Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort

PURPOSE

Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively.

METHODS

ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID.

RESULTS

The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis.

CONCLUSION

Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.

Gene selection for genomic newborn screening: Moving toward consensus?

PURPOSE

Gene selection for genomic newborn screening (gNBS) underpins the validity, acceptability, and ethical application of this technology. Existing gNBS gene lists are highly variable despite being based on shared principles of gene-disease validity, treatability, and age of onset. This study aimed to curate a gNBS gene list that builds upon existing efforts and provide a core consensus list of gene-disease pairs assessed by multiple expert groups worldwide.

METHODS

Our multidisciplinary expert team curated a gene list using an open platform and multiple existing curated resources. We included severe treatable disorders with age of disease onset <5 years with established gene-disease associations and reliable variant detection. We compared the final list with published lists from 5 other gNBS projects to determine consensus genes and to identify areas of discrepancy.

RESULTS

We reviewed 1279 genes and 604 met our inclusion criteria. Metabolic conditions comprised the largest group (25%), followed by immunodeficiencies (21%) and endocrine disorders (15%). We identified 55 consensus genes included by all 6 gNBS research projects. Common reasons for discrepancy included variable definitions of treatability and strength of gene-disease association.

CONCLUSION

We have identified a consensus gene list for gNBS that can be used as a basis for systematic harmonization efforts internationally.

Prospective cohort study of genomic newborn screening: BabyScreen+ pilot study protocol

INTRODUCTION

Newborn bloodspot screening (NBS) is a highly successful public health programme that uses biochemical and other assays to screen for severe but treatable childhood-onset conditions. Introducing genomic sequencing into NBS programmes increases the range of detectable conditions but raises practical and ethical issues. Evidence from prospectively ascertained cohorts is required to guide policy and future implementation. This study aims to develop, implement and evaluate a genomic NBS (gNBS) pilot programme.

METHODS AND ANALYSIS

The BabyScreen+ study will pilot gNBS in three phases. In the preimplementation phase, study materials, including education resources, decision support and data collection tools, will be designed. Focus groups and key informant interviews will also be undertaken to inform delivery of the study and future gNBS programmes. During the implementation phase, we will prospectively recruit birth parents in Victoria, Australia, to screen 1000 newborns for over 600 severe, treatable, childhood-onset conditions. Clinically accredited whole genome sequencing will be performed following standard NBS using the same sample. High chance results will be returned by genetic healthcare professionals, with follow-on genetic and other confirmatory testing and referral to specialist services as required. The postimplementation phase will evaluate the feasibility of gNBS as the primary aim, and assess ethical, implementation, psychosocial and health economic factors to inform future service delivery.

ETHICS AND DISSEMINATION

This project received ethics approval from the Royal Children's Hospital Melbourne Research Ethics Committee: HREC/91500/RCHM-2023, HREC/90929/RCHM-2022 and HREC/91392/RCHM-2022. Findings will be disseminated to policy-makers, and through peer-reviewed journals and conferences.

National increase in the community supply of take-home naloxone associated with a mass media campaign in Scotland: a segmented time series analysis

BACKGROUND

Take-home naloxone (THN) programmes have been associated with reductions in opioid-related mortality. In response to high rates of drug-related deaths in Scotland, the Scottish Government commissioned the 'How to save a life' (HTSAL) mass media campaign to: (1) increase awareness of drug-related deaths and how to respond to an overdose, and (2) increase the supply of THN. The aim of this study was to assess the effect of the campaign on the supply of THN.

METHODS

We used an interrupted time series design to assess the effect of the HTSAL mass media campaign on the national community supply of THN. The study time period was August 2020-December 2021. We modelled two key dates: the start of the campaign (week beginning (w/b) 30th of August 2021) and after the end of the main campaign (w/b 25th of October 2021).

RESULTS

The total number of THN kits distributed in the community in Scotland during the study period was 27,064. The mean number of THN kits distributed per week (relative to the pre-campaign period), increased by 126% during the campaign and 57% post-campaign. In segmented regression analyses, the pre-campaign trend in the number of THN kits supplied was increasing by an average of 1% each week (RR=1.01, 95% CI 1.01 to 1.01, p<0.001). Once the campaign started, a significant change in level was observed, and the number of kits increased by 75% (RR=1.75, 95% CI 1.29 to 2.40, p<0.001). The trend during the campaign was stable (i.e. not increasing or decreasing) but a significant change in level was observed when the campaign ended, and the number of THN kits supplied decreased by 32% (RR=0.68, 95% CI 0.46 to 0.98, p = 0.042). The trend during the post-campaign period was stable.

CONCLUSIONS

The HTSAL campaign had a short term, but large and significant impact, on the community supply of THN in Scotland. Mass media campaigns could be combined with other interventions and strategies to maintain the increased uptake of THN outside of campaign periods.

SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability

SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.

