Quantifying single nucleotide variant detection sensitivity in exome sequencing

BACKGROUND: The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS: Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give “power estimates” for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5–15% of heterozygous and 1–4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the “missing heritability” of quantitative traits

The nonlinear time-dependent response of isotactic polypropylene

Tensile creep tests, tensile relaxation tests and a tensile test with a constant rate of strain are performed on injection-molded isotactic polypropylene at room temperature in the vicinity of the yield point. A constitutive model is derived for the time-dependent behavior of semi-crystalline polymers. A polymer is treated as an equivalent network of chains bridged by permanent junctions. The network is modelled as an ensemble of passive meso-regions (with affine nodes) and active meso-domains (where junctions slip with respect to their positions in the bulk medium with various rates). The distribution of activation energies for sliding in active meso-regions is described by a random energy model. Adjustable parameters in the stress--strain relations are found by fitting experimental data. It is demonstrated that the concentration of active meso-domains monotonically grows with strain, whereas the average potential energy for sliding of junctions and the standard deviation of activation energies suffer substantial drops at the yield point. With reference to the concept of dual population of crystalline lamellae, these changes in material parameters are attributed to transition from breakage of subsidiary (thin) lamellae in the sub-yield region to fragmentation of primary (thick) lamellae in the post-yield region of deformation.Comment: 29 pages, 12 figure

High-Accuracy X-Ray Diffraction Analysis of Phase Evolution Sequence During Devitrification of Cu50Zr50 Metallic Glass

Real-time high-energy X-ray diffraction (HEXRD) was used to investigate the crystallization kinetics and phase selection sequence for constant-heating-rate devitrification of fully amorphous Cu50Zr50, using heating rates from 10 K/min to 60 K/min (10 °C/min to 60 °C/min). In situ HEXRD patterns were obtained by the constant-rate heating of melt-spun ribbons under synchrotron radiation. High-accuracy phase identification and quantitative assessment of phase fraction evolution though the duration of the observed transformations were performed using a Rietveld refinement method. Results for 10 K/min (10 °C/min) heating show the apparent simultaneous formation of three phases, orthorhombic Cu10Zr7, tetragonal CuZr2 (C11b), and cubic CuZr (B2), at 706 K (433 °C), followed immediately by the dissolution of the CuZr (B2) phase upon continued heating to 789 K (516 °C). Continued heating results in reprecipitation of the CuZr (B2) phase at 1002 K (729 °C), with the material transforming completely to CuZr (B2) by 1045 K (772 °C). The Cu5Zr8 phase, previously reported to be a devitrification product in C50Zr50, was not observed in the present study

Identification of the first ATRIP-deficient patient and novel mutations in ATR define a clinical spectrum for ATR-ATRIP Seckel Syndrome

A homozygous mutational change in the Ataxia-Telangiectasia and RAD3 related (ATR) gene was previously reported in two related families displaying Seckel Syndrome (SS). Here, we provide the first identification of a Seckel Syndrome patient with mutations in ATRIP, the gene encoding ATR-Interacting Protein (ATRIP), the partner protein of ATR required for ATR stability and recruitment to the site of DNA damage. The patient has compound heterozygous mutations in ATRIP resulting in reduced ATRIP and ATR expression. A nonsense mutational change in one ATRIP allele results in a C-terminal truncated protein, which impairs ATR-ATRIP interaction; the other allele is abnormally spliced. We additionally describe two further unrelated patients native to the UK with the same novel, heterozygous mutations in ATR, which cause dramatically reduced ATR expression. All patient-derived cells showed defective DNA damage responses that can be attributed to impaired ATR-ATRIP function. Seckel Syndrome is characterised by microcephaly and growth delay, features also displayed by several related disorders including Majewski (microcephalic) osteodysplastic primordial dwarfism (MOPD) type II and Meier-Gorlin Syndrome (MGS). The identification of an ATRIP-deficient patient provides a novel genetic defect for Seckel Syndrome. Coupled with the identification of further ATR-deficient patients, our findings allow a spectrum of clinical features that can be ascribed to the ATR-ATRIP deficient sub-class of Seckel Syndrome. ATR-ATRIP patients are characterised by extremely severe microcephaly and growth delay, microtia (small ears), micrognathia (small and receding chin), and dental crowding. While aberrant bone development was mild in the original ATR-SS patient, some of the patients described here display skeletal abnormalities including, in one patient, small patellae, a feature characteristically observed in Meier-Gorlin Syndrome. Collectively, our analysis exposes an overlapping clinical manifestation between the disorders but allows an expanded spectrum of clinical features for ATR-ATRIP Seckel Syndrome to be define

Running With the Ball? Making a Play for Sport Heritage Archives in Higher Education Contexts

