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    Proceedings of the 2nd BEAT-PCD conference and 3rd PCD training school: part 1.
    BMC Proc 2018 5;12(Suppl 2). Epub 2018 Mar 5.
    8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.
    Primary ciliary dyskinesia (PCD) is a rare heterogenous condition that causes progressive suppurative lung disease, chronic rhinosinusitis, chronic otitis media, infertility and abnormal situs. 'Better Experimental Approaches to Treat Primary Ciliary Dyskinesia' (BEAT-PCD) is a network of scientists and clinicians coordinating research from basic science through to clinical care with the intention of developing treatments and diagnostics that lead to improved long-term outcomes for patients. BEAT-PCD activities are supported by EU funded COST Action (BM1407). Read More

    Building integrated pathways to independence for diverse biomedical researchers: , the BUILD program at Xavier University of Louisiana.
    BMC Proc 2017 4;11(Suppl 12):28. Epub 2017 Dec 4.
    3BUILD Program Office, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, LA 70125 USA.
    Background And Purpose: Xavier University of Louisiana is a historically Black and Catholic university that is nationally recognized for its science, technology, engineering and mathematics (STEM) curricula. Approximately 73% of Xavier's students are African American, and about 77% major in the biomedical sciences. Xavier is a national leader in the number of STEM majors who go on to receive M. Read More

    Evaluating efforts to diversify the biomedical workforce: the role and function of the Coordination and Evaluation Center of the Diversity Program Consortium.
    BMC Proc 2017 4;11(Suppl 12):27. Epub 2017 Dec 4.
    1Department of Medicine, David Geffen School of Medicine, Division of Geriatrics, University of California, Los Angeles, CA 90095 USA.
    Background: The National Institutes of Health (NIH)-funded Diversity Program Consortium (DPC) includes a Coordination and Evaluation Center (CEC) to conduct a longitudinal evaluation of the two signature, national NIH initiatives - the Building Infrastructure Leading to Diversity (BUILD) and the National Research Mentoring Network (NRMN) programs - designed to promote diversity in the NIH-funded biomedical, behavioral, clinical, and social sciences research workforce. Evaluation is central to understanding the impact of the consortium activities. This article reviews the role and function of the CEC and the collaborative processes and achievements critical to establishing empirical evidence regarding the efficacy of federally-funded, quasi-experimental interventions across multiple sites. Read More

    Advancing research opportunities and promoting pathways in graduate education: a systemic approach to BUILD training at California State University, Long Beach (CSULB).
    BMC Proc 2017 4;11(Suppl 12):26. Epub 2017 Dec 4.
    4College of Natural Sciences & Mathematics, California State University, Long Beach, CA 90840 USA.
    Background And Purpose: First-generation college graduates, racial and ethnic minorities, people with disabilities, and those from disadvantaged backgrounds are gravely underrepresented in the health research workforce representing behavioral health sciences and biomedical sciences and engineering (BHS/BSE). Furthermore, relative to their peers, very few students from these underrepresented groups (URGs) earn scientific bachelor's degrees with even fewer earning doctorate degrees. Therefore, programs that engage and retain URGs in health-related research careers early on in their career path are imperative to promote the diversity of well-trained research scientists who have the ability to address the nation's complex health challenges in an interdisciplinary way. Read More

    Enabling full representation in science: the San Francisco BUILD project's agents of change affirm science skills, belonging and community.
    BMC Proc 2017 4;11(Suppl 12):25. Epub 2017 Dec 4.
    4Department of Biology, San Francisco State University, San Francisco, CA 94132 USA.
    Background: The underrepresentation of minority students in the sciences constrains innovation and productivity in the U.S. The SF BUILD project mission is to remove barriers to diversity by taking a "fix the institution" approach rather than a "fix the student" one. Read More

    Think 500, not 50! A scalable approach to student success in STEM.
    BMC Proc 2017 4;11(Suppl 12):24. Epub 2017 Dec 4.
    Office of the Provost, University of Maryland, Baltimore County, Baltimore, MD 21250 USA.
    Background: UMBC, a diverse public research university, "builds" upon its reputation in producing highly capable undergraduate scholars to create a comprehensive new model, STEM BUILD at UMBC. This program is designed to help more students develop the skills, experience and motivation to excel in science, technology, engineering, and mathematics (STEM). This article provides an in-depth description of STEM BUILD at UMBC and provides the context of this initiative within UMBC's vision and mission. Read More

    A research-based inter-institutional collaboration to diversify the biomedical workforce: ReBUILDetroit.
    BMC Proc 2017 4;11(Suppl 12):23. Epub 2017 Dec 4.
    2Department of Biology, University of Detroit-Mercy, Detroit, MI 48221 USA.
    Background And Purpose: Faced with decades of severe economic decline, the city of Detroit, Michigan (USA) is on the cusp or reinventing itself. A Consortium was formed of three higher education institutions that have an established mission to serve an urban population and a vested interest in the revitalization of the health, welfare, and economic opportunity in the Detroit metro region that is synergistic with national goals to diversify the biomedical workforce. The purpose of this article is to describe the rationale, approach, and model of the Research Enhancement for BUILDing Detroit (ReBUILDetroit) Consortium, as a cross-campus collaborative for students, faculty, and institutional development. Read More

