Cosmological parameter estimation with QUaD CMB polarization and temperature experiment

In this thesis we examine the theoretical origin and statistical features of the Cosmic Microwave Background radiation. We particularly focus on the CMB power spectra and cosmological parameter estimation from QUaD CMB experiment data in order to derive implications for the concordance cosmological model. In chapter 4 we present a detailed parameter estimation analysis of the combined polarization and temperature power spectra from the second and third season observations of the QUaD experiment. QUaD has for the first time detected multiple acoustic peaks in the polarization spectrum, allowing meaningful parameter analyses from the polarization data alone. In a standard 6-parameter ACDM parameter estimation analysis we find the QUaD TT power spectrum to be in very good agreement with previous results. However, the QUaD polarization data shows some tension with ACDM model. The origin of this 1−2σ tension remains unclear, and may point to new physics, residual systematics or simple random chance. Combining polarization and temperature data we find an acceptable fit, and show that our results are dominated by the polarization signal. We combine QUaD with the five-year data from the WMAP satellite and the SDSS Luminous Red Galaxies 4th data release power spectrum, and extend our analysis to constrain the tensor-to-scalar ratio and the primordial isocurvature perturbations. Our analysis sets a benchmark for future polarization experiments. In chapter 5 we outline and test a new semi-analytical approach for the estimation of the pseudo- temperature and polarization CMB power spectra for experiments with incomplete sky coverage. We propose a method for constructing the mode-mode coupling matrices which connect the temperature and polarization pseudo-Cℓ’s to the unbiased all-sky bandpowers in the flat sky approximation. We apply this method to the apodization masks of the QUaD CMB experiment and we show that the true underlying bandpowers can be reconstructed from the simulated QUaD-like pseudo-Cℓ’s to high precision. We further investigate the possibility of extending the proposed analytical flat sky approach to the exact calculation of the PCL covariance matrices over a large range of multipoles and we find that the numerical calculation is extremely computationally expensive. The flat sky pseudo-Cℓ and covariances methods presented in this chapter are still work in progress and require more testing

Holistic cancer genome profiling for every patient.

Technological advances in the ability to read the human genome have accelerated the speed of sequencing, such that today we can perform whole genome sequencing (WGS) in one day. Until recently, genomic studies have largely been limited to seeking novel scientific discoveries. The application of new insights gained through cancer WGS into the clinical domain, have been relatively limited. Looking ahead, a vast amount of data can be generated by genomic studies. Of note, excellent organisation of genomic and clinical data permits the application of machine-learning methods which can lead to the development of clinical algorithms that could assist future clinicians and genomicists in the analysis and interpretation of individual cancer genomes. Here, we describe what can be gleaned from holistic whole cancer genome profiling and argue that we must build the infrastructure and educational frameworks to support the modern clinical genomicist to prepare for a future where WGS will be the norm

A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer.

Mammary tumors in dogs hold great potential as naturally occurring breast cancer models in translational oncology, as they share the same environmental risk factors, key histological features, hormone receptor expression patterns, prognostic factors, and genetic characteristics as their human counterparts. We aimed to develop in vitro tools that allow functional analysis of canine mammary tumors (CMT), as we have a poor understanding of the underlying biology that drives the growth of these heterogeneous tumors. We established the long-term culture of 24 organoid lines from 16 dogs, including organoids derived from normal mammary epithelium or benign lesions. CMT organoids recapitulated key morphological and immunohistological features of the primary tissue from which they were derived, including hormone receptor status. Furthermore, genetic characteristics (driver gene mutations, DNA copy number variations, and single-nucleotide variants) were conserved within tumor-organoid pairs. We show how CMT organoids are a suitable model for in vitro drug assays and can be used to investigate whether specific mutations predict therapy outcomes. Specifically, certain CMT subtypes, such as PIK3CA mutated, estrogen receptor-positive simple carcinomas, can be valuable in setting up a preclinical model highly relevant to human breast cancer research. In addition, we could genetically modify the CMT organoids and use them to perform pooled CRISPR/Cas9 screening, where library representation was accurately maintained. In summary, we present a robust 3D in vitro preclinical model that can be used in translational research, where organoids from normal, benign as well as malignant mammary tissues can be propagated from the same animal to study tumorigenesis

An interactive genome browser of association results from the UK10K cohorts project.

UNLABELLED: High-throughput sequencing technologies survey genetic variation at genome scale and are increasingly used to study the contribution of rare and low-frequency genetic variants to human traits. As part of the Cohorts arm of the UK10K project, genetic variants called from low-read depth (average 7×) whole genome sequencing of 3621 cohort individuals were analysed for statistical associations with 64 different phenotypic traits of biomedical importance. Here, we describe a novel genome browser based on the Biodalliance platform developed to provide interactive access to the association results of the project. AVAILABILITY AND IMPLEMENTATION: The browser is available at http://www.uk10k.org/dalliance.html. Source code for the Biodalliance platform is available under a BSD license from http://github.com/dasmoth/dalliance, and for the LD-display plugin and backend from http://github.com/dasmoth/ldserv

Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3.

