Philip Cooley

Philip Cooley
RTI International | RTI International · Division of Survey and Computing Sciences

About

83
Publications
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Introduction
Genome Wide Association Studies (GWAS) compare the DNA of participants having different phenotypes for a particular trait. These participants may be people with a disease (cases) and similar people without the disease (controls). Each study participant person provides a sample of DNA, from which millions of genetic variants are read using Single Nucleotide Polymorphism (SNP) arrays. If one type of the variant (one allele) is more frequent in people with the disease, the variant is said to be associated with the disease. The associated SNPs are then considered to mark a genetic region of the human genome that may influence the risk of disease. GWAS investigate the entire genome, in contrast to methods that specifically test a small number of pre-specified genetic regions. GWAS identify SNPs
Skills and Expertise

Publications

Publications (83)
Chapter
Noncommunicable diseases (NCDs) are the main cause of death worldwide. In addition, the incidence, prevalence, and death rates from NCDs are expected to increase in the future. No single discipline can address the issues of prevention, early detection, access to care, and appropriate treatment that are needed to improve outcomes for NCDs; this grow...
Book
The objective of this book is to describe procedures for analyzing genome-wide association studies (GWAS). Some of the material is unpublished and contains commentary and unpublished research; other chapters (Chapters 4 through 7) have been published in other journals. Each previously published chapter investigates a different genomics model, but a...
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Many published influenza models treat each simulation day as a weekday and do not distinguish weekend days. Consequently, the weekend effect on influenza transmission has not been fully explored. To assess whether distinguishing between weekday and weekend transmissions in simulation models of flu-like infectious disease models matters, this study...
Article
Influenza vaccination is administered throughout the influenza disease season, even as late as March. Given such timing, what is the value of vaccinating the population earlier than currently being practiced? We used real data on when individuals were vaccinated in Allegheny County, Pennsylvania, and the following 2 models to determine the value of...
Article
From 2003 to 2013, RTI International served as the data repository for the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK). RTI worked closely with two sample repository partners to build and maintain the Central Repository (CR) that made data and samples available to approved requestors. In this paper, we recap aspects of est...
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Mathematical and computational models provide valuable tools that help public health planners to evaluate competing health interventions, especially for novel circumstances that cannot be examined through observational or controlled studies, such as pandemic influenza. The spread of diseases like influenza depends on the mixing patterns within the...
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The National Institute of Diabetes and Digestive Disease (NIDDK) Central Data Repository (CDR) is a web-enabled resource available to researchers and the general public. The CDR warehouses clinical data and study documentation from NIDDK funded research, including such landmark studies as The Diabetes Control and Complications Trial (DCCT, 1983–93)...
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Background States’ pandemic influenza plans and school closure statutes are intended to guide state and local officials, but most faced a great deal of uncertainty during the 2009 influenza H1N1 epidemic. Questions remained about whether, when, and for how long to close schools and about which agencies and officials had legal authority over school...
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This paper investigates epistatic scenarios in a genome-wide association studies (GWAS) context using a qualitative association model, to assess the statistical models that reliably predict associations between a qualitative phenotype (i.e., a disease diagnosis) and a pair of interacting genes. We employed the concept of relative risk, which is the...
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The interactions of people using public transportation in large metropolitan areas may help spread an influenza epidemic. An agent-based model computer simulation of New York City's (NYC's) five boroughs was developed that incorporated subway ridership into a Susceptible-Exposed-Infected-Recovered disease model framework. The model contains a total...
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When influenza vaccines are in short supply, allocating vaccines equitably among different jurisdictions can be challenging. But justice is not the only reason to ensure that poorer counties have the same access to influenza vaccines as do wealthier ones. Using a detailed computer simulation model of the Washington, D.C., metropolitan region, we fo...
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During the 2009 H1N1 influenza epidemic, policy makers debated over whether, when, and how long to close schools. While closing schools could have reduced influenza transmission thereby preventing cases, deaths, and health care costs, it may also have incurred substantial costs from increased childcare needs and lost productivity by teachers and ot...
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Increasingly, researchers are turning to computational models to understand the interplay of important variables on systems' behaviors. Although researchers may develop models that meet the needs of their investigation, application limitations-such as nonintuitive user interface features and data input specifications-may limit the sharing of these...
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In 2005, RTI International researchers developed methods to generate synthesized population data on US households for the US Synthesized Population Database. These data are used in agent-based modeling, which simulates large-scale social networks to test how changes in the behaviors of individuals affect the overall network. Group quarters are resi...
