ZNF711 is one of eleven zinc-finger genes on the X chromosome that have been associated with X-linked intellectual disability. This association is confirmed by the clinical findings in 20 new cases in addition to 11 cases previously reported. No consistent growth aberrations, craniofacial dysmorphology, malformations or neurologic findings are associated with alterations in ZNF711. The intellectual disability is typically mild and coexisting autism occurs in half of the cases. Carrier females show no manifestations. A ZNF711-specific methylation signature has been identified which can assist in identifying new cases and in confirming the pathogenicity of variants in the gene.

A recurrence risk of under 1% is usually quoted for parents of children who have apparently de novo genetic conditions. Since 2018, our service has offered digital droplet PCR (ddPCR) testing to determine parental mosaicism rates for apparently de novo variants identified in children with syndromic disorders Aim: To determine the rate of parental mosaicism in a cohort of New Zealand families with apparently de novo pathogenic variants. Method: Specific assays were designed for each pathogenic variant. DNA derived from varying combinations of leukocytes, urothelial buccal and semen was tested by ddPCR for the pathogenic variants identified in the affected children. Results: 102 trio cases have been analysed. Seven parents were identified as being mosaic (6.8%). There is a preponderance of paternal mosaicism (6 of 7 being paternally derived) and two couples had a recurrence of the condition in a second child. Conclusion: This small cohort demonstrates a higher rate of parental mosaicism compared to the typically quoted recurrence risk of <1% and has implications for genetic counselling and genetic testing provision.

Int22h1/Int22h2-mediated Xq28 duplications are associated with intellectual disability of varying degree, neurobehavioural phenotypes and recurrent sinopulmonary infection and atopy in affected males. Heterozygous females may have mild intellectual disability whereas, to date, all reported hemizygous males have moderate-to-severe intellectual disability. We present the case of a healthy, neurotypical adult man with a university education, who was ascertained following investigation of his daughter’s multiple congenital anomalies. Both father and daughter have the common 0.5Mb duplication of Xq28 between breakpoints 154124170 and 154555780 (GRCh37/hg19). We discuss the molecular investigation of this unexpected finding and review the literature of this well-described copy number variant (CNV).

Goldenhar syndrome or oculo-auriculo-vertebral spectrum (OAVS) is a complex developmental disorder characterized by asymmetric ear anomalies, hemifacial microsomia, ocular and vertebral defects. We aimed at identifying and characterizing a new gene associated with OAVS. Two affected brothers with OAVS were analyzed by exome sequencing that revealed a missense variant (p.(Asn358Ser)) in the EYA3 gene. EYA3 screening was then performed in 122 OAVS patients that identified the same variant in one individual from an unrelated family. Segregation assessment in both families showed incomplete penetrance and variable expressivity. We investigated this variant in cellular models to determine its pathogenicity and demonstrated an increased half-life of the mutated protein without impact on its ability to dephosphorylate H2AFX following DNA repair pathway induction. Proteomics performed on this cellular model revealed four significantly predicted upstream regulators which are PPARGC1B, YAP1, NFE2L2 and MYC. Moreover, eya3 knocked-down zebrafish embryos developed specific craniofacial abnormalities corroborating previous animal models and supporting its involvement in the OAVS. Additionally, EYA3 gene expression was deregulated in vitro by retinoic acid exposure. EYA3 is the second recurrent gene identified to be associated with OAVS. Moreover, based on protein interactions and related diseases, we suggest the DNA repair as a key molecular pathway involved in craniofacial development.

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.

Abstract 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.

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.

Pediatric PulmonologyVolume 55, Issue 4 p. 855-857 LETTER TO THE EDITOR Use of ultra-rapid whole-exome sequencing to diagnose congenital central hypoventilation syndrome Shivanthan Shanthikumar MBBS, Corresponding Author Shivanthan Shanthikumar MBBS shivanthan.shanthikumar@rch.org.au orcid.org/0000-0001-6000-3180 Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Australia Department of Paediatrics, University of Melbourne, Melbourne, Australia Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia Correspondence Shivanthan Shanthikumar, Respiratory Medicine, Royal Children's Hospital, 50 Flemington Road, Parkville, Melbourne, VIC 3052, Australia. Email: shivanthan.shanthikumar@rch.org.auSearch for more papers by this authorAjay Kevat MBBS, Ajay Kevat MBBS orcid.org/0000-0001-9881-6478 Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Australia Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, AustraliaSearch for more papers by this authorRachel Stapleton MB, ChB, Rachel Stapleton MB, ChB Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, AustraliaSearch for more papers by this authorSebastian Lunke PhD, Sebastian Lunke PhD Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia Department of Pathology, University of Melbourne, Melbourne, Australia Australian Genomics Health Alliance, AustraliaSearch for more papers by this authorZornitza Stark DM, Zornitza Stark DM Department of Paediatrics, University of Melbourne, Melbourne, Australia Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia Australian Genomics Health Alliance, AustraliaSearch for more papers by this authorMoya Vandeleur PhD, Moya Vandeleur PhD Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, AustraliaSearch for more papers by this author Shivanthan Shanthikumar MBBS, Corresponding Author Shivanthan Shanthikumar MBBS shivanthan.shanthikumar@rch.org.au orcid.org/0000-0001-6000-3180 Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Australia Department of Paediatrics, University of Melbourne, Melbourne, Australia Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia Correspondence Shivanthan Shanthikumar, Respiratory Medicine, Royal Children's Hospital, 50 Flemington Road, Parkville, Melbourne, VIC 3052, Australia. Email: shivanthan.shanthikumar@rch.org.auSearch for more papers by this authorAjay Kevat MBBS, Ajay Kevat MBBS orcid.org/0000-0001-9881-6478 Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Australia Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, AustraliaSearch for more papers by this authorRachel Stapleton MB, ChB, Rachel Stapleton MB, ChB Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, AustraliaSearch for more papers by this authorSebastian Lunke PhD, Sebastian Lunke PhD Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia Department of Pathology, University of Melbourne, Melbourne, Australia Australian Genomics Health Alliance, AustraliaSearch for more papers by this authorZornitza Stark DM, Zornitza Stark DM Department of Paediatrics, University of Melbourne, Melbourne, Australia Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia Australian Genomics Health Alliance, AustraliaSearch for more papers by this authorMoya Vandeleur PhD, Moya Vandeleur PhD Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, AustraliaSearch for more papers by this author First published: 14 February 2020 https://doi.org/10.1002/ppul.24686Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume55, Issue4April 2020Pages 855-857 RelatedInformation