Epitranscriptome modifications are required for structure and function of RNA and defects in these pathways have been associated with human disease. Here we identify the RNA target for the previously uncharacterized 5-methylcytosine (m(5)C) methyltransferase NSun3 and link m(5)C RNA modifications with energy metabolism. Using whole-exome sequencing, we identified loss-of-function mutations in NSUN3 in a patient presenting with combined mitochondrial respiratory chain complex deficiency. Patient-derived fibroblasts exhibit severe defects in mitochondrial translation that can be rescued by exogenous expression of NSun3. We show that NSun3 is required for deposition of m(5)C at the anticodon loop in the mitochondrially encoded transfer RNA methionine (mt-tRNA(Met)). Further, we demonstrate that m(5)C deficiency in mt-tRNA(Met) results in the lack of 5-formylcytosine (f(5)C) at the same tRNA position. Our findings demonstrate that NSUN3 is necessary for efficient mitochondrial translation and reveal that f(5)C in human mitochondrial RNA is generated by oxidative processing of m(5)C.This work was funded by the Medical Research Council (MRC; as part of the core funding for the Mitochondrial Biology Unit MC_U105697135 and by the G0801904 grant), the European Research Council (ERC; 310360), Cancer Research UK (CR-UK; C10701/ A15181), European Commission (FP7/2007-2013, under grant agreement number no.262055 (ESGI), as a Transnational Access project of the European Sequencing and Genotyping Infrastructure), core support grant from the Wellcome Trust and MRC to the Wellcome Trust-MRC Cambridge Stem Cell Institute, the European Commission (Horizon2020, under grant agreement number 633974), the Bundesministerium fur Bildung und Forschung (BMBF) (through the German Network for mitochondrial disorders (mitoNET, 01GM1113C) and through the European network for mitochondrial disorders (E-Rare project GENOMIT, 01GM1207)) and by EMBO (ALFT 701-2013).This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1203

The QUaD Galactic Plane Survey. I. Maps and Analysis of Diffuse Emission

We present a survey of ~800 deg$^{2}$ of the galactic plane observed with the QUaD telescope. The primary products of the survey are maps of Stokes I, Q, and U parameters at 100 and 150 GHz, with spatial resolution of 5' and 3'.5, respectively. Two regions are covered, spanning approximately 245°-295° and 315°-5° in the galactic longitude l and –4° < b < +4° in the galactic latitude b. At 0°.02 square pixel size, the median sensitivity is 74 and 107 kJy sr$^{–1}$ at 100 GHz and 150 GHz respectively in I, and 98 and 120 kJy sr$^{–1}$ for Q and U. In total intensity, we find an average spectral index of α = 2.35 ± 0.01(stat) ± 0.02(sys) for |b| ≤ 1°, indicative of emission components other than thermal dust. A comparison to published dust, synchrotron, and free-free models implies an excess of emission in the 100 GHz QUaD band, while better agreement is found at 150 GHz. A smaller excess is observed when comparing QUaD 100 GHz data to the WMAP five-year W band; in this case, the excess is likely due to the wider bandwidth of QUaD. Combining the QUaD and WMAP data, a two-component spectral fit to the inner galactic plane (|b| ≤ 1°) yields mean spectral indices of α s = –0.32 ± 0.03 and α$_{d}$ = 2.84 ± 0.03; the former is interpreted as a combination of the spectral indices of synchrotron, free-free, and dust, while the second is largely attributed to the thermal dust continuum. In the same galactic latitude range, the polarization data show a high degree of alignment perpendicular to the expected galactic magnetic field direction, and exhibit mean polarization fraction 1.38 ± 0.08(stat) ± 0.1(sys)% at 100 GHz and 1.70 ± 0.06(stat) ± 0.1(sys)% at 150 GHz. We find agreement in polarization fraction between QUaD 100 GHz and the WMAP W band, the latter giving 1.1% ± 0.4%.Astronom

Parameter Estimation From Improved Measurements of the Cosmic Microwave Background From QUaD

We evaluate the contribution of cosmic microwave background (CMB) polarization spectra to cosmological parameter constraints. We produce cosmological parameters using high-quality CMB polarization data from the ground-based QUaD experiment and demonstrate for the majority of parameters that there is significant improvement on the constraints obtained from satellite CMB polarization data. We split a multi-experiment CMB data set into temperature and polarization subsets and show that the best-fit confidence regions for the ΛCDM six-parameter cosmological model are consistent with each other, and that polarization data reduces the confidence regions on all parameters. We provide the best limits on parameters from QUaD EE/BB polarization data and we find best-fit parameters from the multi-experiment CMB data set using the optimal pivot scale of k$_{p}$ = 0.013 Mpc$^{–1}$ to be {h$^{2}$Ω$_{c}$, h$^{2}$Ω$_{b}$, H$_{0}$, A$_{s}$, n$_{s}$, τ} = {0.113, 0.0224, 70.6, 2.29 × 10$^{-9}$, 0.960, 0.086}.Astronom

Common genetic variation drives molecular heterogeneity in human iPSCs.

