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)

Genome Dynamics of Campylobacter jejuni in Response to Bacteriophage Predation

Campylobacter jejuni is a leading cause of food-borne illness. Although a natural reservoir of the pathogen is domestic poultry, the degree of genomic diversity exhibited by the species limits the application of epidemiological methods to trace specific infection sources. Bacteriophage predation is a common burden placed upon C. jejuni populations in the avian gut, and we show that amongst C. jejuni that survive bacteriophage predation in broiler chickens are bacteriophage-resistant types that display clear evidence of genomic rearrangements. These rearrangements were identified as intra-genomic inversions between Mu-like prophage DNA sequences to invert genomic segments up to 590 kb in size, the equivalent of one-third of the genome. The resulting strains exhibit three clear phenotypes: resistance to infection by virulent bacteriophage, inefficient colonisation of the broiler chicken intestine, and the production of infectious bacteriophage CampMu. These genotypes were recovered from chickens in the presence of virulent bacteriophage but not in vitro. Reintroduction of these strains into chickens in the absence of bacteriophage results in further genomic rearrangements at the same locations, leading to reversion to bacteriophage sensitivity and colonisation proficiency. These findings indicate a previously unsuspected method by which C. jejuni can generate genomic diversity associated with selective phenotypes. Genomic instability of C. jejuni in the avian gut has been adopted as a mechanism to temporarily survive bacteriophage predation and subsequent competition for resources, and would suggest that C. jejuni exists in vivo as families of related meta-genomes generated to survive local environmental pressures

Evidence for a lineage of virulent bacteriophages that target Campylobacter.

BACKGROUND: Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in such therapies is a thorough understanding of their genetic complement, genome stability and their ecology to avoid the dissemination or mobilisation of phage or bacterial virulence and toxin genes. Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism. RESULTS: Sequencing and genome analysis was performed for two Campylobacter bacteriophages. The genomes were extremely similar at the nucleotide level (> or = 96%) with most differences accounted for by novel insertion sequences, DNA methylases and an approximately 10 kb contiguous region of metabolic genes that were dissimilar at the sequence level but similar in gene function between the two phages. Both bacteriophages contained a large number of radical S-adenosylmethionine (SAM) genes, presumably involved in boosting host metabolism during infection, as well as evidence that many genes had been acquired from a wide range of bacterial species. Further bacteriophages, from the UK Campylobacter typing set, were screened for the presence of bacteriophage structural genes, DNA methylases, mobile genetic elements and regulatory genes identified from the genome sequences. The results indicate that many of these bacteriophages are related, with 10 out of 15 showing some relationship to the sequenced genomes. CONCLUSIONS: Two large virulent Campylobacter bacteriophages were found to show very high levels of sequence conservation despite separation in time and place of isolation. The bacteriophages show adaptations to their host and possess genes that may enhance Campylobacter metabolism, potentially advantaging both the bacteriophage and its host. Genetic conservation has been shown to extend to other Campylobacter bacteriophages, forming a highly conserved lineage of bacteriophages that predate upon campylobacters and indicating that highly adapted bacteriophage genomes can be stable over prolonged periods of time

Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease

The interplay of transcription factors and cis-regulatory elements (CREs) orchestrates the dynamic and diverse genetic programs that assemble the human central nervous system (CNS) during development and maintain its function throughout life. Genetic variation within CREs plays a central role in phenotypic variation in complex traits including the risk of developing disease. We took advantage of the retina, a well-characterized region of the CNS known to be affected by pathogenic variants in CREs, to establish a roadmap for characterizing regulatory variation in the human CNS. This comprehensive analysis of tissue-specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, and retinal pigment epithelium/choroid) reveals features of regulatory element evolution that shape tissue-specific gene expression programs and defines regulatory elements with the potential to contribute to Mendelian and complex disorders of human vision

