Comparison of the ABC and ACMG systems for variant classification.

The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.

Mapping Two Decades of Paediatric Down Syndrome Research Literature.

Background: While research has led to significant advancements in the health and life expectancy of children with Down Syndrome (DS), there remains a significant burden of disease and health inequity. Further research, focused on areas of greatest need, is imperative to address this. An understanding of what research has been undertaken, and any existing gaps, helps to guide future academic efforts. Methods: We utilised an epistemological approach to summarise two decades of paediatric DS literature. Publications were categorised according to the country of origin, methodology, primary health themes and subcategory research themes. Results: Across 5,800 paediatric DS publications we demonstrate a general increase in the number of publications in this field between 2000 and 2014, with a trending decline thereafter. The majority of publications were affiliated with Institutions based in Western countries. The majority of studies utilised a cross-sectional methodology (33.3%), while relatively few were interventional (5.6%), qualitative (2.7%) or mixed-method studies (1.6%). Most publications focused on development & cognition (13.1%), neurology (9.9%) and oncology (9.8%), with fewer focusing on genitourinary health (0.9%), growth (0.9%), mortality (0.9%) and child protection (0.2%). Conclusion: These findings highlight areas of relative paucity within the paediatric DS literature which may warrant increased academic attention.

A Formative Study of the Implementation of Whole Genome Sequencing in Northern Ireland.

Background: The UK 100,000 Genomes Project was a transformational research project which facilitated whole genome sequencing (WGS) diagnostics for rare diseases. We evaluated experiences of introducing WGS in Northern Ireland, providing recommendations for future projects. Methods: This formative evaluation included (1) an appraisal of the logistics of implementing and delivering WGS, (2) a survey of participant self-reported views and experiences, (3) semi-structured interviews with healthcare staff as key informants who were involved in the delivery of WGS and (4) a workshop discussion about interprofessional collaboration with respect to molecular diagnostics. Results: We engaged with >400 participants, with detailed reflections obtained from 74 participants including patients, caregivers, key National Health Service (NHS) informants, and researchers (patient survey n = 42; semi-structured interviews n = 19; attendees of the discussion workshop n = 13). Overarching themes included the need to improve rare disease awareness, education, and support services, as well as interprofessional collaboration being central to an effective, mainstreamed molecular diagnostic service. Conclusions: Recommendations for streamlining precision medicine for patients with rare diseases include administrative improvements (e.g., streamlining of the consent process), educational improvements (e.g., rare disease training provided from undergraduate to postgraduate education alongside genomics training for non-genetic specialists) and analytical improvements (e.g., multidisciplinary collaboration and improved computational infrastructure).

Variants in GNAI1 cause a syndrome associated with variable features including developmental delay, seizures, and hypotonia.

PURPOSE: Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene. METHODS: Through large cohort trio-based exome sequencing and international data-sharing, we identified 24 unrelated individuals with NDD phenotypes and a variant in GNAI1, which encodes the inhibitory Gαi1 subunit of heterotrimeric G-proteins. We collected detailed genotype and phenotype information for each affected individual. RESULTS: We identified 16 unique variants in GNAI1 in 24 affected individuals; 23 occurred de novo and 1 was inherited from a mosaic parent. Most affected individuals have a severe neurodevelopmental disorder. Core features include global developmental delay, intellectual disability, hypotonia, and epilepsy. CONCLUSION: This collaboration establishes GNAI1 variants as a cause of NDDs. GNAI1-related NDD is most often characterized by severe to profound delays, hypotonia, epilepsy that ranges from self-limiting to intractable, behavior problems, and variable mild dysmorphic features.

Heterozygous lamin B1 and lamin B2 variants cause primary microcephaly and define a novel laminopathy.