Book
The objective of this work was to help frame the ongoing discussion of America’s energy future in the context of all three dimensions—technology, economics, and social sciences—and to draw attention to research needs pertaining to the intersection of the societal factors domain with technology and economics. We hope that the proposed research will...
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The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repository makes data and biospecimens from NIDDK-funded research available to the broader scientific community. It thereby facilitates: the testing of new hypotheses without new data or biospecimen collection; pooling data across several studies to increase statis...
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Nearly one thousand human genome wide association studies (GWAS) have examined over 210 diseases and traits and found over 1,200 SNP associations. With improved genotyping technologies and the growing number of available markers, case-control Genome Wide Association Studies (GWAS) have become a key tool for investigating complex diseases. This stud...
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Assess influenza vaccination among commuters using mass transit in New York City (NYC). We used the 2006 NYC Community Health Survey (CHS) to analyze the prevalence of influenza immunization by commuting behaviors and to understand what socioeconomic and geographic factors may explain any differences found. Vaccination prevalence is significantly l...
Article
Background In December 2009, when the H1N1 influenza pandemic appeared to be subsiding, public health officials and unvaccinated individuals faced the question of whether continued H1N1 immunization was still worthwhile.PurposeTo delineate what combinations of possible mechanisms could generate a third pandemic wave and then explore whether vaccina...
Article
Background In December 2009, when the H1N1 influenza pandemic appeared to be subsiding, public health officials and unvaccinated individuals faced the question of whether continued H1N1 immunization was still worthwhile. Purpose To delineate what combinations of possible mechanisms could generate a third pandemic wave and then explore whether vacci...
Article
In December 2009, when the H1N1 influenza pandemic appeared to be subsiding, public health officials and unvaccinated individuals faced the question of whether continued H1N1 immunization was still worthwhile. To delineate what combinations of possible mechanisms could generate a third pandemic wave and then explore whether vaccinating the populati...
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Communicable-disease transmission models are useful for the testing of prevention and intervention strategies. Agent-based models (ABMs) represent a new and important class of the many types of disease transmission models in use. Agent-based disease models benefit from their ability to assign disease transmission probabilities based on characterist...
Article
In the fall 2009, the University of Pittsburgh Models of Infectious Disease Agent Study (MIDAS) team employed an agent-based computer simulation model (ABM) of the greater Washington, DC, metropolitan region to assist the Office of the Assistant Secretary of Public Preparedness and Response, Department of Health and Human Services, to address sever...
Article
There remains substantial debate over the impact of school closure as a mitigation strategy during an influenza pandemic. The ongoing 2009 H1N1 influenza pandemic has provided an unparalleled opportunity to test interventions with the most up-to-date simulations. To assist the Allegheny County Health Department during the 2009 H1N1 influenza pandem...
Article
Better understanding the possible effects of vaccinating employees is important and can help policymakers and businesses plan vaccine distribution and administration logistics, especially with the current H1N1 influenza vaccine in short supply. This article aims to determine the effects of varying vaccine coverage, compliance, administration rates,...
Article
The Advisory Committee on Immunization Practices has identified health care workers (HCWs) as a priority group to receive influenza vaccine. Although the importance of HCW to the health care system is well understood, the potential role of HCW in transmission during an epidemic has not been clearly established. Using a standard SIR (Susceptible-Inf...
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Population-based variability in protein expression patterns, especially in humans, is often observed but poorly understood. Moreover, very little is known about how interindividual genetic variation contributes to protein expression patterns. To begin to address this, we describe elements of technical and biological variations contributing to expre...
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The choice of a statistical method significantly affects the power profiles of Genome Wide Association (GWA) predictions. Previous simulation studies of a single synthetic phenotype marker determined that the gene model or mode of inheritance (MOI) was a major influence on power. In this paper, the authors compare the power profiles of GWA statisti...
Article
The choice of a statistical method significantly affects the power profiles of Genome Wide Association (GWA) predictions. Previous simulation studies of a single synthetic phenotype marker determined that the gene model or mode of inheritance (MOI) was a major influence on power. In this paper, the authors compare the power profiles of GWA statisti...
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Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications providing historical evidence about epidemics. An ontology has been developed for MIDAS to support the collec...
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This study assesses the impact of Telephone Audio Computer-Assisted Self-Interviewing (T-ACASI) on the reporting of sensitive (mainly heterosexual) behaviours. A randomized experiment was embedded in a telephone survey that drew probability samples of the populations of the USA (N = 1543) and Baltimore city (N = 744). Respondents were randomly assi...
