A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers.

The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and translate these to clinical care.

Indigenous Australian genomes show deep structure and rich novel variation.

The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama-Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000-35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.

The landscape of genomic structural variation in Indigenous Australians.

Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.

Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data.

Addressing Indigenous rights and interests in genetic resources has become increasingly challenging in an open science environment that promotes unrestricted access to genomic data. Although Indigenous experiences with genetic research have been shaped by a series of negative interactions, there is increasing recognition that equitable benefits can only be realized through greater participation of Indigenous communities. Issues of trust, accountability and equity underpin Indigenous critiques of genetic research and the sharing of genomic data. This Perspectives article highlights identified issues for Indigenous communities around the sharing of genomic data and suggests principles and actions that genomic researchers can adopt to recognize community rights and interests in data.

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

FastHPOCR: Pragmatic, fast and accurate concept recognition using the Human Phenotype Ontology.

MOTIVATION: Human Phenotype Ontology (HPO)-based phenotype concept recognition underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing adoption of large language models (LLM) for natural language understanding has led to several LLM-based solutions, we argue that their intrinsic resource-intensive nature is not suitable for realistic management of the phenotype concept recognition (CR) lifecycle. Consequently, we propose to go back to the basics and adopt a dictionary-based approach that enables both an immediate refresh of the ontological concepts as well as efficient re-analysis of past data. RESULTS: We developed a dictionary-based approach using a pre-built large collection of clusters of morphologically-equivalent tokens-to address lexical variability and a more effective concept recognition step by reducing the entity boundary detection strictly to candidates consisting of tokens belonging to ontology concepts. Our method achieves state-of-the-art results (0.76 F1 on the GSC+ corpus) and a processing efficiency of 10,000 publication abstracts in 5s. AVAILABILITY: FastHPOCR is available as a Python package installable via pip. The source code is available at https://github.com/tudorgroza/fast_hpo_cr. A Java implementation of FastHPOCR will be made available as part of the Fenominal Java library available at https://github.com/monarch-initiative/fenominal. The up-to-date GCS-2024 corpus is available at https://github.com/tudorgroza/code-for-papers/tree/main/gsc-2024.

Use of privacy-preserving record linkage to examine the dispensing of pharmaceutical benefits scheme medicines to pregnant women in Western Australia.

PURPOSE: Medications are commonly used during pregnancy to manage pre-existing conditions and conditions that arise during pregnancy. However, not all medications are safe to use in pregnancy. This study utilized privacy-preserving record linkage (PPRL) to examine medications dispensed under the national Pharmaceutical Benefits Scheme (PBS) to pregnant women in Western Australia (WA) overall and by medication safety category. METHODS: In this retrospective, cross-sectional, population-based study, state perinatal records (Midwives Notification Scheme) were linked with national PBS dispensing data using PPRL. Live and stillborn neonates born between 2012 and 2019 in WA were included. The proportion of pregnancies during which the mother was dispensed a PBS medication was calculated, overall and by medication safety category. Factors associated with PBS medication dispensing were examined using logistic regression. RESULTS: PPRL linkage identified matching records for 97.4% of women with perinatal records. A total of 271 739 pregnancies were identified, with 158 585 (58.4%) pregnancies involving the dispensing of at least one PBS medication. Category A medications (those considered safe in pregnancy) were the most commonly dispensed (n = 119 126, 43.8%) followed by B3 (n = 51 135, 18.8%) and B1 (n = 42 388, 15.6%) medication (those with unknown safety). Over the study period, the dispensing of PBS medications in pregnancy increased (OR: 1.06, 95%CI: 1.06, 1.07). The strongest predictor of medication dispensing in pregnancy was pre-pregnancy dispensing (OR: 3.61, 95%CI: 3.54, 3.68). Other factors associated with medication use in pregnancy were smoking, older maternal age, obesity, and prior pregnancies. CONCLUSION: Privacy preserving record linkage provides a way to link cross-jurisdictional data while preserving patient confidentiality and data security. The dispensing of PBS medication in pregnancy was common and increased over time, with approximately 60% of women dispensed at least one medication during pregnancy.

An evaluation of GPT models for phenotype concept recognition.

OBJECTIVE: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. MATERIALS AND METHODS: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. RESULTS: The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. CONCLUSION: Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.

Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data.

Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment "to leveraging the benefits of genomics in the health system for all Australians." They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.

Hospitalizations from Birth to 28 Years in a Population Cohort of Individuals Born with Five Rare Craniofacial Anomalies in Western Australia.

