A harmonized public resource of deeply sequenced diverse human genomes.

Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from 80 populations in the HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftOver and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.

A harmonized public resource of deeply sequenced diverse human genomes.

Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.

Comprehensive metagenomic analysis of blastic plasmacytoid dendritic cell neoplasm.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a hematologic malignancy believed to originate from plasmacytoid dendritic cells (pDCs), the immune cells responsible for producing type 1 interferons during infection. Nearly all patients with BPDCN have prominent skin involvement, with cutaneous infiltration occupying the dermis and subcutis. One half of patients present with BPDCN cells only in the skin, with no evidence of disease elsewhere. Because normal pDCs are rare or absent in cutaneous sites, and they only traffic to the skin after activation by pathogen or inflammation, our aim was to determine if a microorganism is associated with BPDCN. We performed RNA sequencing in BPDCN skin and bone marrow, with cutaneous T-cell lymphoma (CTCL) and normal skin as controls. GATK-PathSeq was used to identify known microbial sequences. Bacterial reads in BPDCN skin were components of normal flora and did not distinguish BPDCN from controls. We then developed a new computational tool, virID (Viral Identification and Discovery; https://github.com/jnoms/virID), for identification of microbial-associated reads remaining unassigned after GATK-PathSeq. We found no evidence for a known or novel virus in BPDCN skin or bone marrow, despite confirming that virID could identify Merkel cell polyomavirus in Merkel cell carcinoma, human papillomavirus in head and neck squamous cell carcinoma, and Kaposi's sarcoma herpesvirus in Kaposi's sarcoma in a blinded fashion. Thus, at the level of sensitivity used here, we found no clear pathogen linked to BPDCN.

GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts.

Summary: We present an updated version of our computational pipeline, PathSeq, for the discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaryotic hosts. This pipeline is available in the Genome Analysis Toolkit (GATK) as a suite of configurable tools that can report the microbial composition of DNA or RNA short-read sequencing samples and identify unknown sequences for downstream assembly of novel organisms. GATK PathSeq enables sample analysis in minutes at low cost. In addition, these tools are built with the GATK engine and Apache Spark framework, providing robust, rapid parallelization of read quality filtering, host subtraction and microbial alignment in workstation, cluster and cloud environments. Availability and implementation: These tools are available as a part of the GATK at https://github.com/broadinstitute/gatk. Supplementary information: Supplementary data are available at Bioinformatics online.

Not quite type 1 or type 2, what now? Review of monogenic, mitochondrial, and syndromic diabetes.

Diabetes mellitus is a heterogeneous group of conditions defined by resultant chronic hyperglycemia. Given the increasing prevalence of diabetes mellitus and the increasing understanding of genetic etiologies, we present a broad review of rare genetic forms of diabetes that have differing diagnostic and/or treatment implications from type 1 and type 2 diabetes. Advances in understanding the genotype-phenotype associations in these rare forms of diabetes offer clinically available examples of evolving precision medicine where defining the correct genetic etiology can radically alter treatment approaches. In this review, we focus on forms of monogenic diabetes, mitochondrial diabetes, and syndromic diabetes.

Knowledge about Age-Related Decline in Fertility and Oocyte Cryopreservation: A National Survey.

CONTEXT: Women worldwide are delaying childbearing, but are they aware of the age-related decline in fertility? AIMS: The aim of this study is to investigate awareness of age-related decline in fertility and oocyte cryopreservation. SETTINGS AND DESIGN: A primary analysis of a cross-sectional electronic survey with a nationally representative sample of nulliparous women aged 25-45 years. SUBJECTS AND METHODS: A national online survey performed March 4-March 9, 2016. STATISTICAL ANALYSIS USED: A linear regression model and ANOVA tests were performed. RESULTS: A total of 1213 women completed the survey. A significant difference was discovered in fecundity knowledge between women who identified as in a partnership compared to those who did not. Partnered women were more likely to respond "know a lot" about the age-related decline in fertility, whereas unpartnered women were more likely to respond "never heard of it" (P < 0.01). Partnered women are also more likely to respond that they would have made different life choices had they been more knowledgeable about fertility at a younger age (P = 0.01). The majority of the survey population had heard of oocyte cryopreservation but did not know much about it. CONCLUSIONS: Slightly over half of participants had an understanding of the natural age-related decline in fertility. Having a partner significantly increased the likelihood that a woman reported more knowledge about fertility. More effort is necessary to educate all women on assisted reproductive technologies and the natural age-related decline in fertility, specifically single women of childbearing age.

Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue.

Ectopic heartbeats can trigger reentrant arrhythmias, leading to ventricular fibrillation and sudden cardiac death. Such events have been attributed to perturbed Ca2+ handling in cardiac myocytes leading to spontaneous Ca2+ release and delayed afterdepolarizations (DADs). However, the ways in which perturbation of specific molecular mechanisms alters the probability of ectopic beats is not understood. We present a multiscale model of cardiac tissue incorporating a biophysically detailed three-dimensional model of the ventricular myocyte. This model reproduces realistic Ca2+ waves and DADs driven by stochastic Ca2+ release channel (RyR) gating and is used to study mechanisms of DAD variability. In agreement with previous experimental and modeling studies, key factors influencing the distribution of DAD amplitude and timing include cytosolic and sarcoplasmic reticulum Ca2+ concentrations, inwardly rectifying potassium current (IK1) density, and gap junction conductance. The cardiac tissue model is used to investigate how random RyR gating gives rise to probabilistic triggered activity in a one-dimensional myocyte tissue model. A novel spatial-average filtering method for estimating the probability of extreme (i.e. rare, high-amplitude) stochastic events from a limited set of spontaneous Ca2+ release profiles is presented. These events occur when randomly organized clusters of cells exhibit synchronized, high amplitude Ca2+ release flux. It is shown how reduced IK1 density and gap junction coupling, as observed in heart failure, increase the probability of extreme DADs by multiple orders of magnitude. This method enables prediction of arrhythmia likelihood and its modulation by alterations of other cellular mechanisms.

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca(2+) spark that requires supercomputing resources for execution. We also present tools for simulating models encoded in the SBML and CellML model description languages, thus demonstrating how Galaxy's reproducible research features can be leveraged by existing technologies. Finally, we demonstrate how the Galaxy workflow editor can be used to compose integrative models from constituent submodules. This work represents an important novel approach, to our knowledge, to making computational simulations more accessible to the broader scientific community.

Real-time detection of an extreme scattering event: Constraints on Galactic plasma lenses.

Extreme scattering events (ESEs) are distinctive fluctuations in the brightness of astronomical radio sources caused by occulting plasma lenses in the interstellar medium. The inferred plasma pressures of the lenses are ~10(3) times the ambient pressure, challenging our understanding of gas conditions in the Milky Way. Using a new survey technique, we discovered an ESE while it was in progress. Here we report radio and optical follow-up observations. Modeling of the radio data demonstrates that the lensing structure is a density enhancement and the lens is diverging, ruling out one of two competing physical models. Our technique will uncover many more ESEs, addressing a long-standing mystery of the small-scale gas structure of our Galaxy.

Modeling calcium regulation of contraction, energetics, signaling, and transcription in the cardiac myocyte.

Calcium (Ca(2+)) plays many important regulatory roles in cardiac muscle cells. In the initial phase of the action potential, influx of Ca(2+) through sarcolemmal voltage-gated L-type Ca(2+) channels (LCCs) acts as a feed-forward signal that triggers a large release of Ca(2+) from the junctional sarcoplasmic reticulum (SR). This Ca(2+) drives heart muscle contraction and pumping of blood in a process known as excitation-contraction coupling (ECC). Triggered and released Ca(2+) also feed back to inactivate LCCs, attenuating the triggered Ca(2+) signal once release has been achieved. The process of ECC consumes large amounts of ATP. It is now clear that in a process known as excitation-energetics coupling, Ca(2+) signals exert beat-to-beat regulation of mitochondrial ATP production that closely couples energy production with demand. This occurs through transport of Ca(2+) into mitochondria, where it regulates enzymes of the tricarboxylic acid cycle. In excitation-signaling coupling, Ca(2+) activates a number of signaling pathways in a feed-forward manner. Through effects on their target proteins, these interconnected pathways regulate Ca(2+) signals in complex ways to control electrical excitability and contractility of heart muscle. In a process known as excitation-transcription coupling, Ca(2+) acting primarily through signal transduction pathways also regulates the process of gene transcription. Because of these diverse and complex roles, experimentally based mechanistic computational models are proving to be very useful for understanding Ca(2+) signaling in the cardiac myocyte.