PURPOSE: Lamins are the major component of nuclear lamina, maintaining structural integrity of the nucleus. Lamin A/C variants are well established to cause a spectrum of disorders ranging from myopathies to progeria, termed laminopathies. Phenotypes resulting from variants in LMNB1 and LMNB2 have been much less clearly defined. METHODS: We investigated exome and genome sequencing from the Deciphering Developmental Disorders Study and the 100,000 Genomes Project to identify novel microcephaly genes. RESULTS: Starting from a cohort of patients with extreme microcephaly, 13 individuals with heterozygous variants in the two human B-type lamins were identified. Recurrent variants were established to be de novo in nine cases and shown to affect highly conserved residues within the lamin ɑ-helical rod domain, likely disrupting interactions required for higher-order assembly of lamin filaments. CONCLUSION: We identify dominant pathogenic variants in LMNB1 and LMNB2 as a genetic cause of primary microcephaly, implicating a major structural component of the nuclear envelope in its etiology and defining a new form of laminopathy. The distinct nature of this lamin B-associated phenotype highlights the strikingly different developmental requirements for lamin paralogs and suggests a novel mechanism for primary microcephaly warranting future investigation.

Presentation and Investigation of Pediatric Bone and Joint Infections in the Pediatric Emergency Department.

OBJECTIVE: The objective of this study was to evaluate the presenting features of bone and joint infections with a view to identify distinguishing trends that will be useful for pediatric emergency departments. METHODS: We performed a retrospective review of patient records over a 12-year period in the pediatric emergency department of a large regional pediatric teaching center serving a diverse population. RESULTS: There were 88 cases of osteoarticular infections during the study period. Pain, fever, and impaired function were commonly reported, but overall, there was inconsistency in the presenting features. Inflammatory makers were sensitive tools, particularly in combination. When C-reactive protein, total white cell count, and erythrocyte sedimentation rate were all abnormal, 98% of bone and joint infections were identified.Causative organisms were identified in only 38% of cases, mostly from cultures of synovial fluid and bone. Streptococcal organisms were significantly more likely to be isolated in children under 5 years than in children over 5 years (P = <0.014). Staphylococcal organisms were significantly more likely to be isolated in children over 5 years than in children under 5 years (P = <0.001). Identification of virulent organisms such as Panton-Valentine leukocidin Staphylococcus aureus and methicillin-resistant S. aureus in our study should prompt review of diagnostic techniques and antibiotic choices. CONCLUSIONS: Overall, children under 5 years were significantly more likely to be diagnosed with septic arthritis than osteomyelitis (P = 0. 006). Children over 12 years were significantly more likely to be diagnosed with osteomyelitis than septic arthritis (P = 0. 019). These trends are useful to consider at presentation and in cases of diagnostic uncertainty.

Increased household financial strain, the Great Recession and child health-findings from the UK Millennium Cohort Study.

BACKGROUND: There is a growing body of evidence associating financial strain (FS) with poor health but most of this research has been cross-sectional and adult-focused. During the 'Great Recession' many UK households experienced increased FS. The primary aim of this study was to determine the impact of increased FS on child health. METHODS: We analysed the Millennium Cohort Study, a longitudinal study of children born in the UK between 2000 and 2002. Surveys at 7 years (T1, 2008) and 11 years (T2, 2012) spanned the 'Great Recession'. Three measures of increased FS were defined; 'became income poor' (self-reported household income dropped below the 'poverty line' between T1 and T2); 'developed difficulty managing' (parental report of being 'financially comfortable' at T1 and finding it 'difficult to manage' at T2); 'felt worse off' (parental report of feeling financially 'worse off' at T2 compared with T1). Poisson regression was used to estimate risk ratios (RR), adjusted risk ratios (aRR) and 95% CIs for six child health outcomes: measured overweight/obesity, problematic behaviour as scored by parents and teachers, and parental reports of fair/poor general health, long-standing illness and bedwetting at T2 (N=13 112). In subanalyses we limited our sample to those who were above the poverty line at T2. RESULTS: Compared with those who were not financially strained at both time points, children in households which experienced increased FS were at an increased risk of all unhealthy outcomes examined. In most cases, these increased risks persisted after adjustment for confounding and when limiting the sample to those above the poverty line. CONCLUSIONS: FS is associated with a range of new or continued poor child health outcomes. During times of widespread economic hardship, such as the 'Great Recession', measures should be taken to buffer children and their families from the impact of FS, and these should not be limited to those who are income poor.

Financial Strain, Parental Smoking, and the Great Recession: An Analysis of the UK Millennium Cohort Study.

