Population-based germline breast cancer gene association studies and meta-analysis to inform wider mainstream testing.

BACKGROUND: Germline genetic testing, previously restricted to familial and young-onset breast cancer, is now offered increasingly broadly to patients with 'population-type' breast cancer in mainstream oncology clinics, with wide variation in the genes included. PATIENTS AND METHODS: Weighted meta-analysis was carried out for three population-based case-control studies (BRIDGES, CARRIERS and UK Biobank) comprising in total 101 397 women with breast cancer and 312 944 women without breast cancer, to quantify 37 putative breast cancer susceptibility genes (BCSGs) for the frequency of pathogenic variants (PVs) in unselected, 'population-type' breast cancer cases and their association with breast cancer and its subtypes. RESULTS: Meta-analysed odds ratios (ORs) and frequencies of PVs in 'population-type' breast cancer cases were generated for BRCA1 (OR 8.73, 95% confidence interval (CI) 7.47-10.20; 1 in 101), BRCA2 (OR 5.68, 95% CI 5.13-6.30; 1 in 68) and PALB2 (OR 4.30, 95% CI 3.68-5.03; 1 in 187). For both CHEK2 (OR 2.40, 95% CI 2.21-2.62; 1 in 73) and ATM (OR 2.16, 95% CI 1.93-2.41; 1 in 132) subgroup analysis showed a stronger association with oestrogen receptor-positive disease. The magnitude of association and frequency of PVs were low for RAD51C (OR 1.53, 95% CI 1.29-2.04; 1 in 913), RAD51D (OR 1.76, 95% CI 1.29-2.41; 1 in 1079) and BARD1 (OR 2.34, 95% CI 1.85-2.97; 1 in 672); frequencies and associations were higher when the analysis was restricted to triple-negative breast cancers. The PV frequency in 'population-type' breast cancer cases was very low for 'syndromic' BCSGs TP53 (1 in 1844), STK11 (1 in 11 525), CDH1 (1 in 2668), PTEN (1 in 3755) and NF1 (1 in 1470), with metrics of association also modest ranging from OR 3.62 (95% CI 1.98-6.61) for TP53 down to OR 1.60 (95% CI 0.48-5.30) for STK11. CONCLUSIONS: These metrics reflecting 'population-type' breast cancer will be informative in defining the appropriate gene set as we continue to expand to germline testing to an increasingly unselected group of breast cancer cases.

Discovering Quantum Phase Transitions with Fermionic Neural Networks.

Deep neural networks have been very successful as highly accurate wave function Ansätze for variational Monte Carlo calculations of molecular ground states. We present an extension of one such Ansatz, FermiNet, to calculations of the ground states of periodic Hamiltonians, and study the homogeneous electron gas. FermiNet calculations of the ground-state energies of small electron gas systems are in excellent agreement with previous initiator full configuration interaction quantum Monte Carlo and diffusion Monte Carlo calculations. We investigate the spin-polarized homogeneous electron gas and demonstrate that the same neural network architecture is capable of accurately representing both the delocalized Fermi liquid state and the localized Wigner crystal state. The network converges on the translationally invariant ground state at high density and spontaneously breaks the symmetry to produce the crystalline ground state at low density, despite being given no a priori knowledge that a phase transition exists.

Estimating anisotropy directly via neural timeseries.

An isotropic dynamical system is one that looks the same in every direction, i.e., if we imagine standing somewhere within an isotropic system, we would not be able to differentiate between different lines of sight. Conversely, anisotropy is a measure of the extent to which a system deviates from perfect isotropy, with larger values indicating greater discrepancies between the structure of the system along its axes. Here, we derive the form of a generalised scalable (mechanically similar) discretized field theoretic Lagrangian that allows for levels of anisotropy to be directly estimated via timeseries of arbitrary dimensionality. We generate synthetic data for both isotropic and anisotropic systems and, by using Bayesian model inversion and reduction, show that we can discriminate between the two datasets - thereby demonstrating proof of principle. We then apply this methodology to murine calcium imaging data collected in rest and task states, showing that anisotropy can be estimated directly from different brain states and cortical regions in an empirical in vivo biological setting. We hope that this theoretical foundation, together with the methodology and publicly available MATLAB code, will provide an accessible way for researchers to obtain new insight into the structural organization of neural systems in terms of how scalable neural regions grow - both ontogenetically during the development of an individual organism, as well as phylogenetically across species.

Quasiparticle Effective Mass of the Three-Dimensional Fermi Liquid by Quantum Monte Carlo.

