Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels.

BACKGROUND: Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. PATIENTS AND METHODS: We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. RESULTS: We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. CONCLUSIONS: There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy.

The prediction of hospital admission in children with acute asthma.

OBJECTIVE: To determine whether a single assessment of children at the time of presentation to the emergency department would discriminate accurately between those requiring admission and those who could be managed at home and to examine the appropriateness of these decisions. METHODOLOGY: Fifty-three children were assessed using a table recommended by Australian and New Zealand respiratory paediatricians, which categorizes children as probably being able to manage at home (group 1), may need admission to hospital (group 2) and certainly need admission to hospital (group 3) on the basis of oximetry, presence of wheeze and pulsus paradoxus. RESULTS: Nine out of 11 children assigned to group 1 were managed at home and 15/17 who were predicted to require admission were admitted. No individual component of the assessment dominated the decision made. Of the 25 children allocated to group 2, 18 were admitted. CONCLUSIONS: The method employed was highly predictive of outcome for half of the children who presented with asthma. However, 25/53 (47%) were assigned by the table to a recommendation for further assessment; this limits its usefulness.

Assessment of airway inflammation in children with acute asthma using induced sputum.

The aims of this study were: to assess the safety of a sputum induction method using inhaled normal saline in children with acute asthma; and to investigate changes in sputum cell counts between acute exacerbations of asthma and its resolution. Ultrasonically nebulized normal saline was used to induce sputum from children (n = 8) presenting with acute asthma within 1 h of arrival and again at least 14 days later, after resolution of the exacerbation. Children received pretreatment with bronchodilator, and peak expiratory flow (PEF) was monitored throughout the procedure. Samples were analysed for total cell count, differential cell counts, and for eosinophils and neutrophils using specific immunochemical stains. Sputum induction was performed without adverse effect in each child with acute asthma. The mean fall in PEF from baseline during sputum induction was 5.3% during the acute attack and 3.4% at resolution. A shorter nebulization time was required to induce sputum in acute asthma than at follow-up (7.8 vs 13.9 min; p = 0.04). During acute asthma, there was an intense cellular infiltrate (mean total cell count 34 x 10(6) cells.mL-1), which resolved after recovery (1.9 x 10(6) cells.mL-1) (p = 0.04). The infiltrate was heterogenous, comprising eosinophils (6.7 x 10(6) cells.mL-1), neutrophils (5.4 x 10(6) cells.mL-1) and mast cells (0.47 x 10(6) cells.mL-1). Resolution of the exacerbation was accompanied by a significant fall in eosinophils and neutrophils (p < or = 0.04). Normal saline induction of sputum can be used to assess airway inflammation in acute asthma. Children with acute asthma have intense airway inflammation that is heterogeneous and involves neutrophils, eosinophils and mast cells.

Eosinophil apoptosis and the resolution of airway inflammation in asthma.

Asthma is accompanied by the accumulation of potentially damaging eosinophils within inflamed airways. How eosinophils may be removed from the airways is not clear. The phagocytic removal of eosinophils in vitro requires that they undergo apoptosis, a form of cell death. We postulated that eosinophil apoptosis may occur in vivo, promoting the removal of airway eosinophils and the resolution of inflammation in asthma. We examined eosinophil apoptosis in sputum samples obtained from 11 subjects during an asthma exacerbation and 2 wk after corticosteroid treatment of the exacerbation. Airway function improved following corticosteroid treatment, and eosinophilic inflammation subsided, with significant decreases occurring in the number of airway eosinophils and the percentage of activated eosinophils. The proportion of apoptotic airway eosinophils increased significantly following corticosteroid treatment, and eosinophil products were apparent within macrophages. Our findings indicate that eosinophil apoptosis is clinically relevant in asthma. Apoptosis may represent a mechanism that promotes the resolution of eosinophilic inflammation in asthma.