Accuracy of genotype imputation in Nelore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for stealth supersymmetry in events with jets, either photons or leptons, and low missing transverse momentum in pp collisions at 8 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for physics beyond the standard model in final states with a lepton and missing transverse energy in proton-proton collisions at root s = 8 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for physics beyond the standard model in events with two leptons, jets, and missing transverse momentum in pp collisions at root s=8 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Strategies for genotype imputation in composite beef cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Improving IRT parameter estimates with small sample sizes: Evaluating the efficacy of a new data augmentation technique

The 3PL model is a flexible and widely used tool in assessment. However, it suffers from limitations due to its need for large sample sizes. This study introduces and evaluates the efficacy of a new sample size augmentation technique called Duplicate, Erase, and Replace (DupER) Augmentation through a simulation study. Data are augmented using several variations of DupER Augmentation (based on different imputation methodologies, deletion rates, and duplication rates), analyzed in BILOG-MG 3, and results are compared to those obtained from analyzing the raw data. Additional manipulated variables include test length and sample size. Estimates are compared using seven different evaluative criteria. Results are mixed and inconclusive. DupER augmented data tend to result in larger root mean squared errors (RMSEs) and lower correlations between estimates and parameters for both item and ability parameters. However, some DupER variations produce estimates that are much less biased than those obtained from the raw data alone. For one DupER variation, it was found that DupER produced better results for low-ability simulees and worse results for those with high abilities. Findings, limitations, and recommendations for future studies are discussed. Specific recommendations for future studies include the application of Duper Augmentation (1) to empirical data, (2) with additional IRT models, and (3) the analysis of the efficacy of the procedure for different item and ability parameter distributions.

Search for supersymmetry in final states with jets, missing transverse energy and one charged lepton with the ATLAS-experiment

Im Jahr 2011 wurde am Large Hadron Collider mit dem ATLAS Experiment ein Datensatz von 4.7 inversen Femtobarn bei einer Schwerpunktsenergie von 7 TeV aufgezeichnet. Teil des umfangreichen Physikprogrammes des ATLAS Experiments ist die Suche nach Physik jenseits des Standardmodells. Supersymmetrie - eine neue Symmetrie zwischen Bosonen und Fermionen - wird als aussichtsreichester Kandidat für neue Physik angesehen, und zahlreiche direkte und indirekte Suchen nach Supersymmetrie wurden in den letzten Jahrzehnten bereits durchgeführt. In der folgenden Arbeit wird eine direkte Suche nach Supersymmetrie in Endzuständen mit Jets, fehlender Transversalenergie und genau einem Elektron oder Myon durchgeführt. Der analysierte Datensatz von 4.7 inversen Femtobarn umfasst die gesamte Datenmenge, welche am ATLAS Experiment bei einer Schwerpunktsenergie von 7 TeV aufgezeichnet wurde. Die Ergebnisse der Analyse werden mit verschiedenen anderen leptonischen Suchkanälen kombiniert, um die Sensitivität auf diversen supersymmetrischen Produktions- und Zerfallsmodi zu maximieren. Die gemessenen Daten sind kompatibel mit der Standardmodellerwartung, und neue Ausschlussgrenzen in verschiedenen supersymmetrischen Modellen werden berechnet.

Search for supersymmetry using final states with one lepton, jets, and missing transverse momentum with the ATLAS detector in √s=7 TeV pp collisions

This Letter presents the first search for supersymmetry in final states containing one isolated electron or muon, jets, and missing transverse momentum from √s=7  TeV proton-proton collisions at the LHC. The data were recorded by the ATLAS experiment during 2010 and correspond to a total integrated luminosity of 35  pb(-1). No excess above the standard model background expectation is observed. Limits are set on the parameters of the minimal supergravity framework, extending previous limits. Within this framework, for A(0)=0 GeV, tanβ=3, and μ>0 and for equal squark and gluino masses, gluino masses below 700 GeV are excluded at 95% confidence level.

Search for diphoton events with large missing transverse energy in 7 TeV proton-proton collisions with the ATLAS detector

A search for diphoton events with large missing transverse energy is presented. The data were collected with the ATLAS detector in proton-proton collisions at √s=7 TeV at the CERN Large Hadron Collider and correspond to an integrated luminosity of 3.1 pb⁻¹. No excess of such events is observed above the standard model background prediction. In the context of a specific model with one universal extra dimension with compactification radius R and gravity-induced decays, values of 1/R<729 GeV are excluded at 95% C. L., providing the most sensitive limit on this model to date.