According to Landau's Fermi liquid theory, the main properties of the quasiparticle excitations of an electron gas are embodied in the effective mass m^{*}, which determines the energy of a single quasiparticle, and the Landau interaction function, which indicates how the energy of a quasiparticle is modified by the presence of other quasiparticles. This simple paradigm underlies most of our current understanding of the physical and chemical behavior of metallic systems. The quasiparticle effective mass of the three-dimensional homogeneous electron gas has been the subject of theoretical controversy, and there is a lack of experimental data. In this Letter, we deploy diffusion Monte Carlo (DMC) methods to calculate m^{*} as a function of density for paramagnetic and ferromagnetic three-dimensional homogeneous electron gases. The DMC results indicate that m^{*} decreases when the density is reduced, especially in the ferromagnetic case. The DMC quasiparticle energy bands exclude the possibility of a reduction in the occupied bandwidth relative to that of the free-electron model at density parameter r_{s}=4, which corresponds to Na metal.

Conservation laws by virtue of scale symmetries in neural systems.

In contrast to the symmetries of translation in space, rotation in space, and translation in time, the known laws of physics are not universally invariant under transformation of scale. However, a special case exists in which the action is scale invariant if it satisfies the following two constraints: 1) it must depend upon a scale-free Lagrangian, and 2) the Lagrangian must change under scale in the same way as the inverse time, [Formula: see text]. Our contribution lies in the derivation of a generalised Lagrangian, in the form of a power series expansion, that satisfies these constraints. This generalised Lagrangian furnishes a normal form for dynamic causal models-state space models based upon differential equations-that can be used to distinguish scale symmetry from scale freeness in empirical data. We establish face validity with an analysis of simulated data, in which we show how scale symmetry can be identified and how the associated conserved quantities can be estimated in neuronal time series.

The microscopic Einstein-de Haas effect.

The Einstein-de Haas (EdH) effect, where the spin angular momentum of electrons is transferred to the mechanical angular momentum of atoms, was established experimentally in 1915. While a semiclassical explanation of the effect exists, modern electronic structure methods have not yet been applied to model the phenomenon. In this paper, we investigate its microscopic origins by means of a noncollinear tight-binding model of an O2 dimer, which includes the effects of spin-orbit coupling, coupling to an external magnetic field, and vector Stoner exchange. By varying an external magnetic field in the presence of spin-orbit coupling, a torque can be generated on the dimer, validating the presence of the EdH effect. The avoided energy level crossings and the rate of change of magnetic field determine the evolution of the spin. We also find that the torque exerted on the nuclei by the electrons in a time-varying B field is not only due to the EdH effect. The other contributions arise from field-induced changes in the electronic orbital angular momentum and from the direct action of the Faraday electric field associated with the time-varying magnetic field.

The risk of breast cancer in BRCA1 and BRCA2 mutation carriers without a first-degree relative with breast cancer.

The objective of this study was to estimate the lifetime risk of breast cancer in women with a BRCA1 or BRCA2 mutation with and without at least 1 first-degree relative with breast cancer. A total of 2835 women with a BRCA1 or BRCA2 mutation were followed. Age- and gene-specific breast cancer rates were calculated. The relative risks of breast cancer for subjects with a family history of breast cancer, compared to no family history were calculated. The mean age at baseline was 41.1 years, and they were followed for a mean of 6.0 years. The estimated penetrance of breast cancer to age 80 years was 60.8% for BRCA1 and 63.1% for BRCA2. For all BRCA carriers, the penetrance of breast cancer to age 80 for those with no first-degree relative with breast cancer was 60.4% and 63.3% for those with at least 1 first-degree relative with breast cancer. The risk of breast cancer for BRCA carriers with no first-degree relative with breast cancer is substantial, and as a result, clinical management for these women should be the same as those for women with an affected relative.

Breast cancer in systemic lupus erythematosus (SLE): receptor status and treatment.

Objective There is a decreased risk of breast cancer in systemic lupus erythematosus (SLE) versus the general population; little is known regarding the receptor status of breast cancers in SLE, or treatment. Methods Breast cancer cases occurring after SLE diagnosis were ascertained through linkage with tumor registries. We determined breast cancer positivity for estrogen receptors (ER), progesterone receptors (PR), and/or Human Epidermal Growth Factor Receptor 2 (HER2), as well as cancer treatment. Results We obtained information on ER, PR, and/or HER2 status for 63 SLE patients with breast cancer. Fifty-three had information on ER and/or PR status; 36 of these (69%) were ER positive. Thirty-six of the 63 had information on HER2 status; of these, 26 had complete information on all three receptors. Twenty-one of these 26 (81%) were HER2 negative; seven of 26(27%) were triple negative. All but one patient underwent surgery; 11.5% received both non-tamoxifen chemotherapy and radiotherapy, 16.4% radiotherapy without non-tamoxifen chemotherapy, and 14.7% received non-tamoxifen chemotherapy without radiotherapy. Conclusion ER positivity was similar to historical general population figures, with a trend toward a higher proportion of triple-negative breast cancers in SLE (possibly reflecting the relatively young age of our SLE patients).

