Specialist multidisciplinary input maximises rare disease diagnoses from whole genome sequencing

Diagnostic whole genome sequencing (WGS) is increasingly used in rare diseases. However, standard, semi-automated WGS analysis may overlook diagnoses in complex disorders. Here, we show that specialist multidisciplinary analysis of WGS, following an initial 'no primary findings' (NPF) report, improves diagnostic rates and alters management. We undertook WGS in 102 adults with diagnostically challenging primary mitochondrial disease phenotypes. NPF cases were reviewed by a genomic medicine team, thus enabling bespoke informatic approaches, co-ordinated phenotypic validation, and functional work. We enhanced the diagnostic rate from 16.7% to 31.4%, with management implications for all new diagnoses, and detected strong candidate disease-causing variants in a further 3.9% of patients. This approach presents a standardised model of care that supports mainstream clinicians and enhances diagnostic equity for complex disorders, thereby facilitating access to the potential benefits of genomic healthcare. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project: http://www.genomicsengland.co.uk .

Genome sequencing reveals underdiagnosis of primary ciliary dyskinesia in bronchiectasis

BACKGROUND

Bronchiectasis can result from infectious, genetic, immunological and allergic causes. 60-80% of cases are idiopathic, but a well-recognised genetic cause is the motile ciliopathy, primary ciliary dyskinesia (PCD). Diagnosis of PCD has management implications including addressing comorbidities, implementing genetic and fertility counselling and future access to PCD-specific treatments. Diagnostic testing can be complex; however, PCD genetic testing is moving rapidly from research into clinical diagnostics and would confirm the cause of bronchiectasis.

METHODS

This observational study used genetic data from severe bronchiectasis patients recruited to the UK 100,000 Genomes Project and patients referred for gene panel testing within a tertiary respiratory hospital. Patients referred for genetic testing due to clinical suspicion of PCD were excluded from both analyses. Data were accessed from the British Thoracic Society audit, to investigate whether motile ciliopathies are underdiagnosed in people with bronchiectasis in the UK.

RESULTS

Pathogenic or likely pathogenic variants were identified in motile ciliopathy genes in 17 (12%) out of 142 individuals by whole-genome sequencing. Similarly, in a single centre with access to pathological diagnostic facilities, 5-10% of patients received a PCD diagnosis by gene panel, often linked to normal/inconclusive nasal nitric oxide and cilia functional test results. In 4898 audited patients with bronchiectasis, <2% were tested for PCD and <1% received genetic testing.

CONCLUSIONS

PCD is underdiagnosed as a cause of bronchiectasis. Increased uptake of genetic testing may help to identify bronchiectasis due to motile ciliopathies and ensure appropriate management.

Lung macrophages from bacille Calmette-Guérin-vaccinated guinea pigs suppress T cell proliferation but restrict intracellular growth of M. tuberculosis after recombinant guinea pig interferon-gamma activation

The guinea pig model of low-dose pulmonary tuberculosis has been used to study the pathogenesis of infection as well as the mechanisms of bacille Calmette-Guérin (BCG) vaccine-induced resistance. We investigated the function of lung cells from naive and BCG-vaccinated guinea pigs after enzymatic digestion of lung tissue with collagenase and DNase I. The total lung digest cells proliferated poorly to purified protein derivative (PPD) but comparatively better to ConA as assessed by [(3)H]-thymidine uptake. However, the non-adherent population obtained after plastic adherence of lung digests showed an enhanced response to concanavalin A (ConA) and PPD. Therefore, proliferation to ConA and PPD of nylon wool-purified T cells co-cultured with peritoneal (PMøs), alveolar (AMøs) or lung macrophages (LMøs) was assessed. Co-cultures of lung T cells and PMøs showed maximum proliferation to PPD, whereas proliferation was suppressed significantly by the addition of AMøs or LMøs. The response of T cells to ConA was unaffected in co-cultures. Incubation of co-cultures with recombinant guinea pig interferon-gamma (rgpIFN-gamma) did not reverse the suppression. In contrast, rgpIFN-gamma-treated plastic adherent LMøs that were non-specific esterase-positive were capable of reducing the intracellular growth of Mycobacterium tuberculosis. Similarly, total, non-adherent and adherent lung digest cells from BCG-vaccinated guinea pigs showed IFN-gamma and tumour necrosis factor (TNF)-alpha mRNA expression in response to ConA, lipopolysaccharide or PPD by reverse transcription-polymerase chain reaction followed by release of TNF protein but not IFN. These studies indicate that rgp-IFN-gamma-treated lung tissue macrophages from BCG-vaccinated guinea pigs are defective for inducing antigen-specific proliferation in T cells, but control the intracellular accumulation of virulent M. tuberculosis.