The diverse pleiotropic effects of spliceosomal protein PUF60: A case series of Verheij syndrome

Verheij syndrome (VRJS) is a rare craniofacial spliceosomopathy presenting with craniofacial dysmorphism, multiple congenital anomalies and variable neurodevelopmental delay. It is caused by single nucleotide variants (SNVs) in PUF60 or interstitial deletions of the 8q24.3 region. PUF60 encodes a splicing factor which forms part of the spliceosome. To date, 36 patients with a sole diagnosis of VRJS due to disease-causing PUF60 SNVs have been reported in peer-reviewed publications. Although the depth of their phenotyping has varied greatly, they exhibit marked phenotypic heterogeneity. We report 10 additional unrelated patients, including the first described patients of Khmer, Indian, and Vietnamese ethnicities, and the eldest patient to date, with 10 heterozygous PUF60 variants identified through exome sequencing, 8 previously unreported. All patients underwent deep phenotyping identifying variable dysmorphism, growth delay, neurodevelopmental delay, and multiple congenital anomalies, including several unique features. The eldest patient is the only reported individual with a germline variant and neither neurodevelopmental delay nor intellectual disability. In combining these detailed phenotypic data with that of previously reported patients (n = 46), we further refine the known frequencies of features associated with VRJS. These include neurodevelopmental delay/intellectual disability (98%), axial skeletal anomalies (74%), appendicular skeletal anomalies (73%), oral anomalies (68%), short stature (66%), cardiac anomalies (63%), brain malformations (48%), hearing loss (46%), microcephaly (41%), colobomata (38%), and other ocular anomalies (65%). This case series, incorporating three patients from previously unreported ethnic backgrounds, further delineates the broad pleiotropy and mutational spectrum of PUF60 pathogenic variants.

P-402 The association between embryo morphology and first trimester miscarriage after single blastocyst transfer

Study question

Can standard morphological assessment of blastocyst quality accurately predict first trimester miscarriage?

Summary answer

Decreasing trophectoderm and inner cell mass grade equally predicted first trimester miscarriage independently. After adjusting for confounders, poor embryo quality was not associated with miscarriage.

What is known already

Embryo quality determined by morphological assessment is a well-established predictor of successful implantation and live birth with in vitro fertilization treatment. Chromosomal abnormalities account for over half of first trimester miscarriages, and links between ploidy status and embryo morphology have been demonstrated. However, the association between blastocyst morphology and first trimester miscarriage is still poorly understood with consensus opinion yet to be established.

Study design, size, duration

This single centre retrospective cohort study included 2020 fresh and frozen single embryo transfers between October 2010 and October 2020. Blastocyst degree of expansion, inner cell mass (ICM) grade, and trophectoderm (TE) grade were compared for 354 pregnancies ending in first trimester miscarriage and 1666 pregnancies that surpassed 12 weeks of gestation. The association between blastocyst morphology and miscarriage was examined by logistic regression analysis.

Participants/materials, setting, methods

All single blastocyst transfers over a 10-year period resulting in first trimester miscarriage or pregnancy beyond 12 weeks of gestation were included in our analysis. Cycles involving donor oocytes, preimplantation genetic testing, resulting in biochemical pregnancy, or ectopic pregnancy were excluded. Differences between groups were analysed with chi-square and logistic regression analysis. Odds ratios (aOR) for miscarriage versus ongoing pregnancy were adjusted for maternal age, cycle type, blastocyst expansion, ICM grade, and TE grade.

Main results and the role of chance

Out of 2020 single embryo transfer cycles, a total of 354 resulted in first trimester miscarriage (17.5%). Independently, miscarriage rates increased with decreasing ICM grade (A to C; 14.6%, 18.9%, and 26.5%, p = 0.003) and TE grade (A to C; 14.6%, 17.7%, and 26.6%, p = 0.004). Univariate logistic regression showed higher risks of miscarriage with ICM grade C compared to ICM grade A (OR 2.241, 95%CI 1.292-3.886, p = 0.004), TE grade C compared to TE grade A (OR 2.116, 95%CI 1.360 – 3.292, p = 0.001), and expansion grades of 1 and 2 compared to expansion of 5 and 6 (OR 2.514, 95%CI 1.477 – 4.278, p = 0.001). After multivariable logistic regression adjusting for maternal age at embryo transfer, cycle type, and all morphological parameters (degree of expansion, ICM, and TE), only expansion grade of 1 and 2 showed a statistically significant association with first trimester miscarriage.

Limitations, reasons for caution

The main limitation of this study is the retrospective design of the analysis, and subjective nature of embryo morphological assessment. There may also be residual confounding by unknown or unmeasured confounders such as paternal age or maternal BMI.

Wider implications of the findings

Embryo selection for transfer should continue to be guided by standard morphological assessment. Decreasing grade of ICM and TE are both positively associated with an increased miscarriage risk, while poorly expanded blastocysts are most predictive of first trimester miscarriage. Patients undergoing embryo transfer should be adequately counselled about these risks.