    A new approach to mentoring for research careers: the National Research Mentoring Network.
    BMC Proc 2017 4;11(Suppl 12):22. Epub 2017 Dec 4.
    1Institute for Clinical and Translational Research, University of Wisconsin, Madison, WI 53705 USA.
    Background And Purpose: Effective mentorship is critical to the success of early stage investigators, and has been linked to enhanced mentee productivity, self-efficacy, and career satisfaction. The mission of the National Research Mentoring Network (NRMN) is to provide all trainees across the biomedical, behavioral, clinical, and social sciences with evidence-based mentorship and professional development programming that emphasizes the benefits and challenges of diversity, inclusivity, and culture within mentoring relationships, and more broadly the research workforce. The purpose of this paper is to describe the structure and activities of NRMN. Read More

    Critical race theory as a bridge in science training: the California State University, Northridge BUILD PODER program.
    BMC Proc 2017 4;11(Suppl 12):21. Epub 2017 Dec 4.
    4Department of Educational Psychology and Counseling, Co-Director, Center for Assessment, Research, and Evaluation (CARE), Northridge, CA 91330-8265 USA.
    Background And Purpose: Unconscious bias and explicit forms of discrimination continue to pervade academic institutions. Multicultural and diversity training activities have not been sufficient in making structural and social changes leading to equity, therefore, a new form of critical consciousness is needed to train diverse scientists with new research questions, methods, and perspectives. The purpose of this paper is to describe Building Infrastructure Leading to Diversity (BUILD); Promoting Opportunities for Diversity in Education and Research (PODER), which is an undergraduate biomedical research training program based on transformative framework rooted in Critical Race Theory (CRT). Read More

    BUILD EXITO: a multi-level intervention to support diversity in health-focused research.
    BMC Proc 2017 4;11(Suppl 12):19. Epub 2017 Dec 4.
    1School of Community Health, College of Urban and Public Affairs, Portland State University, Portland, OR 97207 USA.
    Background And Purpose: As part of the NIH BUILD initiative to diversify the scientific workforce, the EXITO project is a large multi-institutional effort to provide comprehensive support and training for undergraduates from traditionally underrepresented student populations who aspire to health-related research careers. Portland State University, a major public urban university that prioritizes student access and opportunity, and Oregon Health & Science University, a research-intensive academic health center, lead the EXITO network comprised of eleven 2-year and 4-year institutions of higher education spanning Oregon, Washington, Alaska, Hawaii, Guam, American Samoa, and the Northern Mariana Islands. The EXITO project aims for impact in biomedical research by training diverse scholars from indigenous and underserved communities affected by adverse health disparities. Read More

    An entrepreneurial training model to enhance undergraduate training in biomedical research.
    BMC Proc 2017 4;11(Suppl 12):18. Epub 2017 Dec 4.
    1ASCEND Center for Biomedical Research, Division of Research & Economic Development, Morgan State University, Baltimore, MD USA.
    Background: Undergraduate students who are interested in biomedical research typically work on a faculty member's research project, conduct one distinct task (e.g., running gels), and, step by step, enhance their skills. Read More

    Enhancing research careers: an example of a US national diversity-focused, grant-writing training and coaching experiment.
    BMC Proc 2017 4;11(Suppl 12):16. Epub 2017 Dec 4.
    6Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108 USA.
    Background And Purpose: Preparing a successful research proposal is one of the most complex skills required of professional scientists, yet this skill is rarely if ever, taught. A major goal of the National Research Mentoring Network (NRMN) in the United States (U.S. Read More

    A participatory approach to evaluating a national training and institutional change initiative: the BUILD longitudinal evaluation.
    BMC Proc 2017 4;11(Suppl 12):15. Epub 2017 Dec 4.
    5Department of Community Health Sciences, Fielding School of Public Health, and UCLA Center for Health Policy Research, University of California, Los Angeles, CA 90095 USA.
    Background And Purpose: The National Institutes of Health (NIH) funds training programs to increase the numbers and skills of scientists who obtain NIH research grants, but few programs have been rigorously evaluated. The sizeable recent NIH investment in developing programs to increase the diversity of the NIH-funded workforce, implemented through the Diversity Program Consortium (DPC), is unusual in that it also funds a Consortium-wide evaluation plan, which spans the activities of the 10 BUilding Infrastructure Leading to Diversity (BUILD) awardees and the National Research Mentoring Network (NRMN). The purpose of this article is to describe the evaluation design and innovations of the BUILD Program on students, faculty, and institutions of the 10 primarily undergraduate BUILD sites. Read More

