Statistics and Probability Commons^™

Evaluating The Concordance Between Sequencing, Imputation And Microarray Genotype Calls In The Gaw18 Data, Ally Rogers, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Genotype errors are well known to increase type I errors and/or decrease power in related tests of genotypephenotype association, depending on whether the genotype error mechanism is associated with the phenotype. These relationships hold for both single and multimarker tests of genotype-phenotype association. To assess the potential for genotype errors in Genetic Analysis Workshop 18 (GAW18) data, where no gold standard genotype calls are available, we explored concordance rates between sequencing, imputation, and microarray genotype calls. Our analysis shows that missing data rates for sequenced individuals are high and that there is a modest amount of called genotype discordance between …

Genetic Analysis Workshop 18: Methods And Strategies For Analyzing Human Sequence And Phenotype Data In Members Of Extended Pedigrees, Heike Bickeboller, Julia N. Bailey, Joseph Beyene, Rita M. Cantor, Heather J. Cordell, Robert C. Culverhouse, Corinne D. Engelman, David W. Fardo, Saurabh Ghosh, Inke R. Konig, Justo Lorenzo Bermejo, Phillip E. Melton, Stephanie A. Santorico, Glen A. Satten, Lei Sun, Nathan L. Tintle, Andreas Ziegler, Jean W. Maccluer, Laura Almasy

Faculty Work Comprehensive List

Genetic Analysis Workshop 18 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence data from a pedigree-based sample. In this article we present an overview of the data sets and the contributions that analyzed these data. The family data, donated by the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples Consortium, included sequence-level genotypes based on sequencing and imputation, genome-wide association genotypes from prior genotyping arrays, and phenotypes from longitudinal assessments. The contributions from individual research groups were extensively discussed before, during, and after the workshop in theme-based discussion groups before being submitted …

A 2-Step Penalized Regression Method For Family-Based Next-Generation Sequencing Association Studies, Xiuhua Ding, Shaoyong Su, Kannabiran Nandakumar, Xiaoling Wang, David W. Fardo

Biostatistics Faculty Publications

Large-scale genetic studies are often composed of related participants, and utilizing familial relationships can be cumbersome and computationally challenging. We present an approach to efficiently handle sequencing data from complex pedigrees that incorporates information from rare variants as well as common variants. Our method employs a 2-step procedure that sequentially regresses out correlation from familial relatedness and then uses the resulting phenotypic residuals in a penalized regression framework to test for associations with variants within genetic units. The operating characteristics of this approach are detailed using simulation data based on a large, multigenerational cohort.

Modeling Of Multivariate Longitudinal Phenotypes In Family Genetic Studies With Bayesian Multiplicity Adjustment, Lili Ding, Brad G. Kurowski, Hua He, Eileen S. Alexander, Tesfaye B. Mersha, David Fardo, Xue Zhang, Valentina V. Pilipenko, Leah Kottyan, Lisa J. Martin

Biostatistics Faculty Publications

Genetic studies often collect data on multiple traits. Most genetic association analyses, however, consider traits separately and ignore potential correlation among traits, partially because of difficulties in statistical modeling of multivariate outcomes. When multiple traits are measured in a pedigree longitudinally, additional challenges arise because in addition to correlation between traits, a trait is often correlated with its own measures over time and with measurements of other family members. We developed a Bayesian model for analysis of bivariate quantitative traits measured longitudinally in family genetic studies. For a given trait, family-specific and subject-specific random effects account for correlation among family …

Application Of Family-Based Tests Of Association For Rare Variants To Pathways, Brian Greco, Alexander Luedtke, Allison Hainline, Carolina Alvarez, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Pathway analysis approaches for sequence data typically either operate in a single stage (all variants within all genes in the pathway are combined into a single, very large set of variants that can then be analyzed using standard “gene-based” test statistics) or in 2-stages (gene-based p values are computed for all genes in the pathway, and then the gene-based p values are combined into a single pathway p value). To date, little consideration has been given to the performance of gene-based tests (typically designed for a smaller number of single-nucleotide variants [SNVs]) when the number of SNVs in the gene …