Trial registration number

Not applicable

P-282 Blastocyst transfer in advanced maternal age: Single versus double embryo transfer

Study question

Is there a role for elective single blastocyst transfer (eSBT) in advanced maternal age?

Summary answer

Double blastocyst transfer (DBT) versus eSBT resulted in higher live birth rates except for those undergoing their first cycle.

What is known already

Women with advanced maternal age are generally considered poorer prognosis patients with lower live birth rates compared to their younger counterparts. This often results in a higher likelihood of double embryo transfer in this group. This is not without risk as multiple pregnancy is associated with significant maternal and neonatal morbidity especially with advancing maternal age. In older women with blastocysts available for transfer, it is unclear who should be recommended double versus elective single transfer. The concept of the “good-prognosis” older woman remains elusive.

Study design, size, duration

This was a retrospective observational study looking at 511 IVF/ICSI cycles between January 2010 and January 2020. Treatment cycle details and clinical outcomes were entered prospectively into a dedicated clinic database. Data was retrieved and analysed using SPSS V25.

Participants/materials, setting, methods

The study was conducted in a large London IVF centre. Data was collected on women aged 40 or above undergoing an IVF/ICSI cycle with eSBT (Group 1, n = 79) or DBT (Group 2, n = 430). Women with more than three previous IVF attempts were excluded. eSBT was defined as a single blastocyst transfer with at least one further blastocyst available for cryopreservation. Subgroup analysis was performed for those undergoing their first cycle.

Main results and the role of chance

Data from 511 cycles was analysed. The mean age was 40.6±1.2years. The live birth rate was 27%. Group 1 was marginally younger (40.2±0.6 v 40.8±1.2, p &lt; 0.005) and was more likely to be undergoing their first IVF cycle (84% v 68%, p = 0.003). Those in Group 1 had more eggs collected (13.6±7.3 v 11.3±5.5, p = 0.009), more zygotes (8.9±4.7 v 7.3±3.6) formed and more blastocysts frozen (3.4±2.6 v 1.1±1.7, p &lt; 0005). More women in Group 1 had a top quality blastocyst (expansion of &gt; 2 and inner cell mass and trophectoderm of AA, AB, BA or BB) transfer (91% v 71%, p &lt; 0.005).

After logistic regression controlling for maternal age, number of previous IVF cycles and blastocyst quality, Group 1 had a lower likelihood of livebirth (aOR 0.550, 95%CI 0.306-0.988) but with a significantly lower multiple pregnancy rate (0% v 24%, p = 0.024).

Importantly, for those undergoing their first IVF cycle (n = 359), there was no difference in live birth rate in the two groups (aOR 0.617, 95%CI 0.329-1.156) after controlling for age and blastocyst quality but Group 2 had a higher multiple pregnancy rate (24% v 0%, p = 0.020).

Limitations, reasons for caution

This study is limited by its retrospective nature putting it at risk of information bias as it relied on accurate documentation of studied variables into the patient database. The study did not examine cumulative birth rates of fresh and subsequent frozen cycles in Group 1.

Wider implications of the findings

Women should have individualised counseling about number of blastocysts to transfer taking into account their circumstances. Those undergoing their first IVF attempt and with a blastocyst available for transfer, should be counselled that DBT is associated with a higher multiple pregnancy rate with no increase in overall live birth rate.

Trial registration number

Not Applicable

Is faster better? An economic evaluation of rapid and ultra-rapid genomic testing in critically ill infants and children

PURPOSE

To evaluate whether the additional cost of providing increasingly faster genomic results in pediatric critical care is outweighed by reductions in health care costs and increases in personal utility.

METHODS

Hospital costs and medical files from a cohort of 40 children were analyzed. The health economic impact of rapid and ultra-rapid genomic testing, with and without early initiation, relative to standard genomic testing was evaluated.

RESULTS

Shortening the time to results led to substantial economic and personal benefits. Early initiation of ultra-rapid genomic testing was the most cost-beneficial strategy, leading to a cost saving of AU$26,600 per child tested relative to standard genomic testing and a welfare gain of AU$12,000 per child tested. Implementation of early ultra-rapid testing of critically ill children is expected to lead to an annual cost saving of AU$7.3 million for the Australian health system and an aggregate welfare gain of AU$3.3 million, corresponding to a total net benefit of AU$10.6 million.

CONCLUSION

Early initiation of ultra-rapid genomic testing can offer substantial economic and personal benefits. Future implementation of rapid genomic testing programs should focus not only on optimizing the laboratory workflow to achieve a fast turnaround time but also on changing clinical practice to expedite test initiation.

Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder

A proper interaction between muscle-derived collagen XXV and its motor neuron-derived receptors protein tyrosine phosphatases σ and δ (PTP σ/δ) is indispensable for intramuscular motor innervation. Despite this, thus far, pathogenic recessive variants in the COL25A1 gene had only been detected in a few patients with isolated ocular congenital cranial dysinnervation disorders. Here we describe five patients from three unrelated families with recessive missense and splice site COL25A1 variants presenting with a recognizable phenotype characterized by arthrogryposis multiplex congenita with or without an ocular congenital cranial dysinnervation disorder phenotype. The clinical features of the older patients remained stable over time, without central nervous system involvement. This study extends the phenotypic and genotypic spectrum of COL25A1 related conditions, and further adds to our knowledge of the complex process of intramuscular motor innervation. Our observations indicate a role for collagen XXV in regulating the appropriate innervation not only of extraocular muscles, but also of bulbar, axial, and limb muscles in the human.

Human papillomavirus (HPV) vaccination across a cascade of knowledge, willingness, and uptake among gay, bisexual, and other men who have sex with men in Canada's three largest cities

BACKGROUND

Some Canadian jurisdictions offer publicly funded HPV vaccine to gay, bisexual, and other men who have sex with men (GBM) aged ≤26 years. We characterized factors associated with being in different stages of HPV vaccination.

METHODS

Engage is a sexual health study of GBM in the three largest Canadian cities recruited via respondent driven sampling (RDS). We categorized participants as: (1) unaware of HPV vaccine, (2) undecided/unwilling to get vaccinated, (3) willing to get vaccinated, (4) vaccinated with one or more doses. Our RDS-II weighted analyses used multinomial logistic regression to identify factors associated with being in earlier stages of the cascade compared to Stage 4.

RESULTS

Across the cities, 26-40%, 7-14%, 33-39%, and 13-28% were in Stages 1 to 4, respectively. Compared to Stage 4, being in earlier stages of the cascade was associated with bisexual-identification (Stage 1: adjusted odds ratio[aOR] = 2.84, 95% confidence interval[CI] = 1.06-7.62; Stage 2: aOR = 3.09, 95%CI = 1.19-8.05), having immigrated to Canada (Stage 1: aOR = 1.79, 95%CI 1.07-2.99), preference to keep same-sex romantic relationships private (Stage 1: aOR = 1.25, 95% CI = 1.05-1.48; Stage 2: aOR = 1.24, 95%CI = 1.05-1.46), not receiving sexual health information (Stage 1: aOR = 0.31, 95% CI = 0.13-0.71; Stage 2: aOR = 0.27, 95%CI = 0.12-0.64), not accessing a health-care provider (Stage 2: aOR = 0.36, 95%CI = 0.15-0.83), and no past hepatitis A/B vaccination (Stage 1: aOR = 0.16, 95% CI = 0.09-0.30; Stage 2: aOR = 0.18, 95%CI = 0.09-0.35; Stage 3: aOR = 0.38, 95%CI = 0.21-0.61).

DISCUSSION

Interventions are needed to reduce social and financial barriers, increase sexual health knowledge, and improve GBM-competent health-care access to increase vaccine uptake among GBM.

Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants

PURPOSE

Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy).

METHODS

A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases.

RESULTS

Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing.

CONCLUSION

RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data.

Lessons learnt from multifaceted diagnostic approaches to the first 150 families in Victoria's Undiagnosed Diseases Program

BACKGROUND

Clinical exome sequencing typically achieves diagnostic yields of 30%-57.5% in individuals with monogenic rare diseases. Undiagnosed diseases programmes implement strategies to improve diagnostic outcomes for these individuals.

AIM

We share the lessons learnt from the first 3 years of the Undiagnosed Diseases Program-Victoria, an Australian programme embedded within a clinical genetics service in the state of Victoria with a focus on paediatric rare diseases.

METHODS

We enrolled families who remained without a diagnosis after clinical genomic (panel, exome or genome) sequencing between 2016 and 2018. We used family-based exome sequencing (family ES), family-based genome sequencing (family GS), RNA sequencing (RNA-seq) and high-resolution chromosomal microarray (CMA) with research-based analysis.

RESULTS

In 150 families, we achieved a diagnosis or strong candidate in 64 (42.7%) (37 in known genes with a consistent phenotype, 3 in known genes with a novel phenotype and 24 in novel disease genes). Fifty-four diagnoses or strong candidates were made by family ES, six by family GS with RNA-seq, two by high-resolution CMA and two by data reanalysis.

CONCLUSION

We share our lessons learnt from the programme. Flexible implementation of multiple strategies allowed for scalability and response to the availability of new technologies. Broad implementation of family ES with research-based analysis showed promising yields post a negative clinical singleton ES. RNA-seq offered multiple benefits in family ES-negative populations. International data sharing strategies were critical in facilitating collaborations to establish novel disease-gene associations. Finally, the integrated approach of a multiskilled, multidisciplinary team was fundamental to having diverse perspectives and strategic decision-making.

Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution

Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.

Recurrent de novo missense variants in GNB2 can cause syndromic intellectual disability

PURPOSE

Binding proteins (G-proteins) mediate signalling pathways involved in diverse cellular functions and comprise Gα and Gβγ units. Human diseases have been reported for all five Gβ proteins. A de novo missense variant in GNB2 was recently reported in one individual with developmental delay/intellectual disability (DD/ID) and dysmorphism. We aim to confirm GNB2 as a neurodevelopmental disease gene, and elucidate the GNB2-associated neurodevelopmental phenotype in a patient cohort.