Oncogenic role of PDK4 in human colon cancer cells.

BACKGROUND: Cancer cells maintain high rates of glycolysis. Pyruvate dehydrogenase kinases (PDK) contribute to this phenomenon, which favours apoptosis resistance and cellular transformation. We previously reported upregulation of PDK4 in normal mucosa of colorectal cancer (CRC) patients compared with controls and in preneoplastic intestine of our mouse model. Decreased methylation of four consecutive PDK4 CpGs was observed in normal mucosa of patients. Although other members of the PDK family have been investigated for transformation potential, PDK4 has not been extensively studied. METHODS: PDK4 methylation in blood of CRC patients and controls was evaluated by pyrosequencing. PDK4 expression in human colon carcinoma cells was down-regulated by RNAi. Cellular migration and invasion, apoptosis and qRT-PCR of key genes were assessed. RESULTS: Pyrosequencing revealed decreased methylation of the same four consecutive CpGs in the blood of patients compared with controls. Cellular migration and invasion were reduced and apoptosis was increased following transient or stable inhibition of PDK4. Expression of vimentin, HIF-1 and VEGFA was reduced. CONCLUSIONS: These studies demonstrate the involvement of PDK4 in transformation. Methylation assessment of PDK4 in the blood may be useful for non-invasive CRC detection. PDK4 should be considered as a target for development of anticancer strategies and therapies.

Ab initio Exchange-Correlation Free Energy of the Uniform Electron Gas at Warm Dense Matter Conditions.

In a recent Letter [T. Dornheim et al., Phys. Rev. Lett. 117, 156403 (2016)PRLTAO0031-900710.1103/PhysRevLett.117.156403], we presented the first quantum Monte Carlo (QMC) results for the warm dense electron gas in the thermodynamic limit. However, a complete parametrization of the exchange-correlation free energy with respect to density, temperature, and spin polarization remained out of reach due to the absence of (i) accurate QMC results below θ=k_{B}T/E_{F}=0.5 and (ii) QMC results for spin polarizations different from the paramagnetic case. Here we overcome both remaining limitations. By closing the gap to the ground state and by performing extensive QMC simulations for different spin polarizations, we are able to obtain the first completely ab initio exchange-correlation free energy functional; the accuracy achieved is an unprecedented ∼0.3%. This also allows us to quantify the accuracy and systematic errors of various previous approximate functionals.

Breast cancer in systemic lupus.

Objective There is a decreased breast cancer risk in systemic lupus erythematosus (SLE) versus the general population. We assessed a large sample of SLE patients, evaluating demographic and clinical characteristics and breast cancer risk. Methods We performed case-cohort analyses within a multi-center international SLE sample. We calculated the breast cancer hazard ratio (HR) in female SLE patients, relative to demographics, reproductive history, family history of breast cancer, and time-dependent measures of anti-dsDNA positivity, cumulative disease activity, and drugs, adjusted for SLE duration. Results There were 86 SLE breast cancers and 4498 female SLE cancer-free controls. Patients were followed on average for 7.6 years. Versus controls, SLE breast cancer cases tended to be white and older. Breast cancer cases were similar to controls regarding anti-dsDNA positivity, disease activity, and most drug exposures over time. In univariate and multivariate models, the principal factor associated with breast cancers was older age at cohort entry. Conclusions There was little evidence that breast cancer risk in this SLE sample was strongly driven by any of the clinical factors that we studied. Further search for factors that determine the lower risk of breast cancer in SLE may be warranted.

No evidence of excessive cancer screening in female noncarriers from BRCA1/2 mutation-positive families.