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Agent-based models simulate large-scale social systems. They assign behaviors and activities to "agents" (individuals) within the population being modeled and then allow the agents to interact with the environment and each other in complex simulations. Agent-based models are frequently used to simulate infectious disease outbreaks, among other uses...
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The model repository (MREP) is a relational database management system (RDBMS) developed under the auspices of models of infectious disease agent study (MIDAS). The purpose of the MREP is to organize and catalog the models, results, and suggestions for using the MIDAS and to store them in a way to allow users to run models from an access-controlled...
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Although telephone surveys provide an economical method for assessing patterns of diagnosed sexually transmitted diseases (STDs) and STD-related behaviors in populations, the requirement that respondents report such information to human telephone interviewers introduces an opportunity for substantial reporting bias. Telephone computer-assisted self...
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Planning a response to an outbreak of a pandemic strain of influenza is a high public health priority. Three research groups using different individual-based, stochastic simulation models have examined the consequences of intervention strategies chosen in consultation with U.S. public health workers. The first goal is to simulate the effectiveness...
Article
The objective of this study was to reconstruct the type A influenza epidemic that occurred in the Research Triangle Park (RTP) region of North Carolina during the 2003–04 flu season. We describe an agent-based influenza transmission model that uses Influenza-like Illness (ILI) data gathered from state agencies to estimate model parameters. The desi...
Article
In a study that examined associations between single nucleotide polymorphism (SNP) loci within the promoter of the PRTN3 gene and the autoimmune disease Wegener’s granulomatosis (WG), we implemented a self-administered pilot survey that captured participants’ demographic data, family relationships, incidence of autoimmune disease among family membe...
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Controlling the incidence and propagation of animal-borne infectious disease, such as avian influenza and foot-and-mouth disease, is important to the agriculture industry and public health officials because of the potentially devastating economic consequences and the possibility of transmission to humans. The lack of national geographic information...
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Development of strategies for mitigating the severity of a new influenza pandemic is now a top global public health priority. Influenza prevention and containment strategies can be considered under the broad categories of antiviral, vaccine and non-pharmaceutical (case isolation, household quarantine, school or workplace closure, restrictions on tr...
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Well-conducted telephone surveys provide an economical means of estimating the prevalence of sexual and reproductive behaviors in a population. There is, however, a nontrivial potential for bias since respondents must report sensitive information to a human interviewer. The National STD and Behavior Measurement Experiment (NSBME) evaluates a new su...
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The National Institute of Diabetes and Digestive and Kidney Diseases have established central repositories for the collection of DNA, biological samples, and clinical data to be catalogued at a single site. Here we present an overview of the site which stores the clinical data and links to biospecimens. The NIDDK Data repository is a web-enabled re...
Article
One result of the publishing of the human genome sequence is the ability to define objects through their position on the consensus sequence. While this has simplified the process of creating order maps for genes on a chromosome, it has created discrepancies between the published cytolocations of human genes, as presented through genetic references,...
Article
Development of strategies for mitigating the severity of a new influenza pandemic is now a top global public health priority. Influenza prevention and containment strategies can be considered under the broad categories of antiviral, vaccine and non-pharmaceutical (case isolation, household quarantine, school or workplace closure, restrictions on tr...
Article
Summary This molecular epidemiology study integrated questionnaire and genotype information to examine a disease susceptibility hypothesis. The study was based on a previously reported association demonstrated between a single nucleotide polymorphism (SNP) identified as A-564G within the promoter of the proteinase-3 gene (PRTN3) and the autoimmune...
Article
Audio computer-assisted self-interviewing (audio-CASI) technologies have become standard tools for collecting information on sensitive measures. However, while the method is commonly applied in the English language, its use is less prevalent in non-English language data collection efforts. One reason for the low occurrence of non-English audio-CASI...
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The prevalence and distribution of gonococcal and chlamydial infections in the general population are poorly understood. Development of nucleic acid amplification tests, such as the ligase chain reaction assay, provides new opportunities to estimate the prevalence of untreated infections in the population. To estimate the overall prevalence of untr...
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This study assessed the differential effects of face-to-face interviewing and audio-computer assisted self-interviewing (audio-CASI) on categories of questions. Syringe exchange program participants (n = 1417) completed face-to-face interviews or audio-CASI. The questionnaire was categorized into the groups "stigmatized behaviors," "neutral behavio...
