Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments

Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution

Inflationary perturbation theory is geometrical optics in phase space

A pressing problem in comparing inflationary models with observation is the accurate calculation of correlation functions. One approach is to evolve them using ordinary differential equations ("transport equations"), analogous to the Schwinger-Dyson hierarchy of in-out quantum field theory. We extend this approach to the complete set of momentum space correlation functions. A formal solution can be obtained using raytracing techniques adapted from geometrical optics. We reformulate inflationary perturbation theory in this language, and show that raytracing reproduces the familiar "delta N" Taylor expansion. Our method produces ordinary differential equations which allow the Taylor coefficients to be computed efficiently. We use raytracing methods to express the gauge transformation between field fluctuations and the curvature perturbation, zeta, in geometrical terms. Using these results we give a compact expression for the nonlinear gauge-transform part of fNL in terms of the principal curvatures of uniform energy-density hypersurfaces in field space.Comment: 22 pages, plus bibliography and appendix. v2: minor changes, matches version published in JCA

Mutational and phenotypic characterisation of hereditary hemorrhagic telangiectasia

Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular dysplasia. Care delivery for HHT patients is impeded by the need for laborious, repeated phenotyping and gaps in knowledge regarding the relationships between causal DNA variants in ENG, ACVRL1, SMAD4 and GDF2, and clinical manifestations. To address this, we analyzed DNA samples from 183 previously uncharacterized, unrelated HHT and suspected HHT cases using the ThromboGenomics high-throughput sequencing platform. We identified 127 rare variants across 168 heterozygous genotypes. Applying modified American College of Medical Genetics and Genomics Guidelines, 106 variants were classified as pathogenic/likely pathogenic and 21 as nonpathogenic (variant of uncertain significance/benign). Unlike the protein products of ACVRL1 and SMAD4, the extracellular ENG amino acids are not strongly conserved. Our inferences of the functional consequences of causal variants in ENG were therefore informed by the crystal structure of endoglin. We then compared the accuracy of predictions of the causal gene blinded to the genetic data using 2 approaches: subjective clinical predictions and statistical predictions based on 8 Human Phenotype Ontology terms. Both approaches had some predictive power, but they were insufficiently accurate to be used clinically, without genetic testing. The distributions of red cell indices differed by causal gene but not sufficiently for clinical use in isolation from genetic data. We conclude that parallel sequencing of the 4 known HHT genes, multidisciplinary team review of variant calls in the context of detailed clinical information, and statistical and structural modeling improve the prognostication and treatment of HHT

Macroscopic superposition states of ultracold bosons in a double-well potential

We present a thorough description of the physical regimes for ultracold bosons in double wells, with special attention paid to macroscopic superpositions (MSs). We use a generalization of the Lipkin-Meshkov-Glick Hamiltonian of up to eight single particle modes to study these MSs, solving the Hamiltonian with a combination of numerical exact diagonalization and high-order perturbation theory. The MS is between left and right potential wells; the extreme case with all atoms simultaneously located in both wells and in only two modes is the famous NOON state, but our approach encompasses much more general MSs. Use of more single particle modes brings dimensionality into the problem, allows us to set hard limits on the use of the original two-mode LMG model commonly treated in the literature, and also introduces a new mixed Josephson-Fock regime. Higher modes introduce angular degrees of freedom and MS states with different angular properties.Comment: 15 pages, 8 figures, 1 table. Mini-review prepared for the special issue of Frontiers of Physics "Recent Progresses on Quantum Dynamics of Ultracold Atoms and Future Quantum Technologies", edited by Profs. Lee, Ueda, and Drummon

A Statistical Approach to Multifield Inflation: Many-field Perturbations Beyond Slow Roll

We study multifield contributions to the scalar power spectrum in an ensemble of six-field inflationary models obtained in string theory. We identify examples in which inflation occurs by chance, near an approximate inflection point, and we compute the primordial perturbations numerically, both exactly and using an array of truncated models. The scalar mass spectrum and the number of fluctuating fields are accurately described by a simple random matrix model. During the approach to the inflection point, bending trajectories and violations of slow roll are commonplace, and 'many-field' effects, in which three or more fields influence the perturbations, are often important. However, in a large fraction of models consistent with constraints on the tilt the signatures of multifield evolution occur on unobservably large scales. Our scenario is a concrete microphysical realization of quasi-single-field inflation, with scalar masses of order $H$, but the cubic and quartic couplings are typically too small to produce detectable non-Gaussianity. We argue that our results are characteristic of a broader class of models arising from multifield potentials that are natural in the Wilsonian sense.Comment: 39 pages, 17 figures. References added. Matches version published in JCA