TRIO LOGIC REGRESSION - DETECTION OF SNP - SNP INTERACTIONS IN CASE-PARENT TRIOS

Statistical approaches to evaluate higher order SNP-SNP and SNP-environment interactions are critical in genetic association studies, as susceptibility to complex disease is likely to be related to the interaction of multiple SNPs and environmental factors. Logic regression (Kooperberg et al., 2001; Ruczinski et al., 2003) is one such approach, where interactions between SNPs and environmental variables are assessed in a regression framework, and interactions become part of the model search space. In this manuscript we extend the logic regression methodology, originally developed for cohort and case-control studies, for studies of trios with affected probands. Trio logic regression accounts for the linkage disequilibrium (LD) structure in the genotype data, and accommodates missing genotypes via haplotype-based imputation. We also derive an efficient algorithm to simulate case-parent trios where genetic risk is determined via epistatic interactions.

A BAYESIAN SHRINKAGE MODEL FOR INCOMPLETE LONGITUDINAL BINARY DATA WITH APPLICATION TO THE BREAST CANCER PREVENTION TRIAL

We consider inference in randomized studies, in which repeatedly measured outcomes may be informatively missing due to drop out. In this setting, it is well known that full data estimands are not identified unless unverified assumptions are imposed. We assume a non-future dependence model for the drop-out mechanism and posit an exponential tilt model that links non-identifiable and identifiable distributions. This model is indexed by non-identified parameters, which are assumed to have an informative prior distribution, elicited from subject-matter experts. Under this model, full data estimands are shown to be expressed as functionals of the distribution of the observed data. To avoid the curse of dimensionality, we model the distribution of the observed data using a Bayesian shrinkage model. In a simulation study, we compare our approach to a fully parametric and a fully saturated model for the distribution of the observed data. Our methodology is motivated and applied to data from the Breast Cancer Prevention Trial.

Culture, risk factors and mortality: can Switzerland add missing pieces to the European puzzle?

BACKGROUND: The aim was to compare cause-specific mortality, self-rated health (SRH) and risk factors in the French and German part of Switzerland and to discuss to what extent variations between these regions reflect differences between France and Germany. METHODS: Data were used from the general population of German and French Switzerland with 2.8 million individuals aged 45-74 years, contributing 176 782 deaths between 1990 and 2000. Adjusted mortality risks were calculated from the Swiss National Cohort, a longitudinal census-based record linkage study. Results were contrasted with cross-sectional analyses of SRH and risk factors (Swiss Health Survey 1992/3) and with cross-sectional national and international mortality rates for 1980, 1990 and 2000. RESULTS: Despite similar all-cause mortality, there were substantial differences in cause-specific mortality between Swiss regions. Deaths from circulatory disease were more common in German Switzerland, while causes related to alcohol consumption were more prevalent in French Switzerland. Many but not all of the mortality differences between the two regions could be explained by variations in risk factors. Similar patterns were found between Germany and France. CONCLUSION: Characteristic mortality and behavioural differentials between the German- and the French-speaking parts of Switzerland could also be found between Germany and France. However, some of the international variations in mortality were not in line with the Swiss regional comparison nor with differences in risk factors. These could relate to peculiarities in assignment of cause of death. With its cultural diversity, Switzerland offers the opportunity to examine cultural determinants of mortality without bias due to different statistical systems or national health policies.

Search for direct slepton and gaugino production in final states with two leptons and missing transverse momentum with the ATLAS detector in pp collisions at sqrts=7 TeV

A search for the electroweak pair production of charged sleptons and weak gauginos decaying into final states with two leptons is performed using 4.7 fb(-1) of proton-proton collision data at root s = 7 TeV recorded with the ATLAS experiment at the Large Hadron Collider. No significant excesses are observed with respect to the prediction from Standard Model processes. In the scenario of direct slepton production, if the sleptons decay directly into the lightest neutralino, left-handed slepton masses between 85 and 195 GeV are excluded at 95% confidence level for a 20 GeV neutralino. Chargino masses between 110 and 340 GeV are excluded in the scenario of direct production of wino-like chargino pairs decaying into the lightest neutralino via an intermediate on-shell charged slepton for a 10 GeV neutralino. The results are also interpreted in the framework of the phenomenological minimal supersymmetric Standard Model.