Recycling manure as cow bedding: potential benefits and risks for UK dairy farms

Material obtained from physical separation of slurry (recycled manure solids; RMS) has been used as bedding for dairy cows in dry climates in the US since the 1970s. Relatively recently, the technical ability to produce drier material has led to adoption of the practice in Europe under different climatic conditions. This review collates the evidence available on benefits and risks of using RMS bedding on dairy farms, with a European context in mind. There was less evidence than expected for anecdotal claims of improved cow comfort. Among animal health risks, only udder health has received appreciable attention. There are some circumstantial reports of difficulties of maintaining udder health on RMS, but no large scale or long term studies of effects on clinical and subclinical mastitis have been published. Existing reports do not give consistent evidence of inevitable problems, nor is there any information on clinical implications for other diseases. The scientific basis for guidelines on management of RMS bedding is limited. Decisions on optimum treatment and management may present conflicts between control of different groups of organisms. There is no information on the influence that such 'recycling' of manure may have on pathogen virulence. The possibility of influence on genetic material conveying antimicrobial resistance is a concern, but little understood. Should UK or other non-US farmers adopt RMS, they are advised to do so with caution, apply the required strategies for risk mitigation, maintain strict hygiene of bed management and milking practices and closely monitor the effects on herd health

MYT1 role in the microtia-craniofacial microsomia spectrum

Q2Background: Craniofacial microsomia (CFM), also known as the oculo-auriculovertebral spectrum, comprises a variable phenotype with the most common features including microtia and mandibular hypoplasia on one or both sides, in addition to lateral oral clefts, epibulbar dermoids, cardiac, vertebral, and renal abnormalities. The etiology of CFM is largely unknown. The MYT1 gene has been reported as a candidate based in mutations found in three unrelated individuals. Additional patients with mutations in this gene are required to establish its causality. We present two individuals with CFM that have rare variants in MYT1 contributing to better understand the genotype and phenotype associated with mutations in this gene. Methods/Results: We conducted genetic analysis using whole-exome and -genome sequencing in 128 trios with CFM. Two novel MYT1 mutations were identified in two participants. Sanger sequencing was used to confirm these mutations. Conclusion: We identified two additional individuals with CFM who carry rare variants in MYT1, further supporting the presumptive role of this gene in the CFM spectrum.N/

Urban Multi-scale Environmental Predictor - an extensive tool for climate services in urban areas

The city based climate service tool UMEP (Urban Multi-scale Environmental Predictor) is a coupled modelling system that combines models essential for urban climate processes and is developed as an extensive QGIS plugin. An application is presented to illustrate its potential, specifically of the identification of heat waves and cold waves in cities. The tool has broad utility for applications related to outdoor thermal comfort, urban energy consumption, climate change mitigation etc. It includes tools to: enable users to input atmospheric and surface data from multiple sources, prepare meteorological data for use in urban areas, undertake simulations and consider scenarios, and compare and visualize different combinations of climate indicators

Urban Multi-scale Environmental Predictor (UMEP) : An integrated tool for city-based climate services

UMEP (Urban Multi-scale Environmental Predictor), a city-based climate service tool, combines models and tools essential for climate simulations. Applications are presented to illustrate UMEP's potential in the identification of heat waves and cold waves; the impact of green infrastructure on runoff; the effects of buildings on human thermal stress; solar energy production; and the impact of human activities on heat emissions. UMEP has broad utility for applications related to outdoor thermal comfort, wind, urban energy consumption and climate change mitigation. It includes tools to enable users to input atmospheric and surface data from multiple sources, to characterise the urban environment, to prepare meteorological data for use in cities, to undertake simulations and consider scenarios, and to compare and visualise different combinations of climate indicators. An open-source tool, UMEP is designed to be easily updated as new data and tools are developed, and to be accessible to researchers, decision-makers and practitioners. (C) 2017 The Authors. Published by Elsevier Ltd.Peer reviewe

Dominant-negative variant in SLC1A4 causes an autosomal dominant epilepsy syndrome.

SLC1A4 is a trimeric neutral amino acid transporter essential for shuttling L-serine from astrocytes into neurons. Individuals with biallelic variants in SLC1A4 are known to have spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM) syndrome, but individuals with heterozygous variants are not thought to have disease. We identify an 8-year-old patient with global developmental delay, spasticity, epilepsy, and microcephaly who has a de novo heterozygous three amino acid duplication in SLC1A4 (L86_M88dup). We demonstrate that L86_M88dup causes a dominant-negative N-glycosylation defect of SLC1A4, which in turn reduces the plasma membrane localization of SLC1A4 and the transport rate of SLC1A4 for L-serine