Interadapt -- An Interactive Tool For Designing And Evaluating Randomized Trials With Adaptive Enrollment Criteria, Aaron Joel Fisher, Harris Jaffee, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

The interAdapt R package is designed to be used by statisticians and clinical investigators to plan randomized trials. It can be used to determine if certain adaptive designs offer tangible benefits compared to standard designs, in the context of investigators’ specific trial goals and constraints. Specifically, interAdapt compares the performance of trial designs with adaptive enrollment criteria versus standard (non-adaptive) group sequential trial designs. Performance is compared in terms of power, expected trial duration, and expected sample size. Users can either work directly in the R console, or with a user-friendly shiny application that requires no programming experience. Several added …

Vitamin D Status And Demographic And Lifestyle Determinants Among Adults In The United States (Nhanes 2001-2006), Yan Cao, Katie L. Callahan, Sreenivas P. Veeranki, Yang Chen, Ying Liu, Shimin Zheng

ETSU Faculty Works

This study looked at risk factors associated with vitamin D levels in the body among a representative sample of adults in the U.S., NHANES III (2001-2006) data were used to assess the relationship between several demographic and health risk factors and vitamin D levels in the body. The Baseline-Category Logit Model was used to test the association between vitamin D level and the potential risk factors age, education, ethnicity, poverty status, physical activity, smoking, alcohol, obesity, diabetes and total cholesterol with both genders. Vitamin D insufficiency and deficiency were significantly associated with age, race, education, physical activity, obesity, diabetes and …

The Impact Of Student Performance On Large-Scale Assessments: A View Of Long-Term Health, Career, And Societal Outcomes, Roman Usatin

Seton Hall University Dissertations and Theses (ETDs)

This study examined the predictive power of student growth for large-scale assessments on meaningful life outcomes, focusing on the three categories of health, career, and societal involvement. Analysis was conducted using the NELS:88/00 dataset–a longitudinal study that followed a nationally-representative sample of over 12,000 eighth grade students from 1988 to 2000, until the students were 26 years old and entered into the work force. The large-scale assessment variables included math and reading performance in the 1988 cognitive batteries administered by NELS. To gauge growth levels, I generated Student Growth Percentiles (SGP) from tests administered by NELS from 1988 to 1992. …

Methods For Exploring Treatment Effect Heterogeneity In Subgroup Analysis: An Application To Global Clinical Trials, I. Manjula Schou, Ian C. Marschner

COBRA Preprint Series

Multi-country randomised clinical trials (MRCTs) are common in the medical literature and their interpretation has been the subject of extensive recent discussion. In many MRCTs, an evaluation of treatment effect homogeneity across countries or regions is conducted. Subgroup analysis principles require a significant test of interaction in order to claim heterogeneity of treatment effect across subgroups, such as countries in a MRCT. As clinical trials are typically underpowered for tests of interaction, overly optimistic expectations of treatment effect homogeneity can lead researchers, regulators and other stakeholders to over-interpret apparent differences between subgroups even when heterogeneity tests are insignificant. In this …

How Sexism Makes The Man: Examining The Relationship Between Masculinity, Ambivalent Sexism, And Gender Stereotyping, Mariah L. Wilkerson

Lawrence University Honors Projects

Masculinity is a precarious social status, meaning it can be lost through social and gender transgressions (Bosson & Vandello, 2011). Men often act in stereotypically masculine ways to reassert their masculinity and restore their social status after it has been threatened. The current study also examines masculinity in a new way, as a collective gender identity (e.g., Tajfel, 1982). I hypothesized that threatened men and men who identify as more masculine will display masculinity through more polarized attitudes towards traditional and nontraditional groups of men and women, endorsing traditional gender stereotypes, and intensified ambivalently sexist attitudes. Two empirical studies tested …

Trend Analysis And Modeling Of Health And Environmental Data: Joinpoint And Functional Approach, Ram C. Kafle

USF Tampa Graduate Theses and Dissertations

The present study is divided into two parts: the first is on developing the statistical analysis and modeling of mortality (or incidence) trends using Bayesian joinpoint regression and the second is on fitting differential equations from time series data to derive the rate of change of carbon dioxide in the atmosphere.