METHODS

We discovered a GNB2 variant in the index case via exome sequencing and sought individuals with GNB2 variants via international data-sharing initiatives. In silico modelling of the variants was assessed, along with multiple lines of evidence in keeping with American College of Medical Genetics and Genomics guidelines for interpretation of sequence variants.

RESULTS

We identified 12 unrelated individuals with five de novo missense variants in GNB2, four of which are recurrent: p.(Ala73Thr), p.(Gly77Arg), p.(Lys89Glu) and p.(Lys89Thr). All individuals have DD/ID with variable dysmorphism and extraneurologic features. The variants are located at the universally conserved shared interface with the Gα subunit, which modelling suggests weaken this interaction.

CONCLUSION

Missense variants in GNB2 cause a congenital neurodevelopmental disorder with variable syndromic features, broadening the spectrum of multisystem phenotypes associated with variants in genes encoding G-proteins.

Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism

ANKRD17 is an ankyrin repeat-containing protein thought to play a role in cell cycle progression, whose ortholog in Drosophila functions in the Hippo pathway as a co-factor of Yorkie. Here, we delineate a neurodevelopmental disorder caused by de novo heterozygous ANKRD17 variants. The mutational spectrum of this cohort of 34 individuals from 32 families is highly suggestive of haploinsufficiency as the underlying mechanism of disease, with 21 truncating or essential splice site variants, 9 missense variants, 1 in-frame insertion-deletion, and 1 microdeletion (1.16 Mb). Consequently, our data indicate that loss of ANKRD17 is likely the main cause of phenotypes previously associated with large multi-gene chromosomal aberrations of the 4q13.3 region. Protein modeling suggests that most of the missense variants disrupt the stability of the ankyrin repeats through alteration of core structural residues. The major phenotypic characteristic of our cohort is a variable degree of developmental delay/intellectual disability, particularly affecting speech, while additional features include growth failure, feeding difficulties, non-specific MRI abnormalities, epilepsy and/or abnormal EEG, predisposition to recurrent infections (mostly bacterial), ophthalmological abnormalities, gait/balance disturbance, and joint hypermobility. Moreover, many individuals shared similar dysmorphic facial features. Analysis of single-cell RNA-seq data from the developing human telencephalon indicated ANKRD17 expression at multiple stages of neurogenesis, adding further evidence to the assertion that damaging ANKRD17 variants cause a neurodevelopmental disorder.

Human papillomavirus (HPV) vaccine uptake among a community-recruited sample of gay, bisexual, and other men who have sex with men in the three largest cities in Canada from 2017 to 2019

INTRODUCTION

In 2015/2016, Canada's largest provinces implemented publicly-funded human papillomavirus (HPV) vaccination programs for gay, bisexual, and other men who have sex with men (GBM) ≤ 26 years old. We sought to describe HPV vaccine uptake among GBM and determine barriers and facilitators to vaccine initiation with a focus on healthcare access and utilization.

METHODS

Engage is a cohort study among GBM aged 16 + years in three Canadian cities recruited from 2017 to 2019 via respondent driven sampling (RDS). Men completed a comprehensive questionnaire at baseline. By publicly-funded vaccine eligibility (≤26 years old = eligible for vaccination, ≥27 years old = ineligible), we described HPV vaccine uptake (initiation = 1 + dose, completion = 3 doses) and explored factors associated with vaccine initiation using Poisson regression. All analyses were weighted with the RDS-II Volz-Heckathorn estimator.

RESULTS

Across the three cities, 26-35% and 14-21% of men ≤ 26 years and 7-26% and 2-9% of men ≥ 27 years initiated and completed HPV vaccination, respectively. Vaccine initiation was significantly associated with STI/HIV testing or visiting a HIV care specialist in the past six months (≤26: prevalence ratio[PR] = 2.15, 95% confidence interval[CI] 1.06-4.36; ≥27: PR = 2.73, 95%CI 1.14-6.51) and past hepatitis A or B vaccination (≤26: PR = 2.88, 95%CI 1.64-5.05; ≥27: PR = 2.03, 95%CI 1.07-3.86). Among men ≥ 27 years old, vaccine initiation was also positively associated with accessing PrEP, living in Vancouver or Toronto, but negatively associated with identifying as Latin American and increasing age. Vaccine initiation was twice as likely among men ≥ 27 years with private insurance versus no insurance.

CONCLUSIONS

Sixty-five to 74% of men eligible for publicly-funded vaccine across the three cities remained unvaccinated against HPV by 2019. High vaccine cost may partly explain even lower uptake among men ≥ 27 years old. Men seeking sexual health care were more likely to initiate vaccination; bundling vaccination with these services may help improve HPV vaccine uptake.

Evidence for 28 genetic disorders discovered by combining healthcare and research data

De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.

Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review

Background

Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases.

