The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes

BACKGROUND: Identifying insertion/deletion polymorphisms (INDELs) with high confidence has been intrinsically challenging in short-read sequencing data. Here we report our approach for improving INDEL calling accuracy by using a machine learning algorithm to combine call sets generated with three independent methods, and by leveraging the strengths of each individual pipeline. Utilizing this approach, we generated a consensus exome INDEL call set from a large dataset generated by the 1000 Genomes Project (1000G), maximizing both the sensitivity and the specificity of the calls. RESULTS: This consensus exome INDEL call set features 7,210 INDELs, from 1,128 individuals across 13 populations included in the 1000 Genomes Phase 1 dataset, with a false discovery rate (FDR) of about 7.0%. CONCLUSIONS: In our study we further characterize the patterns and distributions of these exonic INDELs with respect to density, allele length, and site frequency spectrum, as well as the potential mutagenic mechanisms of coding INDELs in humans. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1333-7) contains supplementary material, which is available to authorized users

PS1-10afx at z = 1.388: Pan-STARRS1 Discovery of a New Type of Superluminous Supernova

We present the Pan-STARRS1 discovery of PS1-10afx, a unique hydrogen-deficient superluminous supernova (SLSN) at redshift z = 1.388. The light curve peaked at z P1 = 21.7 mag, making PS1-10afx comparable to the most luminous known SNe, with Mu = –22.3 mag. Our extensive optical and near-infrared observations indicate that the bolometric light curve of PS1-10afx rose on the unusually fast timescale of ~12 days to the extraordinary peak luminosity of 4.1 × 1044 erg s–1 (M bol = –22.8 mag) and subsequently faded rapidly. Equally important, the spectral energy distribution is unusually red for an SLSN, with a color temperature of ~6800 K near maximum light, in contrast to previous hydrogen-poor SLSNe, which are bright in the ultraviolet (UV). The spectra more closely resemble those of a normal SN Ic than any known SLSN, with a photospheric velocity of ~11, 000 km s–1 and evidence for line blanketing in the rest-frame UV. Despite the fast rise, these parameters imply a very large emitting radius (gsim 5 × 1015 cm). We demonstrate that no existing theoretical model can satisfactorily explain this combination of properties: (1) a nickel-powered light curve cannot match the combination of high peak luminosity with the fast timescale; (2) models powered by the spindown energy of a rapidly rotating magnetar predict significantly hotter and faster ejecta; and (3) models invoking shock breakout through a dense circumstellar medium cannot explain the observed spectra or color evolution. The host galaxy is well detected in pre-explosion imaging with a luminosity near L*, a star formation rate of ~15 M ☉ yr–1, and is fairly massive (~2 × 1010 M ☉), with a stellar population age of ~108 yr, also in contrast to the young dwarf hosts of known hydrogen-poor SLSNe. PS1-10afx is distinct from known examples of SLSNe in its spectra, colors, light-curve shape, and host galaxy properties, suggesting that it resulted from a different channel than other hydrogen-poor SLSNe.Astronom

The functional spectrum of low-frequency coding variation

Background Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. Results The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. Conclusions This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variatio

PS1-14bj: A Hydrogen-poor Superluminous Supernova with a Long Rise and Slow Decay.

We present photometry and spectroscopy of PS1-14bj, a hydrogen-poor superluminous supernova (SLSN) at redshift z = 0.5215 discovered in the last months of the Pan-STARRS1 Medium Deep Survey. PS1-14bj stands out by its extremely slow evolution, with an observed rise of ∼ > 125 restframe days, and exponential decline out to ∼ 250 days past peak at a measured rate of 0.01 mag day−1, consistent with fully-trapped 56Co decay. This is the longest rise time measured in a SLSN to date, and the first SLSN to show a rise time consistent with pair-instability supernova (PISN) models. Compared to other slowly-evolving SLSNe, it is spectroscopically similar to the prototype SN 2007bi at maximum light, though lower in luminosity (Lpeak ≃ 4.6×1043ergs−1) and with a flatter peak than previous events. PS1-14bj shows a number of peculiar properties, including a near-constant color temperature for > 200 days past peak, and strong emission lines from [O III] λ5007 and [O III] λ4363 with a velocity width of ∼3400 km s−1 in its late-time spectra. These both suggest there is a sustained source of heating over very long timescales, and are incompatible with a simple 56Ni-powered/PISN interpretation. A modified magnetar model including emission leakage at late times can reproduce the light curve, in which case the blue continuum and [O III] features are interpreted as material heated and ionized by the inner pulsar wind nebula becoming visible at late times. Alternatively, the late-time heating could be due to interaction with a shell of H-poor circumstellar material.Astronom

Ultra-Luminous Supernovae as a New Probe of the Interstellar Medium in Distant Galaxies

