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Rare diseases, particularly those with great phenotypic and genetic heterogeneity, remain a diagnostic challenge. Broadening the investigative approach through whole genome sequencing (WGS) is anticipated to improve diagnostic yield. Despite this, substantial numbers of patients remain undiagnosed through current 100,000 Genomes Project pipelines. In these cases, the causative mutation may not be prioritised due to lack of evidence associating the gene with a specific phenotype, or as a result of being inadvertently filtered out. A systematic approach to additional data analysis utilising both inheritance model filtering and ranking algorithm tools has been piloted in cases with no primary findings (NPF). Examples of diagnoses secured include a de novo TAB2mutation, causing a connective tissue phenotype with congenital heart disease and a paternally inherited COL7A1mutation, causing a variable penetrance skin blistering disorder, epidermolysis bullosa dystrophica. Identification of causative variants in WGS data remains challenging. Data led approaches to optimising additional review of cases with NPF have the prospect of improving both sensitivity and cost efficiency and may provide earlier diagnosis for individuals with rare disease, ending their diagnostic odyssey. Establishing a standardised approach to reanalysis will be particularly important as we approach the introduction of an NHS clinical sequencing service.

Background and aims Gitelman syndrome (GS) is a rare renal channelopathy with an autosomal recessive type of inheritance, caused by homozygous or compound heterozygous mutations in SLC12A3 gene. The disorder causes metabolic abnormalities and may be overlapped with Barter type 3 syndrome. Methods A 7 year-old boy presented with a history of several episodes of carpopedal spasms and muscle aches in the last few months. The boy has been a relatively healthy child previously. His auxological parameters were within normal range for his sex and age. Diagnostic assessment was achieved by characteristic symptoms, imaging technics, biochemical, hormonal and molecular analyses. Results The biochemical analyses revealed hypokalemia (3.0–3.4 mmol/l), hypomagnesemia (0.64–0.66 mmol/l), hypocalciuria ( A pathogenic variants and also heterozygous for the SLC12A3 c.2944 A>T (p.Ile982Phe) likely pathogenic variant. His mother was a heterozygous for the c.2944 A>T (p.Ile982Phe) mutation, but his father was heterozygous for the other 2 variants (SLC12A3 c.1805_1806del and c.2660+1G>A). Conclusions Herein we present a first child from Macedonia with clinical manifestations and electrolyte imbalances typical for a GS. The results of the molecular analyses were consistent with the diagnosis of GS. The boy is on a high salt diet and oral potassium and magnesium supplements.

We have established the only specialised clinic for renal tubulopathies in children. The clinical diagnosis of these disorders can be challenging, as they are rare and characterized by significant phenotypic variability. Advances in sequencing technologies facilitate the establishment of a molecular diagnosis. We aimed to investigate the diagnostic yield of a next-generation sequencing panel assessing relevant disease genes in children with a clinical diagnosis of a renal tubulopathy followed through three national networks. DNA was amplified with a kit provided by the European Consortium for High-Throughput Research in Rare Kidney Diseases with 9 multiplex PCR reactions producing 571 amplicons to cover 37 genes associated with tubulopathies, followed by massively parallel sequencing and bioinformatic interpretation. Identified mutations were confirmed by Sanger sequencing. Overall, we assessed 384 index patients and 16 siblings. Most common clinical diagnoses were Bartter/Gitelman syndrome (n=174) and distal renal tubular acidosis (n=76). A total of 269 different variants were identified in 27 genes, of which 95 were considered likely and 136 definitely pathogenic and 100 had not been described at annotation. These mutations established a genetic diagnosis in 245 (64%) of the index patients. Genetic testing changed the clinical diagnosis in 16 (4%) of cases and provided insights into the phenotypic spectrum of the respective disorders. Our results demonstrate a high diagnostic yield of genetic testing in children with a clinical diagnosis of a renal tubulopathy, consistent with a predominantly genetic aetiology in known disease genes. Genetic testing helped establish a definitive diagnosis in almost two-thirds of patients and thereby informed prognosis, management and genetic counselling.

Background The 100,000 Genomes Project is a national programme to perform whole genome sequencing (WGS) in families with an undiagnosed rare disorder or cancer. Multiple specialties from GOSH have recruited patients to the pilot study. Here we report on the outcome of the first 111 pilot cases. Methodology Total lymphocyte DNA was extracted (Chemagic Star, Chemagen) and exported to Genomics England for WGS (HiSeqX, Illumina). Prioritised variants were discussed and classified by a multidisciplinary team (MDT) of Clinical Scientists, Consultant Clinical Geneticists and the recruiting clinicians. Variants deemed to be ‘pathogenic’ or ‘likely pathogenic’ were flagged for diagnostic confirmation and clinical reporting. Results Genomics England returned results for 111 cases (probands); 95 (86%) were analysed as trios (proband and both parents). Variant interpretation has been completed for 97 cases (87%). Thirty-six percent of cases (40/111) and a total of 76 variants were discussed at an MDT meeting. Fifty-three percent of variants discussed (40/76) were classified as pathogenic or likely pathogenic, 30% (23/76) were classified as variants of unknown significance and 17% (13/76) were classified as benign or likely benign. This equated to a genetic diagnosis in 27/111 cases (25%) of which 5/111 (5%) were felt to be a partial rather than full explanation of the phenotype. Of the 97 cases where primary analysis was complete, 66/97 (68%) had no primary findings. This included cases in which variants of unknown significance have been detected. Conclusion WGS is a useful tool for rare disease diagnosis especially in patients who have undergone a fruitless diagnostic odyssey. Analysis of GOSH pilot cases has enabled us to develop infrastructure locally to support the return of main programme results. One quarter of GOSH pilot patients should expect a genetic diagnosis from the primary analysis. It is unclear whether this will be an accurate reflection of the diagnostic rate achieved in the main programme due to ongoing refinement of the recruitment and analysis pipelines.