Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases.

BACKGROUND: Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS: We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS: Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS: Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.

Nitrous oxide-induced myeloneuropathy: a case series.

BACKGROUND: Nitrous oxide (N2O) is the second most common recreational drug used by 16- to 24-year-olds in the UK. Neurological symptoms can occur in some people that use N2O recreationally, but most information comes from small case series. METHODS: We describe 119 patients with N2O-myeloneuropathy seen at NHS teaching hospitals in three of the UK's largest cities: London, Birmingham and Manchester. This work summarises the clinical and investigative findings in the largest case series to date. RESULTS: Paraesthesia was the presenting complaint in 85% of cases, with the lower limbs more commonly affected than the upper limbs. Gait ataxia was common, and bladder and bowel disturbance were frequent additional symptoms. The mid-cervical region of the spinal cord (C3-C5) was most often affected on MRI T2-weighted imaging. The number of N2O canisters consumed per week correlated with methylmalonic acid levels in the blood as a measure of functional B12 deficiency (rho (ρ)=0.44, p=0.04). CONCLUSIONS: Preventable neurological harm from N2O abuse is increasingly seen worldwide. Ease of access to canisters and larger cylinders of N2O has led to an apparent rise in cases of N2O-myeloneuropathy in several areas of the UK. Our results highlight the range of clinical manifestations in a large group of patients to improve awareness of risk, aid early recognition, and promote timely treatment.

Home video EEG telemetry.

Long-term electroencephalogram monitoring is often used to help distinguish epileptic from dissociative (non-epileptic) seizures. Home video telemetry now offers many of the benefits in diagnosis previously available only with inpatient video telemetry, which is usually regarded as the 'gold standard'. Here, we describe recent developments in home video telemetry and how we undertake this procedure in our unit.

Classical and Non-classical Presentations of Complement Factor I Deficiency: Two Contrasting Cases Diagnosed via Genetic and Genomic Methods.

Deficiency of complement factor I is a rare immunodeficiency that typically presents with increased susceptibility to encapsulated bacterial infections. However, non-infectious presentations including rheumatological, dermatological and neurological disease are increasingly recognized and require a high-index of suspicion to reach a timely diagnosis. Herein, we present two contrasting cases of complement factor I deficiency: one presenting in childhood with invasive pneumococcal disease, diagnosed using conventional immunoassays and genetics and the second presenting in adolescence with recurrent sterile neuroinflammation, diagnosed via a genomic approach. Our report and review of the literature highlight the wide spectrum of clinical presentations associated with CFI deficiency and the power of genomic medicine to inform rare disease diagnoses.

Susac's syndrome: the value of fundus fluorescein angiography.

A 19-year-old woman presented with a 4-week history of headache, ataxia, vertigo, confusion, intermittent blurred vision in the right eye and intermittent hearing loss. MRI revealed white matter lesions and 'pepper pot' lesions of the corpus callosum. The cerebrospinal fluid had raised protein and lymphocytes. Fundal examination revealed multiple peripheral arterial occlusions in the both eyes confirmed with fundus fluorescein angiography (FFA). A diagnosis of Susac's syndrome was made. The patient was initially treated with steroids, followed by azathioprine and intravenous immunoglobulins (IVIg). Clinical improvement was noted, associated with improvement of the retinal circulation on FFA.

Randomized trial of vein versus dacron patching during carotid endarterectomy: long-term results.

BACKGROUND AND PURPOSE: Overviews of randomized patch trials by the Cochrane Collaboration suggest that a policy of routine patching is preferable to routine primary closure. However, there is no systematic evidence that patch type, whether prosthetic or vein, influences outcome after carotid endarterectomy (CEA). METHODS: Two hundred seventy-three patients were randomized to vein or thin-walled Dacron patch (Hemashield Finesse) closure of the arteriotomy after 276 CEA procedures. Patients were reviewed clinically and with duplex ultrasound scanning at 1, 6, 12, 24, and 36 months or until death. No patients were lost to follow-up. Cumulative statistical analyses are presented for the 264 patients (269 CEAs) who actually received a randomized treatment allocation. RESULTS: Cumulative freedom from death or ipsilateral stroke at 3 years (including operative events) was 93.0% in the Dacron patch group and 95.5% in the vein group P =.42). Cumulative freedom from death or any stroke was 91.5% after Dacron patch closure and 93.9% after vein closure (P =.46). Cumulative freedom from recurrent stenosis greater than 70% or occlusion at 3 years was 92.9% for patients randomized to the Dacron patch group and 98.4% for patients randomized to the vein group (P =.03). At 3 years the incidence of stroke in the carotid territory not operated on was 1.0% in 93 patients with no contralateral internal carotid artery disease at randomization, and increased to 1.3% in 78 patients with 1% to 69% stenosis, and 2.0% in 51 patients with contralateral 70% to 99% stenosis. No late strokes occurred distal to 42 occluded contralateral internal carotid arteries. CONCLUSIONS: Patch type has no influence on early operative risk, no association with enhanced patterns of thrombogenicity in the early postoperative period, and no influence on risk for ipsilateral or any stroke at 3 years. Dacron patches were, however, associated with a significantly higher incidence of recurrent stenosis at 3 years, with most occurring within 6 to 12 months of surgery. However, the higher incidence of recurrent stenosis was not associated with a parallel increase in late stroke, and in this study a program of serial ultrasound surveillance could not have prevented one ipsilateral stroke.