On the Adjacency Matrix of RyR2 Cluster Structures.

In the heart, electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells. This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors (RyR2). Their openings cause cell-wide release of Ca2+, which in turn causes muscle contraction and the generation of the mechanical force required to pump blood. In resting myocytes, RyR2s can also open spontaneously giving rise to spatially-confined Ca2+ release events known as "sparks." RyR2s are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. Our recent work has shown that the spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks. We showed that the probability of a Ca2+ spark occurring when a single RyR2 in the cluster opens spontaneously can be predicted from the precise spatial arrangements of the RyR2s. Thus, "function" follows from "structure." This probability is related to the maximum eigenvalue (λ1) of the adjacency matrix of the RyR2 cluster lattice. In this work, we develop a theoretical framework for understanding this relationship. We present a stochastic contact network model of the Ca2+ spark initiation process. We show that λ1 determines a stability threshold for the formation of Ca2+ sparks in terms of the RyR2 gating transition rates. We recapitulate these results by applying the model to realistic RyR2 cluster structures informed by super-resolution stimulated emission depletion (STED) microscopy. Eigendecomposition of the linearized mean-field contact network model reveals functional subdomains within RyR2 clusters with distinct sensitivities to Ca2+. This work provides novel perspectives on the cardiac Ca2+ release process and a general method for inferring the functional properties of transmembrane receptor clusters from their structure.

Superresolution modeling of calcium release in the heart.

Stable calcium-induced calcium release (CICR) is critical for maintaining normal cellular contraction during cardiac excitation-contraction coupling. The fundamental element of CICR in the heart is the calcium (Ca(2+)) spark, which arises from a cluster of ryanodine receptors (RyR). Opening of these RyR clusters is triggered to produce a local, regenerative release of Ca(2+) from the sarcoplasmic reticulum (SR). The Ca(2+) leak out of the SR is an important process for cellular Ca(2+) management, and it is critically influenced by spark fidelity, i.e., the probability that a spontaneous RyR opening triggers a Ca(2+) spark. Here, we present a detailed, three-dimensional model of a cardiac Ca(2+) release unit that incorporates diffusion, intracellular buffering systems, and stochastically gated ion channels. The model exhibits realistic Ca(2+) sparks and robust Ca(2+) spark termination across a wide range of geometries and conditions. Furthermore, the model captures the details of Ca(2+) spark and nonspark-based SR Ca(2+) leak, and it produces normal excitation-contraction coupling gain. We show that SR luminal Ca(2+)-dependent regulation of the RyR is not critical for spark termination, but it can explain the exponential rise in the SR Ca(2+) leak-load relationship demonstrated in previous experimental work. Perturbations to subspace dimensions, which have been observed in experimental models of disease, strongly alter Ca(2+) spark dynamics. In addition, we find that the structure of RyR clusters also influences Ca(2+) release properties due to variations in inter-RyR coupling via local subspace Ca(2+) concentration ([Ca(2+)]ss). These results are illustrated for RyR clusters based on super-resolution stimulated emission depletion microscopy. Finally, we present a believed-novel approach by which the spark fidelity of a RyR cluster can be predicted from structural information of the cluster using the maximum eigenvalue of its adjacency matrix. These results provide critical insights into CICR dynamics in heart, under normal and pathological conditions.

Symmetry- and solvent-dependent photophysics of fluorenes containing donor and acceptor groups.