Joinpoint regression model identifies significant changes in the trends of the incidence, mortality, and survival of a specific disease in a given population. Bayesian approach of joinpoint regression is widely used in modeling statistical data to identify the points in the trend where the significant changes occur. The purpose …

Pgs: A Tool For Association Study Of High-Dimensional Microrna Expression Data With Repeated Measures, Yinan Zheng, Zhe Fei, Wei Zhang, Justin Starren, Lei Liu, Andrea Baccarelli, Yi Li, Lifang Hou

The University of Michigan Department of Biostatistics Working Paper Series

Motivation: MicroRNAs (miRNAs) are short single-stranded non-coding molecules that usually function as negative regulators to silence or suppress gene expression. Due to interested in the dynamic nature of the miRNA and reduced microarray and sequencing costs, a growing number of researchers are now measuring high-dimensional miRNAs expression data using repeated or multiple measures in which each individual has more than one sample collected and measured over time. However, the commonly used site-by-site multiple testing may impair the value of repeated or multiple measures data by ignoring the inherent dependent structure, which lead to problems including underpowered results after multiple comparison …

Targeted Maximum Likelihood Estimation Using Exponential Families, Iván Díaz, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

Targeted maximum likelihood estimation (TMLE) is a general method for estimating parameters in semiparametric and nonparametric models. Each iteration of TMLE involves fitting a parametric submodel that targets the parameter of interest. We investigate the use of exponential families to define the parametric submodel. This implementation of TMLE gives a general approach for estimating any smooth parameter in the nonparametric model. A computational advantage of this approach is that each iteration of TMLE involves estimation of a parameter in an exponential family, which is a convex optimization problem for which software implementing reliable and computationally efficient methods exists. We illustrate …

Flint International Statistics Conference Agenda, Kettering University

Flint: One City, 100 Years of Variability

Conference Agenda—Keynote Speakers, Invited & Contributed Talks, Posters, Field Trips

• Tuesday, June 24
• Wednesday, June 25
• Thursday, June 26
• Friday, June 27
• Saturday, June 28

Select Sessions:

• Elart von Collani “Statistics as a general tool for all sciences.”
• Francesca Greselin “Measuring inequality at the time of the Great Divergence.”
• Ernest Fokoue “Recent Applications of Statistical Data Mining for Big Data Predictive Analysis.”
• Vladimir Kaishev “Probability and statistics in actuarial applications.”
• Galia Novikova “Data Mining for Software Development Quality Management.”
• Leda Minkova “Stochastic Models and Statistical Applications.”
• Krzysztof Podgorski “Non-Gaussian stochastic models: theory and applications.”
• Kristina Sendova “Risk measures, probability measures …

Extreme Self-Adjoint Extensions Of A Semibounded Q-Difference Operator, Miron B. Bekker, Martin Bohner, Hristo Voulov

Mathematics and Statistics Faculty Research & Creative Works

For a certain q-difference operator introduced and studied in a series of articles by the same authors, we investigate its extreme self-adjoint extensions, i.e., the so-called Friedrichs and Kreǐn extensions. We show that for the interval of parameters under consideration, the Friedrichs extension and the Kreǐn extension are distinct and give values of the parameter in the von Neumann formulas that correspond to those extensions and describe their resolvent operators. A crucial role in our investigation plays the fact that both the Friedrichs and the Kreǐn extensions are scale invariant. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulating Influenza Transmission With Network Data, Henry V. Bongiovi

Statistics

Simulating Influenza Transmission with Real Network Data

Henry Bongiovi BS Statistics, California Polytechnic State University, San Luis Obispo

[email protected]

Keywords: Network Data, Simulation, Education, Influenza, Epidemic

Disease has been humanities arch rival since the dawn of our existence. As such, we have been trying our best to understand its spread and proliferation. One of the most common diseases, Influenza, is also one of the most complex. To understand the complexities of its spread would greatly improve our ability to combat it and other diseases like it. Using R in conjunction with the package statnet, I have created a simulation of …