Numerical evaluation of the bispectrum in multiple field inflation

We present a complete framework for numerical calculation of the power spectrum and bispectrum in canonical inflation with an arbitrary number of light or heavy fields. Our method includes all relevant effects at tree-level in the loop expansion, including (i) interference between growing and decaying modes near horizon exit; (ii) correlation and coupling between species near horizon exit and on superhorizon scales; (iii) contributions from mass terms; and (iv) all contributions from coupling to gravity. We track the evolution of each correlation function from the vacuum state through horizon exit and the superhorizon regime, with no need to match quantum and classical parts of the calculation; when integrated, our approach corresponds exactly with the tree-level Schwinger or 'in-in' formulation of quantum field theory. In this paper we give the equations necessary to evolve all two- and three-point correlation functions together with suitable initial conditions. The final formalism is suitable to compute the amplitude, shape, and scale dependence of the bispectrum in models with |fNL| of order unity or less, which are a target for future galaxy surveys such as Euclid, DESI and LSST. As an illustration we apply our framework to a number of examples, obtaining quantitatively accurate predictions for their bispectra for the first time. Two accompanying reports describe publicly-available software packages that implement the method

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project) will soon allow a broader range of SNPs to be imputed with higher accuracy, thereby increasing power. We describe a genotype imputation method (IMPUTE version 2) that is designed to address the challenges presented by these new datasets. The main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. We find that IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. We also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that IMPUTE v2 outperforms other methods in this setting at both rare and common SNPs, with overall error rates that are 15%–20% lower than those of the closest competing method. One particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of SNPs; we show that our approach to this problem has practical advantages over other suggested solutions

What is the structure of the Roper resonance?

We investigate the structure of the nucleon resonance N^*(1440) (Roper) within a coupled-channel meson exchange model for pion-nucleon scattering. The coupling to pipiN states is realized effectively by the coupling to the sigmaN, piDelta and rhoN channels. The interaction within and between these channels is derived from an effective Lagrangian based on a chirally symmetric Lagrangian, which is supplemented by well known terms for the coupling of the Delta isobar, the omega meson and the 'sigma', which is the name given here to the strong correlation of two pions in the scalar-isoscalar channel. In this model the Roper resonance can be described by meson-baryon dynamics alone; no genuine N^*(1440) (3 quark) resonance is needed in order to fit piN phase shifts and inelasticities.Comment: 55 pages, 14 figure

Extreme genetic fragility of the HIV-1 capsid

Genetic robustness, or fragility, is defined as the ability, or lack thereof, of a biological entity to maintain function in the face of mutations. Viruses that replicate via RNA intermediates exhibit high mutation rates, and robustness should be particularly advantageous to them. The capsid (CA) domain of the HIV-1 Gag protein is under strong pressure to conserve functional roles in viral assembly, maturation, uncoating, and nuclear import. However, CA is also under strong immunological pressure to diversify. Therefore, it would be particularly advantageous for CA to evolve genetic robustness. To measure the genetic robustness of HIV-1 CA, we generated a library of single amino acid substitution mutants, encompassing almost half the residues in CA. Strikingly, we found HIV-1 CA to be the most genetically fragile protein that has been analyzed using such an approach, with 70% of mutations yielding replication-defective viruses. Although CA participates in several steps in HIV-1 replication, analysis of conditionally (temperature sensitive) and constitutively non-viable mutants revealed that the biological basis for its genetic fragility was primarily the need to coordinate the accurate and efficient assembly of mature virions. All mutations that exist in naturally occurring HIV-1 subtype B populations at a frequency >3%, and were also present in the mutant library, had fitness levels that were >40% of WT. However, a substantial fraction of mutations with high fitness did not occur in natural populations, suggesting another form of selection pressure limiting variation in vivo. Additionally, known protective CTL epitopes occurred preferentially in domains of the HIV-1 CA that were even more genetically fragile than HIV-1 CA as a whole. The extreme genetic fragility of HIV-1 CA may be one reason why cell-mediated immune responses to Gag correlate with better prognosis in HIV-1 infection, and suggests that CA is a good target for therapy and vaccination strategies