A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

Economic performance of small ruminants to smallholder farmers in Climate Smart Villages of Nyando

Small ruminant production forms an integral part of the livelihoods of smallholder farmers in Nyando. This paper is part of a study to evaluate the impacts of the small ruminants on the incomes of smallholder farmers adopting “Climate Smart” agricultural practices in the counties of Kericho and Kisumu in Nyando. A cross-sectional survey involving 162 households was conducted in 2018 to elicit information on farmer demographic characteristics, resource endowment, flock dynamics, and revenues from small ruminant production. Results from the analyses of the data collated showed that the small ruminants are an important source of revenue for the smallholder farmers. The number of animals owned varied depending on the size of the land owned. Farmers in Kericho tended to have larger land holdings than in Kisumu (p<0.01) with concurrently larger flock sizes. The farmers however did not have any information on the optimal number of animals that they should keep on their land. In both counties, better prices were received for larger mature animals than for immature animals. The farmers also tended to sell more female than male animals although they stated that the sale of animals was dependent on the availability of the animals and the anticipated returns. Information on the optimal number of animals to rear with specific resources available is needed for the farmers to be able to continually produce and market sheep and goats at a good price

Do rural migrants 'float' in urban China? Neighbouring and neighbourhood sentiment in Beijing

Urban China reached 50% of the nation’s population by 2010, mainly as a result of massive rural–urban migration. There is substantial evidence of their social marginality in terms of occupational and housing opportunities. Here we ask about their incorporation into the neighbourhoods where they live. Rural migrants are called the ‘floating population’ in China, suggesting that their residence in the city is only temporary and that they are unlikely to develop strong local ties. This study contrasts the neighbourhood socialising of migrant tenants with that of urban homeowners who were born in the city. It draws on original survey research in Beijing that included questions on relations with neighbours and neighbourhood sentiment. It is found that migrants are more likely to engage in socialising and exchange of help with neighbours, and consequently their neighbouring helps strengthen their sentiment towards the neighbourhoods where they live. It is argued that contemporary social changes – including rising education and homeownership – may actually reduce neighbouring, while rural migrants’ marginality makes them more dependent on their local social network

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia.

In acute myeloid leukaemia (AML), the cell of origin, nature and biological consequences of initiating lesions, and order of subsequent mutations remain poorly understood, as AML is typically diagnosed without observation of a pre-leukaemic phase. Here, highly purified haematopoietic stem cells (HSCs), progenitor and mature cell fractions from the blood of AML patients were found to contain recurrent DNMT3A mutations (DNMT3A(mut)) at high allele frequency, but without coincident NPM1 mutations (NPM1c) present in AML blasts. DNMT3A(mut)-bearing HSCs showed a multilineage repopulation advantage over non-mutated HSCs in xenografts, establishing their identity as pre-leukaemic HSCs. Pre-leukaemic HSCs were found in remission samples, indicating that they survive chemotherapy. Therefore DNMT3A(mut) arises early in AML evolution, probably in HSCs, leading to a clonally expanded pool of pre-leukaemic HSCs from which AML evolves. Our findings provide a paradigm for the detection and treatment of pre-leukaemic clones before the acquisition of additional genetic lesions engenders greater therapeutic resistance

Balloon Pulmonary Angioplasty: State of the Art

Balloon pulmonary angioplasty (BPA) is a novel technique for the treatment of chronic thromboembolic pulmonary hypertension. While cardiologists need no introduction to the concept of balloon angioplasty, BPA has its own particular challenges. This article aims to provide the reader with an overview of BPA, starting with an introduction to chronic thromboembolic disease (CTED), the standard management of chronic thromboembolic pulmonary hypertension (CTEPH), technical challenges faced when performing BPA and the evidence base supporting its use. The second part of the article will focus on the future of BPA, in particular the areas where research is required to establish an evidence base to justify the role of BPA in CTEPH and CTED treatment

Double valve replacement for acute spontaneous left chordal rupture secondary to chronic aortic incompetence

A 54 years old male with undiagnosed chronic calcific degenerative aortic valve incompetence presented with acute left anterior chordae tendinae rupture resulting in severe left heart failure and cardiogenic shock. He was successfully treated with emergency double valve replacement using mechanical valves. The pathogenesis of acute rupture of the anterior chordae tendinae, without any evidence of infective endocarditis or ischemic heart disease seems to have been attrition of the subvalvular mitral apparatus by the chronic regurgitant jet of aortic incompetence with chronic volume overload. We review the literature with specific focus on the occurrence of this unusual event

Human Colon Microbiota Transform Polycyclic Aromatic Hydrocarbons to Estrogenic Metabolites

Ingestion is an important exposure route for polycyclic aromatic hydrocarbons (PAHs) to enter the human body. Although the formation of hazardous PAH metabolites by human biotransformation enzymes is well documented, nothing is known about the PAH transformation potency of human intestinal microbiota. Using a gastrointestinal simulator, we show that human intestinal microbiota can also bioactivate PAHs, more in particular to estrogenic metabolites. PAH compounds are not estrogenic, and indeed, stomach and small intestine digestions of 62.5 nmol naphthalene, phenanthrene, pyrene, and benzo(a)pyrene showed no estrogenic effects in the human estrogen receptor bioassay. In contrast, colon digests of these PAH compounds displayed estrogenicity, equivalent to 0.31, 2.14, 2.70, and 1.48 nmol 17α-ethynylestradiol (EE2), respectively. Inactivating the colon microbiota eliminated these estrogenic effects. Liquid chromatography–mass spectrometry analysis confirmed the microbial PAH transformation by the detection of PAH metabolites 1-hydroxypyrene and 7-hydroxybenzo(a)pyrene in colon digests of pyrene and benzo(a)pyrene. Furthermore, we show that colon digests of a PAH-contaminated soil (simulated ingestion dose of 5 g/day) displayed estrogenic activity equivalent to 0.58 nmol EE2, whereas stomach or small intestine digests did not. Although the matrix in which PAHs are ingested may result in lower exposure concentrations in the gut, our results imply that the PAH bioactivation potency of colon microbiota is not eliminated by the presence of soil. Moreover, because PAH toxicity is also linked to estrogenicity of the compounds, the PAH bioactivation potency of colon microbiota suggests that current risk assessment may underestimate the risk from ingested PAHs