Methods

We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them.

Results

Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months.

Conclusion

Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.

A cost-effectiveness analysis of genomic sequencing in a prospective versus historical cohort of complex pediatric patients

PURPOSE

Cost-effectiveness evaluations of first-line genomic sequencing (GS) in the diagnosis of children with genetic conditions are limited by the lack of well-defined comparative cohorts. We sought to evaluate the cost-effectiveness of early GS in pediatric patients with complex monogenic conditions compared with a matched historical cohort.

METHODS

Data, including investigation costs, were collected in a prospective cohort of 92 pediatric patients undergoing singleton GS over an 18-month period (2016-2017) with two of the following: a condition with high mortality, multisystem disease involving three or more organs, or severe limitation of daily function. Comparative data were collected in a matched historical cohort who underwent traditional investigations in the years 2012-2013.

RESULTS

GS yielded a diagnosis in 42% while traditional investigations yielded a diagnosis in 23% (p = 0.003). A change in management was experienced by 74% of patients diagnosed following GS, compared with 32% diagnosed following traditional investigations. Singleton GS at a cost of AU$3100 resulted in a mean saving per person of AU$3602 (95% confidence interval [CI] AU$2520-4685). Cost savings occurred across all investigation subtypes and were only minimally offset by clinical management costs.

CONCLUSION

GS in complex pediatric patients saves significant costs and doubles the diagnostic yield of traditional approaches.

Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System

IMPORTANCE

Widespread adoption of rapid genomic testing in pediatric critical care requires robust clinical and laboratory pathways that provide equitable and consistent service across health care systems.

OBJECTIVE

To prospectively evaluate the performance of a multicenter network for ultra-rapid genomic diagnosis in a public health care system.

DESIGN, SETTING, AND PARTICIPANTS

Descriptive feasibility study of critically ill pediatric patients with suspected monogenic conditions treated at 12 Australian hospitals between March 2018 and February 2019, with data collected to May 2019. A formal implementation strategy emphasizing communication and feedback, standardized processes, coordination, distributed leadership, and collective learning was used to facilitate adoption.

EXPOSURES

Ultra-rapid exome sequencing.

MAIN OUTCOMES AND MEASURES

The primary outcome was time from sample receipt to ultra-rapid exome sequencing report. The secondary outcomes were the molecular diagnostic yield, the change in clinical management after the ultra-rapid exome sequencing report, the time from hospital admission to the laboratory report, and the proportion of laboratory reports returned prior to death or hospital discharge.

RESULTS

The study population included 108 patients with a median age of 28 days (range, 0 days to 17 years); 34% were female; and 57% were from neonatal intensive care units, 33% were from pediatric intensive care units, and 9% were from other hospital wards. The mean time from sample receipt to ultra-rapid exome sequencing report was 3.3 days (95% CI, 3.2-3.5 days) and the median time was 3 days (range, 2-7 days). The mean time from hospital admission to ultra-rapid exome sequencing report was 17.5 days (95% CI, 14.6-21.1 days) and 93 reports (86%) were issued prior to death or hospital discharge. A molecular diagnosis was established in 55 patients (51%). Eleven diagnoses (20%) resulted from using the following approaches to augment standard exome sequencing analysis: mitochondrial genome sequencing analysis, exome sequencing-based copy number analysis, use of international databases to identify novel gene-disease associations, and additional phenotyping and RNA analysis. In 42 of 55 patients (76%) with a molecular diagnosis and 6 of 53 patients (11%) without a molecular diagnosis, the ultra-rapid exome sequencing result was considered as having influenced clinical management. Targeted treatments were initiated in 12 patients (11%), treatment was redirected toward palliative care in 14 patients (13%), and surveillance for specific complications was initiated in 19 patients (18%).

CONCLUSIONS AND RELEVANCE

This study suggests feasibility of ultra-rapid genomic testing in critically ill pediatric patients with suspected monogenic conditions in the Australian public health care system. However, further research is needed to understand the clinical value of such testing, and the generalizability of the findings to other health care settings.

Congenital infections in Hong Kong: an overview of TORCH

Congenital infections refer to a group of perinatal infections that may have similar clinical presentations, including rash and ocular findings. TORCH is the acronym that covers these infections (toxoplasmosis, other [syphilis], rubella, cytomegalovirus, herpes simplex virus). There are, however, other important causes of intrauterine/perinatal infections, including enteroviruses, varicella zoster virus, Zika virus, and parvovirus B19. Intrauterine and perinatal infections are significant causes of fetal and neonatal mortality and important contributors to childhood morbidity. A high index of suspicion for congenital infections and awareness of the prominent features of the most common congenital infections can help to facilitate early diagnosis, tailor appropriate diagnostic evaluation, and if appropriate, initiate early treatments. In the absence of maternal laboratory results diagnostic of intrauterine infections, congenital infections should be suspected in newborns with certain clinical features or combinations of clinical features, including hydrops fetalis, microcephaly, seizures, cataract, hearing loss, congenital heart disease, hepatosplenomegaly, jaundice, or rash. Primary prevention of maternal infections during pregnancy is the cornerstone of prevention of congenital infection. Available resources should focus on the promotion of public health.