INTRODUCTION: During the recent "Great Recession," many families in the United Kingdom experienced increased financial strain (FS). The aim of this study was to determine if increases in FS, occurring over the period of the "Great Recession," were associated with increased risks of persistent and relapsed tobacco use among parents. METHODS: We analyzed the Millennium Cohort Study, a longitudinal study of 18819 children born in the United Kingdom between 2000 and 2002. Surveys at 7 (T1, 2008) and 11 years (T2, 2012) spanned the "Great Recession." Three measures of increased FS were defined; "became income poor" (self-reported household income dropped below the "poverty line" between T1 and T2); "developed difficulty managing" (parental report of being "financially comfortable" at T1 and finding it "difficult to manage" at T2); "felt worse off" (parental report of feeling financially "worse off" at T2, compared to T1). Poisson regression was used to estimate risk ratios (RR), adjusted RRs (aRR), and 95% confidence intervals for three outcomes: "persistent tobacco use," "new reported tobacco use," and "relapsed tobacco use." RESULTS: Parents in households which "became income poor" over the period of the "Great Recession" were significantly more likely to report "persistent tobacco use" (aRR = 2.17 [1.83-2.57]) or "new reported tobacco use" (aRR = 1.72 [1.04-2.83]). Ninety-five percent of "new reported tobacco users" had evidence of prior tobacco use suggesting the majority were "relapsed tobacco users." Similar patterns were seen for those who "developed difficulty managing" and "felt worse off." CONCLUSIONS: Increased tobacco use among financially strained families has the potential to widen inequalities and undermine the public health policies that have had positive impacts on tobacco consumption in the United Kingdom. IMPLICATIONS: While several studies have shown that FS is associated with a higher prevalence of tobacco use, heavier smoking, and relapsed tobacco use, most of this work used cross-sectional data and none has focused on parents. We used longitudinal data from the UK Millennium Cohort Study, between 2008 and 2012, to examine the association between FS and parental smoking. We show that parents who experienced increased FS, over the period of the "Great Recession," were more likely to continue using tobacco or to relapse.

Myofibrillar myopathy caused by a mutation in the motor domain of mouse MyHC IIb.

Ariel is a mouse mutant that suffers from skeletal muscle myofibrillar degeneration due to the rapid accumulation of large intracellular protein aggregates. This fulminant disease is caused by an ENU-induced recessive mutation resulting in an L342Q change within the motor domain of the skeletal muscle myosin protein MYH4 (MyHC IIb). Although normal at birth, homozygous mice develop hindlimb paralysis from Day 13, consistent with the timing of the switch from developmental to adult myosin isoforms in mice. The mutated myosin (MYH4(L342Q)) is an aggregate-prone protein. Notwithstanding the speed of the process, biochemical analysis of purified aggregates showed the presence of proteins typically found in human myofibrillar myopathies, suggesting that the genesis of ariel aggregates follows a pathogenic pathway shared with other conformational protein diseases of skeletal muscle. In contrast, heterozygous mice are overtly and histologically indistinguishable from control mice. MYH4(L342Q) is present in muscles from heterozygous mice at only 7% of the levels of the wild-type protein, resulting in a small but significant increase in force production in isolated single fibres and indicating that elimination of the mutant protein in heterozygotes prevents the pathological changes observed in homozygotes. Recapitulation of the L342Q change in the functional equivalent of mouse MYH4 in human muscles, MYH1, results in a more aggregate-prone protein.

Inheritance patterns and phenotypic features of myofibrillar myopathy associated with a BAG3 mutation.

Myofibrillar myopathies are a heterogeneous group of neuromuscular disorders characterized by disintegration of myofibrils. The inheritance pattern is commonly autosomal dominant, but there has been a striking absence of secondary cases noted in a BAG3-associated subtype. We studied three families with BAG3 p.Pro209Leu mutation showing a severe phenotype of myofibrillar myopathy and axonal neuropathy with giant axons. In one family, transmission to a pair of siblings has occurred from their asymptomatic father who showed somatic mosaicism. In two other families, neither of the parents was affected or showed detectable level of somatic mosaicism. These observations suggest that the BAG3 variant of myofibrillar myopathy may result from a spontaneous mutation at an early point of embryonic development and that transmission from a mosaic parent may occur more than once. The study underlines the importance of parental evaluation as it may have implications for genetic counseling.