We present the Pan-STARRS1 discovery and light curves, and follow-up MMT and Gemini spectroscopy of an ultra-luminous supernova (ULSN; dubbed PS1-11bam) at a redshift of z = 1.566 with a peak brightness of MUV ≈ −22.3 mag. PS1-11bam is one of the highest redshift spectroscopically-confirmed SNe known to date. The spectrum is characterized by broad absorption features typical of previous ULSNe (e.g., C II, Si III), and by strong and narrow Mg II and Fe II absorption lines from the interstellar medium (ISM) of the host galaxy, confirmed by an [O II]λ3727 emission line at the same redshift. The equivalent widths of the Fe IIλ2600 and Mg IIλ2803 lines are in the top quartile of the quasar intervening absorption system distribution, but are weaker than those of gamma-ray burst intrinsic absorbers (i.e., GRB host galaxies). We also detect the host galaxy in pre-explosion Pan-STARRS1 data and find that its UV spectral energy distribution is best fit with a young stellar population age of τ∗ ≈ 15 − 45 Myr and a stellar mass of M∗ ≈ (1.1 − 2.6) × 109 M⊙ (for Z = 0.05 − 1 Z⊙). The star formation rate inferred from the UV continuum and [O II]λ3727 emission line is ≈ 10 M⊙ yr−1, higher than in any previous ULSN host. PS1-11bam provides the first direct demonstration that ULSNe can serve as probes of the interstellar medium in distant galaxies. At the present, the depth and red sensitivity of PS1 are uniquely suited to finding such events at cosmologically interesting redshifts (z ∼ 1 − 2); the future combination of LSST and 30-m class telescopes promises to extend this technique to z ∼ 4.Astronom

Toward Characterization of the Type IIP Supernova Progenitor Population: A Statistical Sample of Light Curves from Pan-STARRS1

In recent years, wide-field sky surveys providing deep multiband imaging have presented a new path for indirectly characterizing the progenitor populations of core-collapse supernovae (SNe): systematic light-curve studies. We assemble a set of 76 grizy-band Type IIP SN light curves from Pan-STARRS1, obtained over a constant survey program of 4 yr and classified using both spectroscopy and machine-learning-based photometric techniques. We develop and apply a new Bayesian model for the full multiband evolution of each light curve in the sample. We find no evidence of a subpopulation of fast-declining explosions (historically referred to as "Type IIL" SNe). However, we identify a highly significant relation between the plateau phase decay rate and peak luminosity among our SNe IIP. These results argue in favor of a single parameter, likely determined by initial stellar mass, predominantly controlling the explosions of red supergiants. This relation could also be applied for SN cosmology, offering a standardizable candle good to an intrinsic scatter of lesssim 0.2 mag. We compare each light curve to physical models from hydrodynamic simulations to estimate progenitor initial masses and other properties of the Pan-STARRS1 Type IIP SN sample. We show that correction of systematic discrepancies between modeled and observed SN IIP light-curve properties and an expanded grid of progenitor properties are needed to enable robust progenitor inferences from multiband light-curve samples of this kind. This work will serve as a pathfinder for photometric studies of core-collapse SNe to be conducted through future wide-field transient searches.Astronom

First results from recent JET experiments in Hydrogen and Hydrogen-Deuterium plasmas

The hydrogen campaign completed at JET in 2016 has demonstrated isotope ratio control in JET-ILW using gas puffing and pellets for fuelling, Neutral Beam Injection alone or in combination, with D/H spectroscopy as a diagnostic. The plasma properties such as confinement, L-H threshold, density limit depend on the isotope composition. The L-H transition power increases with the hydrogen concentration with a wide plateau in the range 0.2<nH/(nD+nH)<0.8. Energy confinement is significantly lower in hydrogen than in comparable deuterium ELMy H-mode plasmas, suggesting an isotope mass scaling that is stronger than in IPB98(y,2). In L-mode, the isotope dependence of confinement is weaker. The H-mode density limit in hydrogen is up to 35% lower than in heuterium, whilst it is found to be higher in L-mode. The lower ion mass leads to reduced tungsten sputtering in hydrogen plasmas. During the campaign, the nD/(nD+nH) ratio dropped to ~1% in only a few discharges after the last deliberate introduction of deuterium, although it was seen to rise again to ~2% with several seconds of exposure of the divertor tiles to ~10MW of auxiliary heating. Several ICRH scenarios were also tested in hydrogen plasmas

Systematic Uncertainties Associated with the Cosmological Analysis of the First Pan-STARRS1 Type Ia Supernova Sample

We probe the systematic uncertainties from the 113 Type Ia supernovae (SN Ia) in the Pan-STARRS1 (PS1) sample along with 197 SN Ia from a combination of low-redshift surveys. The companion paper by Rest et al. (2013) describes the photometric measurements and cosmological inferences from the PS1 sample. The largest systematic uncertainty stems from the photometric calibration of the PS1 and low-z samples. We increase the sample of observed Calspec standards from 7 to 10 used to define the PS1 calibration system. The PS1 and SDSS-II calibration systems are compared and discrepancies up to ∼ 0.02 mag are recovered. We find uncertainties in the proper way to treat intrinsic colors and reddening produce differences in the recovered value of w up to 3%. We estimate masses of host galaxies of PS1 supernovae and detect an insignificant difference in distance residuals of the full sample of 0.037±0.031 mag for host galaxies with high and low masses. Assuming flatness and including systematic uncertainties in our analysis of only SNe measurements, we find w =−1.120+0.360 −0.206(Stat)+0.269 −0.291(Sys). With additional constraints from BAO, CMB (Planck) and H0 measurements, we find w = −1.166+0.072 −0.069 and Ωm = 0.280+0.013 −0.012 (statistical and systematic errors added in quadrature). Significance of the inconsistency with w = −1 depends on whether we use Planck or WMAP measurements of the CMB: wBAO+H0+SN+WMAP = −1.124+0.083−0.065.Astronom