap apportionment in sub-Saharan Africa (ABC-DO): a prospective cohort study.

BACKGROUND: Breast cancer is the second leading cause of death from cancer in women in sub-Saharan Africa, yet there are few well characterised large-scale survival studies with complete follow-up data. We aimed to provide robust survival estimates in women in this setting and apportion the survival gaps. METHODS: The African Breast Cancer-Disparities in Outcomes (ABC-DO) prospective cohort study was done at eight hospitals across five sub-Saharan African countries (Namibia, Nigeria, South Africa, Uganda, and Zambia). We prospectively recruited women (aged ≥18 years) who attended these hospitals with suspected breast cancer. Women were actively followed up by use of a telephone call once every 3 months, and a mobile health application was used to keep a dynamic record of follow-up calls due. We collected detailed sociodemographic, clinical, and treatment data. The primary outcome was 3-year overall survival, analysed by use of flexible proportional mortality models, and we predicted survival under scenarios of modified distributions of risk factors. FINDINGS: Between Sept 8, 2014, and Dec 31, 2017, 2313 women were recruited from these eight hospitals, of whom 85 did not have breast cancer. Of the remaining 2228 women with breast cancer, 58 women with previous treatment or recurrence, and 14 women from small racial groups (white and Asian women in South Africa), were excluded. Of the 2156 women analysed, 1840 (85%) were histologically confirmed, 129 (6%) were cytologically confirmed, and 187 (9%) were clinically confirmed to have breast cancer. 2156 (97%) women were followed up for up to 3 years or up to Jan 1, 2019, whichever was earlier. Up to this date, 879 (41%) of these women had died, 1118 (52%) were alive, and 159 (7%) were censored early. 3-year overall survival was 50% (95% CI 48-53), but we observed variations in 3-year survival between different races in Namibia (from 90% in white women to 56% in Black women) and in South Africa (from 76% in mixed-race women to 59% in Black women), and between different countries (44-47% in Uganda and Zambia vs 36% in Nigeria). 215 (10%) of all women had died within 6 months of diagnosis, but 3-year overall survival remained low in women who survived to this timepoint (58%). Among survival determinants, improvements in early diagnosis and treatment were predicted to contribute to the largest increases in survival, with a combined absolute increase in survival of up to 22% in Nigeria, Zambia, and Uganda, when compared with the contributions of other factors (such as HIV or aggressive subtypes). INTERPRETATION: Large variations in breast cancer survival in sub-Saharan African countries indicate that improvements are possible. At least a third of the projected 416 000 breast cancer deaths that will occur in this region in the next decade could be prevented through achievable downstaging and improvements in treatment. Improving survival in socially disadvantaged women warrants special attention. FUNDING: Susan G Komen and the International Agency for Research on Cancer.

The variability of SMARCA4-related Coffin-Siris syndrome: Do nonsense candidate variants add to milder phenotypes?

SMARCA4 encodes a central ATPase subunit in the BRG1-/BRM-associated factors (BAF) or polybromo-associated BAF (PBAF) complex in humans, which is responsible in part for chromatin remodeling and transcriptional regulation. Variants in this and other genes encoding BAF/PBAF complexes have been implicated in Coffin-Siris Syndrome, a multiple congenital anomaly syndrome classically characterized by learning and developmental differences, coarse facial features, hypertrichosis, and underdevelopment of the fifth digits/nails of the hands and feet. Individuals with SMARCA4 variants have been previously reported and appear to display a variable phenotype. We describe here a cohort of 15 unrelated individuals with SMARCA4 variants from the Coffin-Siris syndrome/BAF pathway disorders registry who further display variability in severity and degrees of learning impairment and health issues. Within this cohort, we also report two individuals with novel nonsense variants who appear to have a phenotype of milder learning/behavioral differences and no organ-system involvement.

Two novel intragenic variants in the FMR1 gene in patients with suspect clinical diagnosis of Fragile X syndrome and no CGG repeat expansion.

The major and most well-studied genetic cause of Fragile-X syndrome (FXS) is expansion of a CGG repeat in the 5'-UTR of the FMR1 gene. Routine testing for this expansion is performed globally. Overall, there is a paucity of intragenic variants explaining FXS, a fact which is being addressed by a more systematic application of whole exome (WES) and whole genome (WGS) sequencing, even in the diagnostic setting. Here we report two families comprising probands with a clinical suspicion of FXS and no CGG repeat expansions. Using WES/WGS we identified deleterious variants within the coding region of FMR1 in both families. In a family from Finland we identified a complex indel c.1021-1028delinsTATTGG in exon 11 of FMR1 which gives rise to a frameshift and a premature termination codon (PTC), p.Asn341Tyrfs*7. Follow-up mRNA and protein studies on a cell line from the proband revealed that although the mRNA levels of FMR1 were not altered, Fragile X Mental Retardation 1 Protein (FMRP) was undetectable. Additionally, we identified a variant, c.881-1G > T, affecting the canonical acceptor splice site of exon 10 of FMR1 in an Australian family. Our findings reinforce the importance of intragenic FMR1 variant testing, particularly in cases with clinical features of FXS and no CGG repeat expansions identified.