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Item does not contain fulltext, Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.

The diagnosis of children with genetic conditions places a significant economic burden on health care services. The lack of well-defined comparative cohorts has been a limitation of health economic studies comparing first-line genomic sequencing (GS) against traditional approaches. Aim(s): To evaluate utility and cost effectiveness of early GS in pediatric patients with complex monogenic conditions compared to a matched historical cohort. Method(s): Data, including diagnosis rate and investigation costs, were collected in a prospective cohort of 92 pediatric patients who underwent singleton GS over an 18-month period (2016-2017). Inclusion required patients to have two of the following: a condition with high morbidity or mortality, a multi-system disease involving three or more organ systems, or severe limitation of daily function. For comparison, data were collected in a historical patient cohort fulfilling the inclusion criteria who underwent traditional investigations in the two years (2012-2013) prior to the availability of clinical genomic sequencing. Result(s): Genomic sequencing yielded a diagnosis in 42% while traditional investigations yielded a diagnosis in 23% (p = 0.003). 75% of diagnosed patients experienced a change in management, compared to 33% of diagnosed patients who underwent traditional investigations. In the GS cohort, four times fewer invasive investigations were observed. Compared to traditional investigations, singleton genomic sequencing at a cost of $3100 AUD resulted in a mean saving per person of $2780 AUD (95%CI $1585-$3974). Conclusion(s): Early genomic sequencing is highly costeffective while doubling the diagnostic yield of traditional approaches and improving the care of patients with complex genetic conditions.

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. METHOD(S): 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. RESULT(S): 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(S): 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.Copyright © 2020 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals LLC.

Contains fulltext : 218289.pdf (Publisher’s version ) (Closed access), MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.

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. Method(s): 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. Result(s): 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(s): GS in complex pediatric patients saves significant costs and doubles the diagnostic yield of traditional approaches.Copyright © 2020, American College of Medical Genetics and Genomics.

Introduction: Standard rapid genomic testing techniques analyse nuclear DNA variants using exome and/or genome sequencing (ES/GS). Rapid mtDNA analysis is not routinely available, particularly in centres performing ES, which does not deliver clinical-grade mtDNA sequencing. We describe our experience using rapid mtDNA sequencing in tandem with an ES-based rapid genomic diagnosis program as part of the Australian Genomics Acute Care flagship. Method(s): Two infants presenting with persistent lactic acidosis and bone marrow failure were recruited for rapid genomic testing. With clinical suspicion of mitochondrial disease, both infants underwent rapid ES and mtDNA sequencing in tandem, the latter using Nextera libraries from a full length mtDNA amplicon. Result(s): ES was non-diagnostic in both infants. mtDNA sequencing identified a single large mtDNA deletion in both infants, diagnostic of Pearson syndrome (MIM 557000). Diagnostic reports were issued within 73 hours 55 minutes and 54 hours 25 minutes, respectively. Both infants avoided invasive bone marrow biopsies and a range of other investigations. Conclusion(s): Rapid mtDNA sequencing in tandem with ES results in additional diagnoses in seriously ill children with suspected mitochondrial pathology, suggesting that ES alone may be insufficient in this setting. When designing rapid genomic diagnosis programs, centres should consider incorporating mtDNA amplification and analysis in individuals with suspected mitochondrial pathology, by combining ES and mtDNA sequencing in tandem, or analysing mtDNA data from GS, which captures the mitochondrial genome.

Multiple studies have shown that genomic testing has a high diagnostic yield and an impact on clinical management for patients with suspected genetic conditions. Therefore, there has been a push worldwide to apply rapid genomic sequencing in critically ill neonatal and pediatric patients. The goal of this study was to investigate the practicality of applying ultrarapid genomic testing for critically ill neonatal and pediatric patients with suspected monogenic conditions in Australia. The study recruited a total of 108 patients prospectively from March 2018 to February 2019, and data were collected until May 2019. Of the 12 hospitals that acted as collaborating sites, 5 were women's hospitals, 3 women's and children's hospitals, and 4 children's hospitals. Eligible patients included those who were admitted to a neonatal or pediatric intensive care unit (NICU or PICU) and were referred to clinical genetics for a possible monogenic condition. Chromosomal microarray was a requirement before enrollment if there was a suspected chromosomal condition. Chromosomal microarrays were performed concurrently with ultrarapid exome sequencing when the probability of a positive result on microarray was low. Additionally, rapid mitochondrial genome sequencing was performed alongside ultrarapid exome sequencing if a mitochondrial condition was suspected. When possible, ultrarapid exome sequencing was performed in both parents as well as the child (trio). The primary outcome of this study measured the time from the last sample received to the ultrarapid exome sequencing report finalized. Other outcomes measured were the diagnostic yield, change in clinical management after the report was finalized, number of reports returned before hospital discharge, and time from admission to the report being finalized. Of the 108 patients enrolled, the median age was 28 days, with a range of 0 days to 17 years. Overall, 34% were female, 57% were NICU admissions, 33% were PICU admissions, and 9% wer

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(s): To prospectively evaluate the performance of a multicenter network for ultra-rapid genomic diagnosis in a public health care system. Design, Setting, and Participant(s): 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. Result(s): 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