OBJECTIVE: To describe trends, age-specific patterns, and factors influencing hospitalizations for 5 rare craniofacial anomalies (CFAs). METHODS: Data on livebirths (1983-2010; n = 721 019) including rare CFA (craniofacial microsomia, mandibulofacial dysostosis, Pierre Robin sequence, Van der Woude syndrome, and frontonasal dysplasia), episodes of death, and demographic and perinatal factors were identified from the Western Australian Register of Developmental Anomalies, Death Registrations and Midwives Notification System. Information on incident craniofacial and noncraniofacial related admissions, length of hospital stay, and intensive care and emergency-related admissions were identified using principal diagnosis and procedural codes were extracted from the Hospital Morbidity Data Collection and linked to other data sources. Associations of hospitalizations by age groups as well as demographic and perinatal factors were expressed as incidence rate ratio (IRR). RESULTS: The incident hospitalizations were 3 times as high for rare CFA (IRR 3.22-3.72) throughout childhood into adolescence than those without. Children with rare CFA had 3-4 times as many potentially preventable hospitalizations until 18 years of age than those without. Specifically, respiratory infections (IRR 2.13-2.35), ear infections (IRR 7.92-26.28), and oral health-related conditions contributed for most noncraniofacial admissions until the adolescence period. A greater incidence of noncraniofacial related hospitalizations was observed among Indigenous children, births with intrauterine growth restrictions, and families with high socioeconomic disadvantage. CONCLUSIONS: Throughout childhood, individuals with rare CFA had greater hospital service use, specifically for potentially preventable conditions, than those without. These population-level findings can inform new preventive strategies and early disease management targeted toward reducing preventable hospitalizations.

Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms.

Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.

Trends in prenatal diagnosis of congenital anomalies in Western Australia between 1980 and 2020: A population-based study.

BACKGROUND: Advances in screening and diagnostics have changed the way in which we identify and diagnose congenital anomalies. OBJECTIVE: To examine changes in rates of prenatal diagnosis of congenital anomalies over time and by demographic characteristics. METHODS: We undertook a population-based retrospective cohort study of all children born in Western Australia between 1980 and 2020 and diagnosed with a congenital anomaly. Age at diagnosis (prenatal, neonatal, infancy, early childhood or childhood) prevalence (all-type and type-specific), and prevalence ratios (PR) were calculated. We fit joinpoint regression models to describe the average annual percentage change (APC) in prenatal diagnosis over time, and log-binomial regression models to estimate the association between prenatal diagnosis and demographic characteristics. RESULTS: Prenatal diagnosis prevalence between the first (1980-1989: 28.3 per 10,000 births) and last (2005-2014: 156.1 per 10,000 births) decades of the study increased 5.5-fold (95% confidence interval [CI] 5.0, 5.9). Substantial increases were observed for cardiovascular (PR 10.7, 95% CI 8.0, 14.6), urogenital (PR 10.5, 95% CI: 8.7, 12.6) and chromosomal anomalies (PR 7.0, 95% CI 5.9, 8.3). Prenatal diagnosis was positively associated with the birth year (adjusted risk ratio [RR] 1.04, 95% CI 1.03, 1.04), advanced maternal age (RR 1.14, 95% CI 1.11, 1.18), multiple anomalies (RR 2.86, 95% CI 2.77, 2.96) and major anomalies (RR 3.75, 95% CI 3.36, 4.19), and inversely associated with remoteness (RR 0.89, 95% CI: 0.83, 0.95) and Aboriginality (RR 0.90, 95% CI 0.83, 0.97). CONCLUSIONS: Increases in prenatal diagnosis of congenital anomalies were observed in Western Australia from 1980 to 2020, reflecting advances in screening. Prenatal diagnosis was less common in remote regions and in Aboriginal children, strengthening calls for increased provision of antenatal care services for these populations.

Prevalence and trends for Aboriginal and Torres Strait Islander children living with cerebral palsy: A birds-eye view.