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This paper describes a new interview data collection system that uses a laptop personal computer equipped with a touch-sensitive video monitor. The touch-screen-based audio computer-assisted self-interviewing system, or touch screen audio-CASI, enhances the ease of use of conventional audio CASI systems while simultaneously providing the privacy of...
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Recent studies have reported on the utility of audio computer-assisted self-interviewing (ACASI) in surveys of human immunodeficiency virus (HIV) risk behaviors that involve a single assessment. This paper reports the results of a test of ACASI within a longitudinal study of HIV risk behavior and infection. Study participants (gay men (n = 1,974) a...
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Recent studies have reported on the utility of audio computer-assisted self-interviewing (ACASI) in surveys of human immunodeficiency virus (HIV) risk behaviors that involve a single assessment. This paper reports the results of a test of ACASI within a longitudinal study of HIV risk behavior and infection. Study participants (gay men ( n =...
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Measurements of drug use and other illicit or stigmatized behaviors are subject to nontrivial underreporting biases. During in-person surveys, respondents are more likely to report such behaviors when interviewed using techniques that maximize interviewee privacy, e.g., use of paper SAQs and audio-CASI rather than questioning by human interviewers....
Article
Audio computer-assisted self interviewing (Audio-CASI) technologies have recently been shown to provide important and sometimes dramatic improvements in the quality of survey measurements. This is particularly true for measurements requiring respondents to divulge highly sensitive information such as their sexual, drug use, or other sensitive behav...
Article
This paper describes a new interview data collection system that uses a personal computer equipped with a telephone interface card. This system, telephone audio computer-assisted self-interviewing or T-ACASI, offers the economy of telephone interviews while providing the privacy of self-administered questionnaires. We describe T-ACASI design consid...
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Diagnostic procedures, used singly or in combination, are crucial in the determination of the presence and prevalence of medical and other conditions. In the absence of a "gold standard," two or more measures or diagnostic tests are often available that may be used to estimate true prevalence. The authors have developed a statistical method with wh...
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Information from 12 studies is combined to estimate the AIDS incubation distribution with greater precision than is possible from a single study. The analysis uses a hierarchy of parametric models based on a four-parameter generalized F distribution. This general model contains four standard two-parameter distributions as special cases. The cases a...
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This article reviews a multimedia application in the area of survey measurement research: adding audio capabilities to a computer-assisted interviewing system. Hardware and software issues are discussed, and potential hardware devices that operate from DOS platforms are reviewed. Three types of hardware devices are considered: PCMCIA devices, paral...
Article
Several large research programs are underway that evaluate the centralized intake model for drug abuse treatment. In this model, the drug abuse treatment facilities in a city do not operate independently; their efforts are coordinated through a small number of intake centers, which handle all patient intake and data management activities. The succe...
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The purpose of this paper is to assess different procedures used in the modeling of the AIDS epidemic that account for changes in the definition of AIDS. Specifically, we assess three methods that adjust for the effect of definition changes on the modeling of HIV reconstructions. Our results suggest that how we account for definition changes is a c...
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This paper describes a model that simulates the spread of HIV and progression to AIDS. The model is based on classical models of disease transmission. It consists of six linked risk groups and tracks the numbers of infectives, AIDS cases, AIDS related deaths, and other deaths of infected persons in each risk group. Parametric functions are used to...
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To evaluate the effect of the assumption of no long reporting delays on estimates of AIDS incidence. Reported AIDS cases must be adjusted for reporting delays to estimate AIDS incidence. We compared the adjustments supplied with the Centers for Disease Control and Prevention (CDC) AIDS Public Information Data Set with a set of adjustments that diff...
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This paper describes an AIDS epidemic model that has been developed to explore the relationships among parameters that characterize that epidemic which include: (1) needle sharing and sexual contacts with individuals within and among distinct risk groups; (2) rates of progression from HIV infection to diagnosis of AIDS; (3) characteristics of viral...
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Consumer spending creates pollution both directly and indirectly, through derived demand relationships. This paper estimates total generation of five air pollutants by family income class based on a large-scale input-output model of production, consumption, family income, and rediduals relationships. Pollution generation is shown to be disproportio...
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Due to the frequent occurrence of missing data in sample surveys, the major techniques for dealing with missing data (primarily imputation methods) have been formulated by survey statisticians in consultation with scientists performing survey research. One approach to the missing value problem is to formulate it as an optimization problem. This for...