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells

Homozygous loss-of-function variants in European cosmopolitan and isolate populations

Homozygous Loss of Function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown - as are the phenotypic effects of losing function for most human genes. Here, we make use of 1,432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation

Oral Abstracts 7: RA ClinicalO37. Long-Term Outcomes of Early RA Patients Initiated with Adalimumab Plus Methotrexate Compared with Methotrexate Alone Following a Targeted Treatment Approach

Background: This analysis assessed, on a group level, whether there is a long-term advantage for early RA patients treated with adalimumab (ADA) + MTX vs those initially treated with placebo (PBO) + MTX who either responded to therapy or added ADA following inadequate response (IR). Methods: OPTIMA was a 78- week, randomized, controlled trial of ADA + MTX vs PBO + MTX in MTX-naïve early (<1 year) RA patients. Therapy was adjusted at week 26: ADA + MTX-responders (R) who achieved DAS28 (CRP) <3.2 at weeks 22 and 26 (Period 1, P1) were re-randomized to withdraw or continue ADA and PBO + MTX-R continued randomized therapy for 52 weeks (P2); IR-patients received open-label (OL) ADA + MTX during P2. This post hoc analysis evaluated the proportion of patients at week 78 with DAS28 (CRP) <3.2, HAQ-DI <0.5, and/or ΔmTSS ≤0.5 by initial treatment. To account for patients who withdrew ADA during P2, an equivalent proportion of R was imputed from ADA + MTX-R patients. Results: At week 26, significantly more patients had low disease activity, normal function, and/or no radiographic progression with ADA + MTX vs PBO + MTX (Table 1). Differences in clinical and functional outcomes disappeared following additional treatment, when PBO + MTX-IR (n = 348/460) switched to OL ADA + MTX. Addition of OL ADA slowed radiographic progression, but more patients who received ADA + MTX from baseline had no radiographic progression at week 78 than patients who received initial PBO + MTX. Conclusions: Early RA patients treated with PBO + MTX achieved comparable long-term clinical and functional outcomes on a group level as those who began ADA + MTX, but only when therapy was optimized by the addition of ADA in PBO + MTX-IR. Still, ADA + MTX therapy conferred a radiographic benefit although the difference did not appear to translate to an additional functional benefit. Disclosures: P.E., AbbVie, Merck, Pfizer, UCB, Roche, BMS—Provided Expert Advice, Undertaken Trials, AbbVie—AbbVie sponsored the study, contributed to its design, and participated in the collection, analysis, and interpretation of the data, and in the writing, reviewing, and approval of the final version. R.F., AbbVie, Pfizer, Merck, Roche, UCB, Celgene, Amgen, AstraZeneca, BMS, Janssen, Lilly, Novartis—Research Grants, Consultation Fees. S.F., AbbVie—Employee, Stocks. A.K., AbbVie, Amgen, AstraZeneca, BMS, Celgene, Centocor-Janssen, Pfizer, Roche, UCB—Research Grants, Consultation Fees. H.K., AbbVie—Employee, Stocks. S.R., AbbVie—Employee, Stocks. J.S., AbbVie, Amgen, AstraZeneca, BMS, Celgene, Centocor-Janssen, GlaxoSmithKline, Lilly, Pfizer (Wyeth), MSD (Schering-Plough), Novo-Nordisk, Roche, Sandoz, UCB—Research Grants, Consultation Fees. R.V., AbbVie, BMS, GlaxoSmithKline, Human Genome Sciences, Merck, Pfizer, Roche, UCB Pharma—Consultation Fees, Research Support. Table 1.Week 78 clinical, functional, and radiographic outcomes in patients who received continued ADA + MTX vs those who continued PBO + MTX or added open-label ADA following an inadequate response ADA + MTX, n/N (%)a PBO + MTX, n/N (%)b Outcome Week 26 Week 52 Week 78 Week 26 Week 52 Week 78 DAS28 (CRP) <3.2 246/466 (53) 304/465 (65) 303/465 (65) 139/460 (30)*** 284/460 (62) 300/460 (65) HAQ-DI <0.5 211/466 (45) 220/466 (47) 224/466 (48) 150/460 (33)*** 203/460 (44) 208/460 (45) ΔmTSS ≤0.5 402/462 (87) 379/445 (86) 382/443 (86) 330/459 (72)*** 318/440 (72)*** 318/440 (72)*** DAS28 (CRP) <3.2 + ΔmTSS ≤0.5 216/462 (47) 260/443 (59) 266/443 (60) 112/459 (24)*** 196/440 (45) 211/440 (48)*** DAS28 (CRP) <3.2 + HAQ-DI <0.5 + ΔmTSS ≤0.5 146/462 (32) 168/443 (38) 174/443 (39) 82/459 (18)*** 120/440 (27)*** 135/440 (31)** aIncludes patients from the ADA Continuation (n = 105) and OL ADA Carry On (n = 259) arms, as well as the proportional equivalent number of responders from the ADA Withdrawal arm (n = 102). bIncludes patients from the MTX Continuation (n = 112) and Rescue ADA (n = 348) arms. Last observation carried forward: DAS28 (CRP) and HAQ-DI; Multiple imputations: ΔmTSS. ***P < 0.001 and **iP < 0.01, respectively, for differences between initial treatments from chi-squar