Contains fulltext : 208539.pdf (publisher's version ) (Closed access), Zinc finger protein 462 (ZNF462) is a relatively newly discovered vertebrate specific protein with known critical roles in embryonic development in animal models. Two case reports and a case series study have described the phenotype of 10 individuals with ZNF462 loss of function variants. Herein, we present 14 new individuals with loss of function variants to the previous studies to delineate the syndrome of loss of function in ZNF462. Collectively, these 24 individuals present with recurring phenotypes that define a multiple congenital anomaly syndrome. Most have some form of developmental delay (79%) and a minority has autism spectrum disorder (33%). Characteristic facial features include ptosis (83%), down slanting palpebral fissures (58%), exaggerated Cupid's bow/wide philtrum (54%), and arched eyebrows (50%). Metopic ridging or craniosynostosis was found in a third of study participants and feeding problems in half. Other phenotype characteristics include dysgenesis of the corpus callosum in 25% of individuals, hypotonia in half, and structural heart defects in 21%. Using facial analysis technology, a computer algorithm applying deep learning was able to accurately differentiate individuals with ZNF462 loss of function variants from individuals with Noonan syndrome and healthy controls. In summary, we describe a multiple congenital anomaly syndrome associated with haploinsufficiency of ZNF462 that has distinct clinical characteristics and facial features.

Purpose: The purpose of the study was to implement and prospectively evaluate the outcomes of a rapid genomic diagnosis program at two pediatric tertiary centers. Method(s): Rapid singleton whole-exome sequencing (rWES) was performed in acutely unwell pediatric patients with suspected monogenic disorders. Laboratory and clinical barriers to implementation were addressed through continuous multidisciplinary review of process parameters. Diagnostic and clinical utility and cost-effectiveness of rWES were assessed. Result(s): Of 40 enrolled patients, 21 (52.5%) received a diagnosis, with median time to report of 16 days (range 9-109 days). A result was provided during the first hospital admission in 28 of 36 inpatients (78%). Clinical management changed in 12 of the 21 diagnosed patients (57%), including the provision of lifesaving treatment, avoidance of invasive biopsies, and palliative care guidance. The cost per diagnosis was AU$13,388 (US$10,453). Additional cost savings from avoidance of planned tests and procedures and reduced length of stay are estimated to be around AU$543,178 (US$424,101). The clear relative advantage of rWES, joint clinical and laboratory leadership, and the creation of a multidisciplinary "rapid team" were key to successful implementation. Conclusion(s): Rapid genomic testing in acute pediatrics is not only feasible but also cost-effective, and has high diagnostic and clinical utility. It requires a whole-of-system approach for successful implementation.Copyright © 2018, American College of Medical Genetics and Genomics.

Objective: While standard rapid genomic testing techniques analyse nuclear DNA variants using whole exome (WES) and/or whole genome (WGS) sequencing, rapid mtDNA analysis is not usually performed. We describe our experience using rapid mtDNA sequencing in tandem with WES in the Australian Genomics Acute Care Genomics flagship. Method(s): Two infants presenting with persistent lactic acidosis and bone marrow failure were recruited for rapid genomic testing. With clinical suspicion of mitochondrial disease, both infants underwent rapid WES and mtDNA sequencing in tandem, the latter using Nextera libraries from a full length mtDNA amplicon. Result(s): WES was non-diagnostic. mtDNA sequencing identified a single large-scale mtDNA deletion in both infants, consistent with Pearson syndrome (MIM 557000). Diagnostic reports were issued within 73 hours 55 minutes and 54 hours 25 minutes, respectively. Both infants avoided invasive bone marrow biopsies and a range of other investigations. Conclusion(s): Rapid mtDNA sequencing in tandem with WES Results in additional diagnoses in seriously ill children with suspected mitochondrial disease, suggesting that WES alone may be insufficient in this setting. When designing rapid genomic diagnostic programs, centres should consider mtDNA analysis, combining WES and mtDNA sequencing in tandem, or analysing mtDNA data from WGS, which captures the mitochondrial genome.Copyright © 2018

Rapid genomic testing is a valuable new diagnostic tool for acutely unwell infants, however exome sequencing does not deliver clinical-grade mitochondrial genome sequencing and may fail to diagnose mitochondrial disorders caused by mitochondrial DNA (mtDNA) variants. Rapid mitochondrial genome sequencing and analysis are not routinely available in rapid genomic diagnosis programmes. We present two critically ill neonates with transfusion-dependent anaemia and persistent lactic acidosis who underwent rapid mitochondrial genome sequencing in tandem with exome sequencing as part of an exome sequencing-based rapid genomic diagnosis programme. No diagnostic variants were identified on examination of the nuclear exome data for either infant. Mitochondrial genome sequencing identified a large mtDNA deletion in both infants, diagnosing Pearson syndrome within 74 and 55 h, respectively. Early diagnosis in the third week of life allowed the avoidance of a range of other investigations and appropriate treatment planning. Rapid mitochondrial genome analysis provides additional diagnostic and clinical utility and should be considered as an adjunct to exome sequencing in rapid genomic diagnosis programmes.Copyright © 2019, The Author(s), under exclusive licence to European Society of Human Genetics.