Three two-photon absorption (2PA) dyes (donor-π-donor (DPA2F), donor-π-acceptor (AF240), and acceptor-π-acceptor (BT2F); specifically, D is Ph2N-, A is 2-benzothiazoyl, and the π-linker is 9,9-diethylfluorene) are examined in a variety of aprotic solvents. Because the 2PA cross section is sensitive to the polarity of the local environment, this report examines the solvent-dependent linear photophysics of the dyes, which are important to understand before probing more complex solid-state systems. The symmetrical dyes show little solvent dependence; however, AF240 has significant solvatochromism observed in the fluorescence spectra and lifetimes and also the transient absorption spectra. A 114 nm bathochromic shift is observed in the fluorescence maximum when going from n-hexane to acetonitrile, whereas the lifetimes increase from 1.25 to 3.12 ns. The excited-state dipole moment for AF240 is found to be 20.1 D using the Lippert equation, with smaller values observed for the symmetrical dyes. Additionally, the femtosecond transient absorption (TA) spectra at time zero show little solvent dependence for DPA2F or BT2F, but AF240 shows a 52 nm hypsochromic shift from n-hexane to acetonitrile. Coupled with the solvatochromism in the fluorescence and large excited-state dipole moment, this is attributed to formation of an intramolecular charge-transfer (ICT) state in polar solvents. By 10 ps in AF240, the maximum TA in acetonitrile has shifted 30 nm, providing direct evidence of a solvent-stabilized ICT state, whose formation occurs in 0.85-2.71 ps, depending on solvent. However, AF240 in nonpolar solvents and the symmetrical dyes in all solvents show essentially no shifts due to a predominantly locally excited (LE) state. Preliminary temperature-dependent fluorescence using frozen glass media supports significant solvent reorganization around the AF240 excited state in polar solvents, and may also support a twisted intramolecular charge-transfer (TICT)-state contribution to the stabilization. Finally, time-dependent density functional theory calculations support ICT in AF240 in polar media and also allow prediction of the 2PA cross sections in the 0-0 band, which are much larger for AF240 than the symmetrical dyes.

Direct measurement of group delay dispersion in metamagnetics for ultrafast pulse shaping.

In this paper, we explore the use of magnetic resonant metamaterials, so called metamagnetics, as dispersive elements for optical pulse shaping. We measure both positive and negative group delay dispersion (GDD) values in a metamagnetic material using the multiphoton interference phase scan (MIIPS) technique and show pulse temporal profiles numerically. The results are compared with finite element models. These GDD properties of metamagnetics, along with previously shown tunability and loss control with gain media, enable their use in ultrashort pulse optical applications.

Femtosecond micromachining in transparent bulk materials using an anamorphic lens.

A unique anamorphic lens design was applied to a circular 780nm femtosecond laser pulse to transform it into an elliptically shaped beam at focus. This lens was developed to give an alternative method of micromachining bulk transparent materials. The challenge for femtosecond laser processing is to control the nonlinear affect of self-focusing, which can occur when using a fast f-number lens. Once the focused spot is dominated by self-focusing the predicted focused beam becomes a filament inside the bulk, which is an undesirable effect. The anamorphic lens resolves this self-focusing by increasing the numerical aperture (NA) and employing an elliptical beam shape. The anamorphic lens was designed to furnish a 2.5mum by 190mum line at focus. Provided the pulse energy is high enough, transparent bulk material will be damaged with a single femtosecond laser pulse. Damage in this text refers to visual change in the index of refraction as observed under an optical microscope. Using this elliptical shape (or line), grating structures were micro-machined on the surface of SiC bulk transparent substrate. SiC was chosen because it is known for its micromachining difficulty and its crystalline structure. From the lack of self-focusing and using energy that is just above the damage threshold the focused line beam generated from the anamorphic lens grating structures produced a line shape nearly identical to the geometrical approximation. In this paper we discuss a new method of writing gratings (or other types of structures) in bulk transparent materials using a single femtosecond laser pulse. We will investigate the grating structures visually (inspected under an optical microscope) and also by use of an atomic force microscopy (AFM). In addition, we test the grating diffraction efficiency (DE) as a function of grating spacing, d.