BACKGROUND: In families with a proven BRCA1/2 mutation, women not carrying the familial mutation should follow the cancer screening recommendations applying to women in the general population. In the present study, we evaluated the cancer screening practices of unaffected noncarriers from families with a proven BRCA mutation, and we assessed the role of family history in their screening practices. METHODS: Self-report data were provided retrospectively by 220 unaffected female noncarriers for periods of up to 10 years (mean: 4.3 years) since disclosure of their BRCA1/2 genetic test result. A ratio for the annual frequency of breast and ovarian cancer screening exams (mammography, breast ultrasonography, breast magnetic resonance imaging, transvaginal or pelvic ultrasound, cancer antigen 125 testing) was calculated as number of screening exams divided by the number of years in the individual observation period. RESULTS: The annual average for mammography exams was 0.15, 0.4, 0.56, and 0.71 in women 30-39, 40-49, 50-59, and 60-69 years of age respectively. The uptake of other breast and ovarian cancer screening exams was very low. Mammography and breast ultrasonography and magnetic resonance imaging were generally more frequent among participants with at least 1 first-degree relative affected by breast cancer. CONCLUSIONS: In most noncarriers, screening practices are consistent with the guidelines concerning women in the general population. When noncarriers adopt screening behaviours that are different from those that would be expected for average-risk women, those behaviours are influenced by their familial cancer history. IMPACT: Decision tools might help female noncarriers to be involved in their follow-up in accordance with their genetic status and their family history, while taking into account the benefits and disadvantages of cancer screening.

Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit.

We perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N=1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F_{xc} of the macroscopic electron gas with an unprecedented accuracy of |ΔV|/|V|,|ΔF_{xc}|/|F|_{xc}∼10^{-3}. A comparison of our new data to the recent parametrization of F_{xc} by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.

Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas.

The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N-body density matrices for uniform electron gas systems of up to 10^{124} matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k-space configuration path-integral formalism disagree by up to ∼10% at certain reduced temperatures T/T_{F}≤0.5 and densities r_{s}≤1. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T/T_{F}≥1 and r_{s}≤2.

Electron Elevator: Excitations across the Band Gap via a Dynamical Gap State.

We use time-dependent density functional theory to study self-irradiated Si. We calculate the electronic stopping power of Si in Si by evaluating the energy transferred to the electrons per unit path length by an ion of kinetic energy from 1 eV to 100 keV moving through the host. Electronic stopping is found to be significant below the threshold velocity normally identified with transitions across the band gap. A structured crossover at low velocity exists in place of a hard threshold. An analysis of the time dependence of the transition rates using coupled linear rate equations enables one of the excitation mechanisms to be clearly identified: a defect state induced in the gap by the moving ion acts like an elevator and carries electrons across the band gap.

Recommendations on breast cancer screening and prevention in the context of implementing risk stratification: impending changes to current policies.

In recent years, risk stratification has sparked interest as an innovative approach to disease screening and prevention. The approach effectively personalizes individual risk, opening the way to screening and prevention interventions that are adapted to subpopulations. The international perspective project, which is developing risk stratification for breast cancer, aims to support the integration of its screening approach into clinical practice through comprehensive tool-building. Policies and guidelines for risk stratification-unlike those for population screening programs, which are currently well regulated-are still under development. Indeed, the development of guidelines for risk stratification reflects the translational aspects of perspective. Here, we describe the risk stratification process that was devised in the context of perspective, and we then explain the consensus-based method used to develop recommendations for breast cancer screening and prevention in a risk-stratification approach. Lastly, we discuss how the recommendations might affect current screening policies.

Characterization of a novel founder MSH6 mutation causing Lynch syndrome in the French Canadian population.

We identified an MSH6 mutation (c.10C>T, p.Gln4*) causing Lynch syndrome (LS) in 11 French Canadian (FC) families from the Canadian province of Quebec. We aimed to investigate the molecular and clinical implications of this mutation among FC carriers and to assess its putative founder origin. We studied 11 probands and 27 family members. Additionally 6433 newborns, 187 colorectal cancer (CRC) cases, 381 endometrial cancer (EC) cases and 179 additional controls, all of them from Quebec, were used. Found in approximately 1 of 400 newborns, the mutation is one of the most common LS mutations described. We have found that this mutation confers a greater risk for EC than for CRC, both in the 11 studied families and in the unselected cases: EC [odds ratio (OR) = 7.5, p < 0.0001] and CRC (OR = 2.2, p = 0.46). Haplotype analyses showed that the mutation arose in a common ancestor, probably around 430-656 years ago, coinciding with the arrival of the first French settlers. Application of the results of this study could significantly improve the molecular testing and clinical management of LS families in Quebec.

Systematic study of finite-size effects in quantum Monte Carlo calculations of real metallic systems.

We present a systematic and comprehensive study of finite-size effects in diffusion quantum Monte Carlo calculations of metals. Several previously introduced schemes for correcting finite-size errors are compared for accuracy and efficiency, and practical improvements are introduced. In particular, we test a simple but efficient method of finite-size correction based on an accurate combination of twist averaging and density functional theory. Our diffusion quantum Monte Carlo results for lithium and aluminum, as examples of metallic systems, demonstrate excellent agreement between all of the approaches considered.

Free-energy coarse-grained potential for C60.

We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C60. Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures.

Interaction picture density matrix quantum Monte Carlo.

The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N-body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.