AIM: To provide a birds-eye view of the trends of cerebral palsy (CP) for Australian Aboriginal and Torres Strait Islander children and young adults. METHOD: Data were obtained for this population-based observational study from the Australian Cerebral Palsy Register (ACPR), birth years 1995 to 2014. The Indigenous status of children was classified by maternal Aboriginal and Torres Strait Islander or non-Indigenous status. Descriptive statistics were calculated for socio-demographic and clinical characteristics. Prenatal/perinatal and post-neonatal birth prevalence was calculated per 1000 live births and per 10 000 live births respectively, and Poisson regression used to assess trends. RESULTS: Data from the ACPR were available for 514 Aboriginal and Torres Strait Islander individuals with CP. Most children could walk independently (56%) and lived in urban or regional areas (72%). One in five children lived in socioeconomically disadvantaged remote/very remote areas. The birth prevalence of prenatal/perinatal CP declined after the mid-2000s from a high of 4.8 (95% confidence interval 3.2-7.0) to 1.9 per 1000 live births (95% confidence interval 1.1-3.2) (2013-2014), with marked declines observed for term births and teenage mothers. INTERPRETATION: The birth prevalence of CP in Aboriginal and Torres Strait Islander children in Australia declined between the mid-2000s and 2013 to 2014. This birds-eye view provides key stakeholders with new knowledge to advocate for sustainable funding for accessible, culturally safe, antenatal and CP services. WHAT THIS PAPER ADDS: Birth prevalence of cerebral palsy (CP) is beginning to decline for Aboriginal and Torres Strait Islanders. Recent CP birth prevalence for Aboriginal and Torres Strait Islanders is 1.9 per 1000 live births. Most children with CP live in more populated areas rather than remote or very remote areas. One in five Aboriginal and Torres Strait Islander children with CP live in socioeconomically disadvantaged remote areas.

Patterns, trends, and factors influencing hospitalizations for craniosynostosis in Western Australia. A population-based study.

Understanding hospital service use among children with a diagnosis of craniosynostosis (CS) is important to improve services and outcomes. This study aimed to describe population-level trends, patterns, and factors influencing hospitalizations for craniosynostosis in Western Australia. Data on live births (1990-2010; n = 554,624) including craniosynostosis, episodes of death, demographic, and perinatal factors were identified from the midwives, birth defects, hospitalizations, and death datasets. Information on craniosynostosis and non-craniosynostosis-related admissions, cumulative length of hospital stay (cLoS), intensive care unit, and emergency department-related admissions were extracted from the hospitalization dataset and linked to other data sources. These associations were examined using negative binomial regression presented as annual percent change and associations of hospitalizations by age groups, demographic, and perinatal factors were expressed as incidence rate ratio (IRR). We found an increasing trend in incident hospitalizations but a marginal decline in cLoS for craniosynostosis over the observed study period. Perinatal conditions, feeding difficulties, nervous system anomalies, respiratory, and other infections contributed to majority of infant non-CS-related admissions.Respiratory infections accounted for about twice the number of admissions for individuals with CS (IRRs 1.94-2.34) across all observed age groups. Higher incidence of non-CS hospitalizations was observed among females, with associated anomalies, to families with highest socioeconomic disadvantage and living in remote areas of the state.   Conclusion: Marginal reduction in the cLoS for CS-related admissions observed over the 21-year period are potentially indicative of improved peri-operative care. However, higher incidence of respiratory infection-related admissions for syndromic synostosis is concerning and requires investigation.

Refining nosology by modelling variation among facial phenotypes: the RASopathies.

BACKGROUND: In clinical genetics, establishing an accurate nosology requires analysis of variations in both aetiology and the resulting phenotypes. At the phenotypic level, recognising typical facial gestalts has long supported clinical and molecular diagnosis; however, the objective analysis of facial phenotypic variation remains underdeveloped. In this work, we propose exploratory strategies for assessing facial phenotypic variation within and among clinical and molecular disease entities and deploy these techniques on cross-sectional samples of four RASopathies: Costello syndrome (CS), Noonan syndrome (NS), cardiofaciocutaneous syndrome (CFC) and neurofibromatosis type 1 (NF1). METHODS: From three-dimensional dense surface scans, we model the typical phenotypes of the four RASopathies as average 'facial signatures' and assess individual variation in terms of direction (what parts of the face are affected and in what ways) and severity of the facial effects. We also derive a metric of phenotypic agreement between the syndromes and a metric of differences in severity along similar phenotypes. RESULTS: CFC shows a relatively consistent facial phenotype in terms of both direction and severity that is similar to CS and NS, consistent with the known difficulty in discriminating CFC from NS based on the face. CS shows a consistent directional phenotype that varies in severity. Although NF1 is highly variable, on average, it shows a similar phenotype to CS. CONCLUSIONS: We established an approach that can be used in the future to quantify variations in facial phenotypes between and within clinical and molecular diagnoses to objectively define and support clinical nosologies.

The Human Phenotype Ontology in 2021.

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

Epidemiology of Hospital Admissions for Craniosynostosis in Australia: A Population-Based Study.

