Capture-based targeted sequencing using a T-cell control in myeloid malignancies and idiopathic cytopenias.

We report on a study of next-generation sequencing in 257 patients undergoing investigations for cytopenias. We sequenced bone marrow aspirates using a target enrichment panel comprising 82 genes and used T cells from paired blood as a control. One hundred and sixty patients had idiopathic cytopenias, 81 had myeloid malignancies and 16 had lymphoid malignancies or other diagnoses. Forty-seven of the 160 patients with idiopathic cytopenias had evidence of somatic pathogenic variants consistent with clonal cytopenias. Only 39 genes of the 82 tested were mutated in the 241 patients with either idiopathic cytopenias or myeloid neoplasms. We confirm that T cells can be used as a control to distinguish between germline and somatic variants. The use of paired analysis with a T-cell control significantly reduced the time molecular scientists spent reporting compared to unpaired analysis. We identified somatic variants of uncertain significance (VUS) in a higher proportion (24%) of patients with myeloid malignancies or clonal cytopenias compared to less than 2% of patients with non-clonal cytopenias. This suggests that somatic VUS are indicators of a clonal process. Lastly, we show that blood depleted of lymphocytes can be used in place of bone marrow as a source of material for sequencing.

Profiles of tobacco smokers and ex-smokers in a large-scale random sample survey across Wales: an unsupervised machine-learning cluster analysis.

BACKGROUND: The Welsh government recently set a target to be smoke-free by 2030, which means reducing the prevalence of tobacco smoking in adults to 5% by then. The goal is to improve health and population life expectancy. To support this strategy, we identified profile groups with different sets of socioeconomic and demographic characteristics within the population of smokers. We compared these profiles to those identified in the ex-smoker population to provide a broader understanding of smokers and inform targeting of interventions and policy. METHODS: We did a cross-sectional study using data from the National Survey for Wales. This survey is a random sample telephone survey of individuals aged 16 years and older across Wales carried out from Sept 1, 2021 to Jan 31, 2022, weighted to be representative of the Welsh population. For the smoking subgroup, we did a weighted hierarchical cluster analysis with multiple imputation to impute missing data and repeated it for ex-smokers. In total, 63 survey variables were used in the analysis. These variables included smoking history, e-cigarette use, sociodemographics, lifestyle factors, individual-level deprivation, general health and long-term conditions, mental health, and wellbeing. FINDINGS: Among the 6407 respondents (weighted proportions: 49% male, 51% female; 28% aged 16-34 years, 46% aged 35-44 years, 26% aged ≥65 years; 95% white, 5% other ethnicity), 841 (13%) smoked and 2136 (33%) were ex-smokers. Four distinctive profiles of smokers were identified, the groups were of relatively comparable size and characterised by similarities described as (1) high-risk alcohol drinkers and without children; (2) single, mostly in social housing, and poor health and mental health; (3) mostly single, younger, tried e-cigarettes, and poor mental health; (4) older couples and poor health; when comparing the groups with each other. Cluster quality and validation statistics were considered fair: silhouette coefficient=0·09, Dunn index (Dunn2)=1·06. Generally, ex-smoker clusters differed from smoking clusters because of themes related to increased sickness, better affluence, employment, and older age (≥75 years). INTERPRETATION: This study suggests that not all smokers are the same, and they do not fall into one coherent group. Smoking cessation interventions to improve the health of ageing populations might need a different approach to consider a wider context or motivations to inform targeted quitting. It is acknowledged that smoking might be underreported because of perceived social unacceptability. FUNDING: Public Health Wales.

Protease inhibitors potentiate chemotherapy-induced neutropenia.

Pharmacokinetic interactions between chemotherapy and highly active antiretroviral therapy (HAART) are described, but there are few data on their clinical relevance. Patients with systemic AIDS-related non-Hodgkin lymphoma (ARL) were treated with concomitant HAART and infusional cyclophosphamide-doxorubicin-etoposide (CDE) chemotherapy. We compared neutropenia according to whether patients received protease inhibitor (PI)-based HAART or non-PI regimens. Differences in survival, response rates, immunologic parameters, and virologic parameters were also investigated. The day-10 (Mann-Whitney U test; P = .012) and day-14 (P = .025) neutrophil counts were significantly lower in patients receiving PIs, though there were no differences in the number of days of granulocyte colony-stimulating factor (G-CSF) administered between groups (P = .16). Grade 3 or 4 infections requiring hospitalization were recorded for a total of 58 (31%) of 190 cycles of CDE: 23 (48%) of 48 when prescribed PIs and 35 (25%) of 142 with concomitant PI-sparing HAART (chi(2) test; P = .0025). There were no statistically significant differences in the response rates, relapse-free survival, or disease-free survival between patients receiving PIs and those not receiving PIs. PI-based HAART appears to significantly potentiate the myelotoxicity of CDE chemotherapy. This potentiation may be a consequence of microsomal enzyme inhibition reducing the metabolism of cytotoxics in this regimen.

The efficacy of ritonavir in the prevention of AIDS-related Kaposi's sarcoma.

Angiogenesis is thought to play a major role in the development of Kaposi's sarcoma (KS), considered by many to be a hyperplastic disorder caused in part by local production of inflammatory cytokines. The antiangiogenic effects of protease inhibitors, in particular ritonavir, have been suggested in laboratory work to lead to regression of KS, and recent data have shown the importance of ritonavir as a model of pharmaceutical development. As our clinical cohort data has shown that non-nucleoside reverse transcriptase inhibitor-based regimens are not inferior to protease inhibitor-based therapy in the prevention of KS, we investigated the specific contribution of ritonavir to chemoprevention of this AIDS-defining illness. In a logistic regression analysis, we found that ritonavir-based therapy confers no advantages compared to other regimens in the prevention of KS. This is consistent with data suggesting that regression of KS is mediated by an overall improvement in immune function and not by the effects of specific antiretrovirals.