Strategies in Rapid Genetic Diagnostics of Critically Ill Children:Experiences From a Dutch University Hospital

Background: Genetic disorders are a substantial cause of infant morbidity and mortality and are frequently suspected in neonatal intensive care units. Non-specific clinical presentation or limitations to physical examination can result in a plethora of genetic testing techniques, without clear strategies on test ordering. Here, we review our 2-years experiences of rapid genetic testing of NICU patients in order to provide such recommendations. Methods: We retrospectively included all patients admitted to the NICU who received clinical genetic consultation and genetic testing in our University hospital. We documented reasons for referral for genetic consultation, presenting phenotypes, differential diagnoses, genetic testing requested and their outcomes, as well as the consequences of each (rapid) genetic diagnostic approach. We calculated diagnostic yield and turnaround times (TATs). Results: Of 171 included infants that received genetic consultation 140 underwent genetic testing. As a result of testing as first tier, 13/14 patients received a genetic diagnosis from QF-PCR; 14/115 from SNP-array; 12/89 from NGS testing, of whom 4/46 were diagnosed with a small gene panel and 8/43 with a large OMIM-morbid based gene panel. Subsequent secondary or tertiary analysis and/or additional testing resulted in five more diagnoses. TATs ranged from 1 day (QF-PCR) to a median of 14 for NGS and SNP-array testing, with increasing TAT in particular when many consecutive tests were performed. Incidental findings were detected in 5/140 tested patients (3.6%). Conclusion: We recommend implementing a broad NGS gene panel in combination with CNV calling as the first tier of genetic testing for NICU patients given the often unspecific phenotypes of ill infants and the high yield of this large panel

A stepwise approach including whole exome sequencing targeting a gene panel for paediatric dilated cardiomyopathy, potentially yields a diagnosis in 50% of patients

Introduction: Dilated cardiomyopathy (DCM) is a progressive disease of heart muscle with an incidence of approximately 0.57 per 100,000 children in the US. The spectrum and frequency of mutations in known DCM genes differ among adults, children, and infants. Aim: To evaluate the diagnostic yield of genome-wide copy number variation (CNV) analysis and trio Whole Exome Sequencing (WES) with targeted analysis of genes implicated in paediatric DCM. Methods: We identified 95 cases (from 85 families) diagnosed with DCM before 18 years of age. Thirteen families with a genetic diagnosis that was previously established by other sequencing techniques were excluded, and 41 families for other reasons. In 31 carefully phenotyped probands CNV-analysis (SNP-array) and trio-WES were performed. Human Phenotype Ontology (HPO)-terms were used for data filtering. Results: A (likely) genetic diagnosis could be made in 14/31 families (45.2%). (Likely) pathogenic heterozygous variants were identified in TNNT2, SCN5A, TTN, MYH7 (4), MYL2 (2) and TPM1, and homozygous variants in SPEG (centronuclear myopathy) and GLB1 (GM1-gangliosidosis) using WES, as well as an 1p36.33p36.32 and an 10q25.2 deletion, using SNP-array. Compound heterozygous mutations in CEP135 (primary microcephaly) were identified in a child with syndromic DCM. Five patients carried autosomal recessive disease mutations that did not explain their phenotypes. Conclusions: WES and CNV-analysis yielded diagnoses for 45% of our cohort. In 8/10 families 'solved' by WES a causal variant in a well-known DCM gene was identified. When CNV-analysis and WES would have been applied as primary tests to all patients, the potential yield could increase to approximately 51%. Combining CNV-analysis with trio-based WES, filtering for variants in a virtual, and flexible gene panel based on patient-specific HPO-terms, represent a comprehensive, personalized, cost-and time-efficient strategy to establish a diagnosis within the genetically highly heterogeneous paediatric DCM cohort. The latter technique provides the ability to stepwise analysis of a subset of genomic data, thereby minimizing the number of variants of unknown significance and preventing incidental findings in a proportion of patients

Rapid Targeted Genomics in Critically Ill Newborns

BACKGROUND: Rapid diagnostic whole-genome sequencing has been explored in critically ill newborns, hoping to improve their clinical care and replace time-consuming and/ or invasive diagnostic testing. A previous retrospective study in a research setting showed promising results with diagnoses in 57%, but patients were highly selected for known and likely Mendelian disorders. The aim of our prospective study was to assess the speed and yield of rapid targeted genomic diagnostics for clinical application. METHODS: We included 23 critically ill children younger than 12 months in ICUs over a period of 2 years. A quick diagnosis could not be made after routine clinical evaluation and diagnostics. Targeted analysis of 3426 known disease genes was performed by using wholegenome sequencing data. We measured diagnostic yield, turnaround times, and clinical consequences. RESULTS: A genetic diagnosis was obtained in 7 patients (30%), with a median turnaround time of 12 days (ranging from 5 to 23 days). We identified compound heterozygous mutations in the EPG5 gene (Vici syndrome), the RMND1 gene (combined oxidative phosphorylation deficiency-11), and the EIF2B5 gene (vanishing white matter), and homozygous mutations in the KLHL41 gene (nemaline myopathy), the GFER gene (progressive mitochondrial myopathy), and the GLB1 gene (GM1-gangliosidosis). In addition, a 1p36.33p36.32 microdeletion was detected in a child with cardiomyopathy. CONCLUSIONS: Rapid targeted genomics combined with copy number variant detection adds important value in the neonatal and pediatric intensive care setting. It led to a fast diagnosis in 30% of critically ill children for whom the routine clinical workup was unsuccessful

Toward an effective exome-based genetic testing strategy in pediatric dilated cardiomyopathy

Purpose: We evaluated the diagnostic yield in pediatric dilated cardiomyopathy (DCM) of combining exome sequencing (ES)based targeted analysis and genome-wide copy-number variation (CNV) analysis. Based on our findings, we retrospectively designed an effective approach for genetic testing in pediatric DCM. Methods: We identified 95 patients (in 85 families) with pediatric onset of DCM. We initially excluded 13 of these families because they already had a genetic diagnosis, leaving a total of 31 probands for singlenucleotide polymorphism (SNP) array and trio-ES. We used Human Phenotype Ontology (HPO)-based filtering for our data analysis. Results: We reached a genetic diagnosis in 15/31 (48.4%) families. ES yielded a diagnosis in 13 probands (13/15; 86.7%), with most variants being found in genes encoding structural cardiomyocyte components. Two large deletions were identified using SNP array. If we had included the 13 excluded families, our estimated yield would have been 54%. Conclusion: We propose a standardized, stepwise analysis of (i) wellknown cardiomyopathy genes, (ii) CNVs, (iii) all genes assigned to HPO cardiomyopathy, and (iv) if appropriate, genes assigned to other HPO terms. This diagnostic approach yields the highest increase at each subsequent step and reduces analytic effort, cost, the number of variants of unknown clinical significance, and the chance of incidental findings