To describe trends, age, and sex-specific patterns of population hospital admissions with a diagnosis of craniosynostosis (CS) in Australia.Population data for hospital separations (in-patient) from public and private hospitals (July 1996-June 2018) were obtained from the publicly available Australian Institute of Health and Welfare (AIHW) National Hospital Morbidity Database.The outcome variables were hospital separation rates (HSR) (number of hospital separations divided by the estimated resident population [ERP] per year) and average length of stay (aLOS) (patient days divided by the number of hospital separations) with a diagnosis of CS. Trends in HSR and aLOS adjusted for age, sex, and type of CS were investigated by negative binomial regression presented as annual percent change (APC).In 8057 admissions identified, we observed no significant change in the annual trend for HSR for the 22-year period. However, a marginal annual decrease of 1.6% (95% CI: -0.7, -2.4) in the aLOS was identified for the same time period. HSR were higher for males, infants, and single suture synostosis. aLOS was 3.8 days (95% CI: 3.8, 3.9) per visit, longer for syndromic conditions.There was a minor reduction in the average length of hospital stay for CS over the 22-year period potentially indicative of improved care. Population-level information on hospitalisations for rare craniofacial conditions can inform research, clinical, and surgical practice.

Epidemiology of Rare Craniofacial Anomalies: Retrospective Western Australian Population Data Linkage Study.

OBJECTIVE: To describe birth prevalence of rare craniofacial anomalies and associations with antenatal and perinatal factors. STUDY DESIGN: All live and stillbirths in Western Australia between 1980 and 2010 were identified from the Western Australian Birth Registrations and the Midwives Notification System (also provides information on antenatal and perinatal factors). Rare craniofacial anomalies (craniosynostosis, craniofacial microsomia, and others [Pierre Robin, Van der Woude, and Treacher Collins syndrome]) were ascertained from the Western Australian Register of Developmental Anomalies and linked to other data sources. Trends in prevalence, adjusted for sex and Indigenous status, were investigated by Poisson regression and presented as annual percent change (APC). Strengths of association of related factors were assessed using multivariable log-binomial regression adjusted for sex, Indigenous status, birth year, socioeconomic disadvantage, and remoteness and reported as risk ratios with 95% CIs. RESULTS: There was a temporal increase in prevalence of metopic synostosis (APC 5.59 [2.32-8.96]) and craniofacial microsomia (Goldenhar syndrome) (APC 4.43 [1.94-6.98]). Rare craniofacial anomalies were more likely among infants born preterm, as twins or greater-order multiples, with growth restriction, to older parents, to mothers undertaking fertility treatments, and with pre-existing medical conditions, specifically epilepsy, diabetes, or hypothyroidism. Prenatal identification of rare craniofacial anomalies was uncommon (0.6%). CONCLUSIONS: Our findings indicate a steady increase over time in prevalence of metopic synostosis and craniofacial microsomia (Goldenhar syndrome). Possible associations of fertility treatments and pre-existing maternal medical conditions with rare craniofacial anomalies require further investigation.

Further evidence for distinct traits associated with RBM10 missense variants.

A case of a missense RBM10 variant in an adult with mild to moderate intellectual disability.

Association between craniofacial anomalies, intellectual disability and autism spectrum disorder: Western Australian population-based study.

BACKGROUND: Accurate knowledge of the relationship between craniofacial anomalies (CFA), intellectual disability (ID) and autism spectrum disorder (ASD) is essential to improve services and outcomes. The aim is to describe the association between CFA, ID and ASD using linked population data. METHODS: All births (1983-2005; n = 566,225) including CFA births (comprising orofacial clefts, craniosynostosis, craniofacial microsomia and mandibulofacial dysostosis) surviving to 5 years were identified from the birth, death, birth defects and midwives population data sets. Linked data from these data sets were followed for a minimum of 5 years from birth until 2010 in the intellectual disability database to identify ID and ASD. These associations were examined using a modified Poisson regression. RESULTS: Prevalence of ID and ASD was higher among CFA (especially with additional anomalies) than those without [prevalence ratio 5.27, 95% CI 4.44, 6.25]. It was higher among CFA than those with other gastrointestinal and urogenital anomalies but lower than nervous system and chromosomal anomalies. Children with CFA and severe ID had a higher proportion of nervous system anomalies. CONCLUSIONS: Findings indicate increased ID and ASD among CFA but lower than nervous system and chromosomal anomalies. This population evidence can improve early identification of ID/ASD among CFA and support service planning. IMPACT: Our study found about one in ten children born with craniofacial anomalies (CFA) are later identified with intellectual disability (ID). Prevalence of ID among CFA was higher than those with other gastrointestinal, urogenital, and musculoskeletal birth defects but lower than those with the nervous system and chromosomal abnormalities. Most children with craniofacial anomalies have a mild-to-moderate intellectual disability with an unknown aetiology. On average, intellectual disability is identified 2 years later for children born with non-syndromic craniofacial anomalies than those with syndromic conditions. Our findings can improve the early identification of ID/ASD among CFA and support service planning.