For considerable time, academia (in particular, the Humanities) has been in an intellectual, economic and pragmatic par des deux with the culture and arts sector (in this case, heritage, museums and archives). In many ways, given their respective pursuits of scientific enquiry and learning, valuable contribution to a knowledge economy, commitment to public enlightenment, and exploration of critical and creative endeavour, a relationship between the sectors makes sense. Unity notwithstanding, the relationships have become increasingly now influenced by (en)forced contextual constraints (e.g., government policy development and intervention, neoliberal market forces, structural and ideological shifts in funding acquisition and allocation, patronage changes and demands, and/or individual political priorities) (Dubuc 2011; McCall and Gray 2014; Watson 2002). Drawing on education and heritage scholarship, and theoretical frameworks of sport culture spaces (Hardy, Loy and Booth 2009; Phillips 2012; Pinson 2017), this paper examines efforts undertaken at one specific Higher Education establishment in the United Kingdom in which institutional agendas (vis-à-vis historical and cultural foci, encouraging ‘impactful’ academic activity, brand exposure, economic efficiency, and community engagement) have contoured, and become entwined with, an embryonic sport heritage and archive project. Recalling similar arrangements elsewhere (Krüger 2014; Reilly, Clayton and Hughson 2014; Reilly 2015), the aim of this case study is to explore how the wider education and cultural policy context have precipitated an increasingly symbiotic and dependent relationship between university and cultural/arts initiatives. The paper considers how the impetus to develop a sports-based (basketball) heritage archive and study centre reflects the current fragilities of the two sectors, yet, concomitantly, reveals the potentials that might be developed from fostering greater intellectual and pragmatic alliances. The paper concludes by advocating the practical, political and ideological usefulness of network formation, sustainability measures and continued cross-sector dialogue

RIP4 inhibits STAT3 signaling to sustain lung adenocarcinoma differentiation.

Loss of epithelial differentiation and extracellular matrix (ECM) remodeling are known to facilitate cancer progression and are associated with poor prognosis in patients with lung cancer. We have identified Receptor-interacting serine/threonine protein kinase 4 (RIP4) as a regulator of tumor differentiation in lung adenocarcinoma (AC). Bioinformatics analyses of human lung AC samples showed that poorly differentiated tumors express low levels of RIP4, whereas high levels are associated with better overall survival. In vitro, lung tumor cells expressing reduced RIP4 levels showed enhanced activation of STAT3 signaling and had a greater ability to invade through collagen. In contrast, overexpression of RIP4 inhibited STAT3 activation, which abrogated interleukin-6-dependent induction of lysyl oxidase, a collagen cross-linking enzyme. In an autochthonous mouse model of lung AC initiated by Kras(G12D) expression with loss of p53, Rip4 knockdown tumors progressed to a poorly differentiated state marked by an increase in Hmga2, reduced Ttf1, and enrichment of genes regulating extracellular remodeling and Jak-Stat signaling. Tail vein injections of cells overexpressing Rip4 showed a reduced potential to invade and form tumors, which was restored by co-expression of Stat3. Altogether, our work has identified that loss of RIP4 enhances STAT3 signaling in lung cancer cells, promoting the expression of ECM remodeling genes and cancer dedifferentiation

Do dividends signal future earnings in the Nordic stock markets?

We study the informational content of dividends on three Nordic civil law markets, where other simultaneous but blurring motives for dividends may be weaker. Using aggregate data on real earnings per share and payout ratios, long time series from 1969 to 2010, and methodologies which address problems of endogeneity, non-stationarity and autocorrelation (including a Vector Error Correction Model approach), we find evidence on dividend signaling in Nordic markets. However, we also find heterogeneity in the relationship between dividends and earnings on markets similar in many respects, suggesting that even small variations in the institutional surroundings may be important for the results

A Theoretical Model of Augmented Reality Acceptance in Urban Cultural Heritage Tourism

Latest mobile technologies have revolutionised the way people experience their environment. Recent research explored the opportunities of using augmented reality (AR) in order to enhance the user experience however, there is only limited research on users’ acceptance of AR in the tourism context. The technology acceptance model is the predominant theory for researching technology acceptance. Previous researchers used the approach of proposing external dimensions based on secondary literature; however missed the opportunity to integrate context specific dimensions. This paper therefore aims to propose an AR acceptance model in the context of urban heritage tourism. Five focus groups, with young British female tourists visiting Dublin and experiencing a mobile AR application, were conducted. The data were analysed using thematic analysis and revealed seven dimensions that should be incorporated into AR acceptance research including information quality, system quality, costs of use, recommendations, personal innovativeness and risk as well as facilitating conditions

Nanoscale Confinement and Fluorescence Effects of Bacterial Light Harvesting Complex LH2 in Mesoporous Silicas

Many key chemical and biochemical reactions, particularly in living cells, take place in confined space at the mesoscopic scale. Toward understanding of physicochemical nature of biomacromolecules confined in nanoscale space, in this work we have elucidated fluorescence effects of a light harvesting complex LH2 in nanoscale chemical environments. Mesoporous silicas (SBA-15 family) with different shapes and pore sizes were synthesized and used to create nanoscale biomimetic environments for molecular confinement of LH2. A combination of UV-vis absorption, wide-field fluorescence microscopy, and in situ ellipsometry supports that the LH2 complexes are located inside the silica nanopores. Systematic fluorescence effects were observed and depend on degree of space confinement. In particular, the temperature dependence of the steady-state fluorescence spectra was analyzed in detail using condensed matter band shape theories. Systematic electronic-vibrational coupling differences in the LH2 transitions between the free and confined states are found, most likely responsible for the fluorescence effects experimentally observed