Canada's Prosthetic Coverage: a Review of Provincial Prosthetic Policy

The Canadian healthcare system serves as an example of equity and federal service to citizens across the world. However, it is not without its challenges. Prosthetic coverage across Canada is highly variable and largely unable to provide equal coverage for Canadian persons living with amputation. Many persons with limb loss are forced to rely upon personal resources, fundraising, or the charity of non-governmental organizations in order to meet this basic healthcare need. This disparity in the Canadian healthcare system is unusual and largely undescribed in the literature. We thus explore the nature of Canadian healthcare prosthetic coverage across Canada, investigating the variability in coverage, presence of prosthetic coverage policies, clarity of policy, eligibility criteria, and interval of prosthetic replacement. Our findings highlight potential areas for improvement within current Canadian healthcare policy.

Febrile neutropenia and its associated hospitalization in breast cancer patients on docetaxel-containing regimen: A retrospective cohort study on duration of prophylactic GCSF administration

PURPOSE

To compare febrile neutropenia (FN) incidence and hospitalization among breast cancer patients on docetaxel with no granulocyte colony-stimulating factors (GCSF) primary prophylaxis (PP), 4/5-day PP, or 7-day PP.

METHODS

We identified 3916 breast cancer patients using docetaxel-cyclophosphamide (TC), doxorubicin-cyclophosphamide then docetaxel (AC-T), fluorouracil-epirubicin-cyclophosphamide then docetaxel (FEC-T), docetaxel-carboplatin-trastuzumab (TJH), or docetaxel-doxorubicin-cyclophosphamide (TAC) from a hospital pharmacy dispensing database in Hong Kong between 2014 and 2016. Patients were offered GCSF within 5 days since administering docetaxel. Outcomes included FN incidence, time to first hospitalization, hospitalization rate, and duration.

RESULTS

In TC regimen, FN incidence (with odds ratio, OR) of patients with no PP, 4/5-day PP, and 7-day PP was 21.69%, 7.95% (OR 0.31, p < 0.001), and 5.33% (OR 0.20, p < 0.001), respectively. In TJH regimen, FN incidence of patients with no PP, 4/5-day PP, and 7-day PP was 38.26%, 8.33% (OR 0.15, p < 0.001), and 8.57% (OR 0.15, p < 0.001), respectively. FN incidence of patients on AC-T regimen with no PP and 4/5-day PP was 20.93% and 6.84%, respectively (OR 0.28, p = 0.005); with FEC-T regimen, the incidence was 9.91% and 4.77%, respectively (OR 0.46, p = 0.035). Only 3.27% FN cases were not hospitalized. Mean (±standard deviation, SD) time to first hospitalization was 8.21 ± 2.44 days. Mean (±SD) duration of hospitalization for patients with no PP, 4/5-day PP, and 7-day PP was 4.66 ± 2.60, 4.37 ± 2.85, and 5.12 ± 2.97 days, respectively.

CONCLUSION

GCSF prophylaxis in breast cancer patients on docetaxel could reduce FN incidence and hospitalization. 4/5-day PP demonstrated similar efficacy to 7-day PP with superior saving benefits on healthcare expenditure.

Hyperinsulinaemic hypoglycaemia: A rare association of vanishing white matter disease

We report two unrelated patients with infantile onset leukoencephalopathy with vanishing white matter (VWM) and hyperinsulinaemic hypoglycaemia. To our knowledge, this association has not been described previously. Both patients had compound heterozygous pathogenic variants in EIF2B4 detected on exome sequencing and absence of other variants which might explain the hyperinsulinism. Hypoglycaemia became apparent at 6 and 8 months, respectively, although in one patient, transient neonatal hypoglycaemia was also documented. One patient responded to diazoxide and the other was managed with continuous nasogastric feeding. We hypothesise that the pathophysiology of hyperinsulinism in VWM may involve dysregulation of transcription of genes related to insulin secretion.

Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions

IMPORTANCE

Optimal use of whole-exome sequencing (WES) in the pediatric setting requires an understanding of who should be considered for testing and when it should be performed to maximize clinical utility and cost-effectiveness.

OBJECTIVES

To investigate the impact of WES in sequencing-naive children suspected of having a monogenic disorder and evaluate its cost-effectiveness if WES had been available at different time points in their diagnostic trajectory.

DESIGN, SETTING, AND PARTICIPANTS

This prospective study was part of the Melbourne Genomics Health Alliance demonstration project. At the ambulatory outpatient clinics of the Victorian Clinical Genetics Services at the Royal Children's Hospital, Melbourne, Australia, children older than 2 years suspected of having a monogenic disorder were prospectively recruited from May 1 through November 30, 2015, by clinical geneticists after referral from general and subspecialist pediatricians. All children had nondiagnostic microarrays and no prior single-gene or panel sequencing.