Gwas Identifies An Nat2 Acetylator Status Tag Single Nucleotide Polymorphism To Be A Major Locus For Skin Fluorescence, Karen M. Eny, Helen L. Lutgers, John Maynard, Barbara E.K. Klein, Kristine E. Lee, Patricia A. Cleary, +20 Additional Authors

Epidemiology Faculty Publications

Aims/hypothesis

Skin fluorescence (SF) is a non-invasive marker of AGEs and is associated with the long-term complications of diabetes. SF increases with age and is also greater among individuals with diabetes. A familial correlation of SF suggests that genetics may play a role. We therefore performed parallel genome-wide association studies of SF in two cohorts.

Methods

Cohort 1 included 1,082 participants, 35–67 years of age with type 1 diabetes. Cohort 2 included 8,721 participants without diabetes, aged 18–90 years.

Results

rs1495741 was significantly associated with SF in Cohort 1 (p < 6 × 10−10), which is known to tag theNAT2 acetylator phenotype. The fast acetylator genotype was associated …

Abcc9 Gene Polymorphism Is Associated With Hippocampal Sclerosis Of Aging Pathology, Peter T. Nelson, Steven Estus, Erin L. Abner, Ishita Parikh, Manasi Malik, Janna H. Neltner, Eseosa Ighodaro, Wang-Xia Wang, Bernard R. Wilfred, Li-San Wang, Walter A. Kukull, Kannabiran Nandakumar, Mark L. Farman, Wayne W. Poon, Maria M. Corrada, Claudia H. Kawas, David H. Cribbs, David A. Bennett, Julie A. Schneider, Eric B. Larson, Paul K. Crane, Otto Valladares, Frederick A. Schmitt, Richard J. Kryscio, Gregory A. Jicha, Charles D. Smith, Stephen W. Scheff, Joshua A. Sonnen, Jonathan L. Haines, Margaret A. Pericak-Vance, Richard Mayeux, Lindsay A. Farrer, Linda J. Van Eldik, Craig Horbinski, Robert C. Green, Marla Gearing, Leonard W. Poon, Patricia L. Kramer, Randall L. Woltjer, Thomas J. Montine, Amanda B. Partch, Alexander J. Rajic, Katierose Richmire, Sarah E. Monsell, Gerard D. Schellenberg, David W. Fardo

Pathology and Laboratory Medicine Faculty Publications

Hippocampal sclerosis of aging (HS-Aging) is a high-morbidity brain disease in the elderly but risk factors are largely unknown. We report the first genome-wide association study (GWAS) with HS-Aging pathology as an endophenotype. In collaboration with the Alzheimer's Disease Genetics Consortium, data were analyzed from large autopsy cohorts: (#1) National Alzheimer's Coordinating Center (NACC); (#2) Rush University Religious Orders Study and Memory and Aging Project; (#3) Group Health Research Institute Adult Changes in Thought study; (#4) University of California at Irvine 90+ Study; and (#5) University of Kentucky Alzheimer's Disease Center. Altogether, 363 HS-Aging cases and 2,303 controls, all pathologically …

Rapid Door-To-Balloon Time (≤ 30 Minutes) In The Treatment Of Acute St-Elevation Myocardial Infarction (Stemi) Is Associated With Reduced Length Of Hospital Stay And Improved Clinical Outcomes, Yassir Nawaz Md, Ataul Qureshi Md, Navin K. Subrayappa Md, Orlando E. Rivera Rn, Bruce Feldman Do, Nainesh C. Patel Md

Department of Medicine

No abstract provided.

Understanding Non-Emergent Pediatric Ed Visits: Using Hospital And Family Centric Data To Inform System Redesign, Deborah Swavely Dnp, Rn, Kathy Baker Mph, Rn, Krista L. Bilger Bsn, Rn, David Zimmerman Mph, Andrew Martin Msn, Rn

Department of Community Health and Health Studies

No abstract provided.