Analytical validation of a next generation sequencing liquid biopsy assay for high sensitivity broad molecular profiling.

Circulating tumor DNA (ctDNA) analysis is being incorporated into cancer care; notably in profiling patients to guide treatment decisions. Responses to targeted therapies have been observed in patients with actionable mutations detected in plasma DNA at variant allele fractions (VAFs) below 0.5%. Highly sensitive methods are therefore required for optimal clinical use. To enable objective assessment of assay performance, detailed analytical validation is required. We developed the InVisionFirst™ assay, an assay based on enhanced tagged amplicon sequencing (eTAm-Seq™) technology to profile 36 genes commonly mutated in non-small cell lung cancer (NSCLC) and other cancer types for actionable genomic alterations in cell-free DNA. The assay has been developed to detect point mutations, indels, amplifications and gene fusions that commonly occur in NSCLC. For analytical validation, two 10mL blood tubes were collected from NSCLC patients and healthy volunteer donors. In addition, contrived samples were used to represent a wide spectrum of genetic aberrations and VAFs. Samples were analyzed by multiple operators, at different times and using different reagent Lots. Results were compared with digital PCR (dPCR). The InVisionFirst assay demonstrated an excellent limit of detection, with 99.48% sensitivity for SNVs present at VAF range 0.25%-0.33%, 92.46% sensitivity for indels at 0.25% VAF and a high rate of detection at lower frequencies while retaining high specificity (99.9997% per base). The assay also detected ALK and ROS1 gene fusions, and DNA amplifications in ERBB2, FGFR1, MET and EGFR with high sensitivity and specificity. Comparison between the InVisionFirst assay and dPCR in a series of cancer patients showed high concordance. This analytical validation demonstrated that the InVisionFirst assay is highly sensitive, specific and robust, and meets analytical requirements for clinical applications

Do cravings predict smoking cessation in smokers calling a national quit line: secondary analyses from a randomised trial for the utility of ‘urges to smoke’ measures

BACKGROUND: Single-item urges to smoke measures have been contemplated as important measures of nicotine dependence This study aimed to prospectively determine the relationships between measures of craving to smoke and smoking cessation, and compare their ability to predict cessation with the Heaviness of Smoking Index, an established measure of nicotine dependence. METHODS: We conducted a secondary analysis of data from the randomised controlled PORTSSS trial. Measures of nicotine dependence, ascertained before making a quit attempt, were the HSI, frequency of urges to smoke (FUTS) and strength of urges to smoke (SUTS). Self-reported abstinence at six months after quitting was the primary outcome measure. Multivariate logistic regression and Receiver Operating Characteristic (ROC) analysis were used to assess associations and abilities of the nicotine dependence measures to predict smoking cessation. RESULTS: Of 2,535 participants, 53.5% were female; the median (Interquartile range) age was 38 (28–50) years. Both FUTS and HSI were inversely associated with abstinence six months after quitting; for each point increase in HSI score, participants were 16% less likely to have stopped smoking (OR 0.84, 95% C.I 0.78-0.89, p < 0.0001). Compared to participants with the lowest possible FUTS scores, those with greater scores had generally lower odds of cessation (p across frequency of urges categories=0.0026). SUTS was not associated with smoking cessation. ROC analysis suggested the HSI and FUTS had similar predictive validity for cessation. CONCLUSIONS: Higher FUTS and HSI scores were inversely associated with successful smoking cessation six months after quit attempts began and both had similar validity for predicting cessation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13011-015-0011-8) contains supplementary material, which is available to authorized users

Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

We conduct a genome-wide association study (GWAS) of educational attainment (EA) in a sample of ~3 million individuals and identify 3,952 approximately uncorrelated genome-wide-significant single-nucleotide polymorphisms (SNPs). A genome-wide polygenic predictor, or polygenic index (PGI), explains 12-16% of EA variance and contributes to risk prediction for ten diseases. Direct effects (i.e., controlling for parental PGIs) explain roughly half the PGI's magnitude of association with EA and other phenotypes. The correlation between mate-pair PGIs is far too large to be consistent with phenotypic assortment alone, implying additional assortment on PGI-associated factors. In an additional GWAS of dominance deviations from the additive model, we identify no genome-wide-significant SNPs, and a separate X-chromosome additive GWAS identifies 57

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

IMechE Design Challenge 2017 outline presentation

Outline of IMechE Competitions and the 1st year UG annual Design Challenge Competition (2017) - Stephen Herd, 13 Jan'17 (6 presentation slides as 3 A4 pages - 2 slides per page) for Referenc

Dosing ketamine for pediatric procedural sedation in the emergency department

Objective: To describe intravenous ketamine dosing regimens for children requiring brief procedural sedation

Potential-Induced Pitting Corrosion of an IrO2(110)−RuO2(110)/Ru(0001)\mathrm{IrO_{2}(110)-RuO_{2}(110)/Ru(0001)} Model Electrode under Oxygen Evolution Reaction Conditions

Sophisticated $\mathrm{IrO_{2}(110)}$-based model electrodes are prepared by deposition of a 10 nm thick single-crystalline $\mathrm{IrO_{2}(110)}$ layer supported on a structure-directing $\mathrm{IrO_{2}(110)-RuO_{2}(110)/Ru(0001)}$ template, exposing a regular array of mesoscopic rooflike structures. With this model electrode together with the dedicated in situ synchrotron based techniques (SXRD, XRR) and ex situ characterization techniques (SEM, ToF-SIMS, XPS), the corrosion process of $\mathrm{IrO_{2}(110)}$ in an acidic environment (pH 0.4) is studied on different length scales. Potential-induced pitting corrosion starts at 1.48 V vs SHE and is initiated at so-called surface grain boundaries, where three rotational domains of $\mathrm{IrO_{2}(110)}$ meet. The most surprising result is, however, that even when the electrode potential is increased to 1.94 V vs SHE 60–70% of the $\mathrm{IrO_{2}}$ film still stays intact down to the mesoscale and atomic scale and no uniform thinning of the $\mathrm{IrO_{2}(110)}$ layer is encountered. Neither flat$\mathrm{IrO_{2}(110)}$ terraces nor single steps are attacked. Ultrathin single-crystalline $\mathrm{IrO_{2}(110)}$ layers seem to be much more stable to anodic corrosion than hitherto expected

Potential-Induced Pitting Corrosion of an IrO2(110)-RuO2(110)/Ru(0001) Model Electrode under Oxygen Evolution Reaction Conditions

Sophisticated IrO2(110)-based model electrodes are prepared by deposition of a 10 nm thick single-crystalline IrO2(110) layer supported on a structure-directing RuO2(110)/Ru(0001) template, exposing a regular array of mesoscopic rooflike structures. With this model electrode together with the dedicated in situ synchrotron based techniques (SXRD, XRR) and ex situ characterization techniques (SEM, ToF-SIMS, XPS), the corrosion process of IrO2(110) in an acidic environment (pH 0.4) is studied on different length scales. Potential-induced pitting corrosion starts at 1.48 V vs SHE and is initiated at so-called surface grain boundaries, where three rotational domains of IrO2(110) meet. The most surprising result is, however, that even when the electrode potential is increased to 1.94 V vs SHE 60-70% of the IrO2 film still stays intact down to the mesoscale and atomic scale and no uniform thinning of the IrO2(110) layer is encountered. Neither flat IrO2(110) terraces nor single steps are attacked. Ultrathin single-crystalline IrO2(110) layers seem to be much more stable to anodic corrosion than hitherto expected

Best practices for the use of meteorite names in publications

International audienc