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. Methods 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. Results 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 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.

We report the results of a pilot project for clinical DNA sequencing in New Zealand. This project aimed to estimate the diagnostic yield of next generation sequencing in the New Zealand clinical environment. Trio whole exome sequencing (WES) was performed on germline DNA of 40 individuals from 12 families with presumptive Mendelian disorders. In addition, both WES and deep targeted sequencing (DTS) was performed on tumours, metastases and corresponding normal blood leukocytes from two cancer patients. For the rare Mendelian disorder cohort, the diagnostic yield was 6/12, including previously recognised pathogenic mutations and novel mutations. In tumour sequence analysis, WES identified somatic single nucleotide mutations and copy number aberrations in both cancer patients; however, DTS was required to obtain clinically informative information. This study showed that diagnostic germline and tumour WES and DTS could be easily undertaken in New Zealand, and identified specific infrastructural challenges that must be solved to facilitate its clinical use.

Aim: Implementation and assessment of rapid genomic testing in a routine diagnostic service.

16q24 deletion involving the ANKRD11 gene, ranging from 137 kb to 2 Mb, have been associated with a microdeletion syndrome characterized by variable cognitive impairment, autism spectrum disorder, facial dysmorphisms with dental anomalies, brain abnormalities essentially affecting the corpus callosum and short stature. On the other hand, patients carrying either deletions encompassing solely ANKRD11 or its loss-of-function variants were reported in association with the KBG syndrome, characterized by a very similar phenotype, including mild-to-moderate intellectual disability, short stature and macrodontia of upper incisors, with inter and intrafamilial variability. To assess whether the haploinsufficiency of ANKRD11-flanking genes, such as ZFPM1, CDH15 and ZNF778, contributed to either the severity of the neurological impairment or was associated with other clinical features, we collected 12 new cases with a 16q24.2q24.3 deletion (de novo in 11 cases), ranging from 343 kb to 2.3 Mb. In 11 of them, the deletion involved the ANKRD11 gene, whereas in 1 case only flanking genes upstream to it were deleted. By comparing the clinical and genetic features of our patients with those previously reported, we show that the severity of the neurological phenotype and the frequency of congenital heart defects characterize the deletions that, besides ANKRD11, contain ZFPM1, CDH15 and ZNF778 as well. Moreover, the presence of thrombocytopenia and astigmatism should be taken into account to distinguish between 16q24 microdeletion syndrome and KBG syndrome. The single patient not deleted for ANKRD11, whose phenotype is characterized by milder psychomotor delay, cardiac congenital malformation, thrombocytopenia and astigmatism, confirms all this data.

Brown-Vialetto-van Laere syndrome is characterized by a progressive sensorimotor neuropathy, optic atrophy, hearing loss, bulbar dysfunction, and respiratory insufficiency. Mutations in SLC52A2 and SLC52A3, encoding riboflavin transporters RFVT2 and RFVT3, respectively, are the genetic basis of this disorder, often referred to as riboflavin transporter deficiency types 2 and 3, respectively. We present cases of both types of riboflavin transporter deficiency, highlighting the distinguishing clinical features of a rapidly progressive motor or sensorimotor axonal neuropathy, optic atrophy, sensorineural hearing loss, and bulbar dysfunction. One child presented with isolated central apnea and hypoventilation, not previously described in genetically confirmed Brown-Vialetto-van Laere, later complicated by diaphragmatic paralysis secondary to phrenic nerve palsy. Magnetic resonance imaging showed T2 hyperintensity in the dorsal spinal cord in 2 children, as well as previously unreported cervical nerve root enlargement and cauda equina ventral nerve root enhancement in 1 child. Novel homozygous mutations were identified in each gene-a NM_024531.4(SLC52A2):c.505C > T, NP_078807.1(SLC52A2):p.(Arg169Cys) variant in SLC52A2 and NM_033409.3(SLC52A3):c.1316G > A, NP_212134.3(SLC52A3):p.(Gly439Asp) variant in SLC52A3. Both treated children showed improvement on high-dose riboflavin supplementation, highlighting the importance of early recognition of this treatable clinical entity.