EXPOSURES

All children underwent singleton WES with targeted phenotype-driven analysis.

MAIN OUTCOMES AND MEASURES

The study examined the clinical utility of a molecular diagnosis and the cost-effectiveness of alternative diagnostic trajectories, depending on timing of WES.

RESULTS

Of 61 children originally assessed, 44 (21 [48%] male and 23 [52%] female) aged 2 to 18 years (mean age at initial presentation, 28 months; range, 0-121 months) were recruited, and a diagnosis was achieved in 23 (52%) by singleton WES. The diagnoses were unexpected in 8 of 23 (35%), and clinical management was altered in 6 of 23 (26%). The mean duration of the diagnostic odyssey was 6 years, with each child having a mean of 19 tests and 4 clinical genetics and 4 nongenetics specialist consultations, and 26 (59%) underwent a procedure while under general anesthetic for diagnostic purposes. Economic analyses of the diagnostic trajectory identified that WES performed at initial tertiary presentation resulted in an incremental cost savings of A$9020 (US$6838) per additional diagnosis (95% CI, A$4304-A$15 404 [US$3263-US$11 678]) compared with the standard diagnostic pathway. Even if WES were performed at the first genetics appointment, there would be an incremental cost savings of A$5461 (US$4140) (95% CI, A$1433-A$10 557 [US$1086- US$8004]) per additional diagnosis compared with the standard diagnostic pathway.

CONCLUSIONS AND RELEVANCE

Singleton WES in children with suspected monogenic conditions has high diagnostic yield, and cost-effectiveness is maximized by early application in the diagnostic pathway. Pediatricians should consider early referral of children with undiagnosed syndromes to clinical geneticists.

Development of the Sports Organization Concussion Risk Assessment Tool (SOCRAT)

OBJECTIVE

In this paper, we describe the development of a novel tool-the Sports Organization Concussion Risk Assessment Tool (SOCRAT)-to assist sport organizations in assessing the overall risk of concussion at a team level by identifying key risk factors.

METHODS

We first conducted a literature review to identify risk factors of concussion using ice hockey as a model. We then developed an algorithm by combining the severity and the probability of occurrence of concussions of the identified risk factors by adapting a risk assessment tool commonly used in engineering applications.

RESULTS

The following risk factors for ice hockey were identified: age, history of previous concussions, previous body checking experience, allowance of body checking, type of helmet worn and the game or practice environment. These risk factors were incorporated into the algorithm, resulting in an individual risk priority number (RPN) for each risk factor and an overall RPN that provides an estimate of the risk in the given circumstances.

CONCLUSION

The SOCRAT can be used to analyse how different risk factors contribute to the overall risk of concussion. The tool may be tailored to organizations to provide: (1) an RPN for each risk factor and (2) an overall RPN that takes into account all the risk factors. Further work is needed to validate the tool based on real data.

Ebola virus disease: An update on current prevention and management strategies

Ebola virus disease (EVD) is characterised by systemic viral replication, immuno-suppression, abnormal inflammatory responses, large volume fluid and electrolyte losses, and high mortality in under-resourced settings. There are various therapeutic strategies targeting EVD including vaccines utilizing different antigen delivery methods, antibody-based therapies and antiviral drugs. These therapies remain experimental, but received attention following their use particularly in cases treated outside West Africa during the 2014-15 outbreak, in which 20 (80%) out of 25 patients survived. Emerging data from current trials look promising and are undergoing further study, however optimised supportive care remains the key to reducing mortality from EVD.

The role of computerised tomography in predicting visual outcome in ocular trauma patients

PURPOSE

Ocular blast injuries in the military setting are particularly associated with significant maxillofacial trauma and/or brain injury. The opportunity to perform a comprehensive ophthalmic evaluation is frequently limited in the acute multiple trauma scenario. We aim to describe the relationship between the clinical effects of acute ocular and orbital blast trauma with the findings on computerised tomography (CT).

METHODS

This was a retrospective consecutive case series of all soldiers with facial and/or suspected ocular injuries. A total of 80 eyes that had suffered blast injuries of varying severity were studied. Assessment of orbital and ocular CT images were performed by military consultant radiologists. A comparison was made with actual clinical findings. Statistical analysis was performed using Fisher's exact test.

RESULTS

No pathological findings were described in 37 of the 80 eyes imaged by orbital and ocular CT scans. Clinically, these eyes and orbits were all found to be intact, or had minor trauma. All foreign bodies and penetrating eye injuries were successfully diagnosed by CT. Absence of an orbital fracture did not rule out a globe injury. However, a corneal or scleral defect was less likely when an orbital fracture was absent.

CONCLUSION

The eye is a delicate structure prone to injury that requires urgent repair if breached. It is difficult to assess thoroughly in the unconscious or distressed patient. In this context, CT imaging is invaluable to be able to make a relatively confident prediction of clinical findings and decide upon the necessity for acute ophthalmic surgical intervention.