    Using collaborative approaches with a multi-method, multi-site, multi-target intervention: evaluating the National Research Mentoring Network.
    BMC Proc 2017 4;11(Suppl 12):14. Epub 2017 Dec 4.
    6Department of Community Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA USA.
    Background And Purpose: The NIH-funded National Research Mentoring Network (NRMN) aims to increase the representation and success of underrepresented groups (URGs) in biomedical research by enhancing the training and career development of individuals from diverse backgrounds, communities, and cultures. The national scope of NRMN, its wide array of innovative programs in mentor and mentee matching and training across the career spectrum, requires a collaborative evaluation strategy that addresses both internal and external evaluation needs. Due to the variety of programs implemented for each target group, the NRMN program is responsible for its own process and short-term outcome evaluations and the national Coordination and Evaluation Center (CEC) is responsible for assessing the medium and long-term effectiveness of the implemented strategies and program sustainability. Read More

    BUILDing BLaST: promoting rural students' biomedical research careers using a culturally responsive, one health approach.
    BMC Proc 2017 4;11(Suppl 12):13. Epub 2017 Dec 4.
    1University of Alaska Fairbanks Biomedical Learning and Student Training Program, Fairbanks, Alaska 99775 USA.
    Background And Purpose: Most postsecondary institutions in the state of Alaska (USA) have a broad mission to serve diverse students, many of whom come from schools in rural villages that are accessible only by plane, boat, or snowmobile. The major research university, the University of Alaska in Fairbanks (UAF), serves a population whereby 40% are from groups recognized as underrepresented in the biomedical workforce. The purpose of this article is to describe the Building Infrastructure Leading to Diversity (BUILD)-supported program in the state of Alaska that seeks to engage students from rural areas with a culturally relevant approach that is centered on the One Health paradigm, integrating human, animal, and environmental health. Read More

    BUILDing SCHOLARS: enhancing diversity among U.S. biomedical researchers in the Southwest.
    BMC Proc 2017 4;11(Suppl 12):12. Epub 2017 Dec 4.
    7Department of Electrical & Computer Engineering, University of Texas at El Paso, El Paso, TX 79968 USA.
    Background And Purpose: With funding from the National Institutes of Health, BUILDing SCHOLARS was established at The University of Texas at El Paso with the goal of implementing, evaluating and sustaining a suite of institutional, faculty and student development interventions in order to train the next generation of biomedical researchers from the U.S. Southwest region, where the need is dire among underserved communities. Read More

    Personalized medicine and Hispanic health: improving health outcomes and reducing health disparities - a National Heart, Lung, and Blood Institute workshop report.
    BMC Proc 2017 3;11(Suppl 11):11. Epub 2017 Oct 3.
    Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8856 USA.
    Persons of Hispanic/Latino descent may represent different ancestries, ethnic and cultural groups and countries of birth. In the U.S. Read More

    Proceedings from the CIH 5th Infectious Diseases Symposium 2016 "Drug Resistant Tuberculosis: Old Disease - New Challenge".
    BMC Proc 2017 4;11(Suppl 10). Epub 2017 Sep 4.
    Center for International Health - CIHLMU, Munich, Germany.
    The 5th CIH Infectious Disease Symposium, Munich, Germany, March 12, 2016 brought together Tuberculosis Experts from developed and low middle-income countries to discuss the control of drug resistance Tuberculosis. The meeting featured 9 presentations: Tuberculosis history and current scenario, Tuberculosis and migration - current scenario in Germany, Mechanism of Tuberculosis resistance development, Epidemiology of resistance - transmission vs. new generation of resistance, The impact of diagnostic in patients beyond - sensitivity and specificity, The Bangladesh regimen - new hope trough old drugs, New drugs and regimens - an overview on studies and Multi and Extensively Drug Resistant Tuberculosis from Europe. Read More

    Meeting report of the 2nd German dialectical behavior therapy for adolescents network meeting.
    BMC Proc 2016 4;10(Suppl 3). Epub 2016 Jul 4.
    Department of Child and Adolescent Psychiatry and Psychotherapy, University Medicine Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
    Over the past 30 years, dialectical behavior therapy has been shown to be an effective treatment for adult borderline personality disorder. The adaptation of DBT for adolescents (DBT-A) in different patient groups has also led to some promising improvements of the respective psychopathology. During the second German DBT-A network meeting in 2015 in Mainz, Germany, a need for further research and innovative approaches in treatment of adolescents became apparent and resulted in controversial discussions. Read More

    Proceedings of the COST action BM1407 inaugural conference BEAT-PCD: translational research in primary ciliary dyskinesia - bench, bedside, and population perspectives.
    BMC Proc 2016 29;10(Suppl 9):66. Epub 2016 Nov 29.
    Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
    Primary ciliary dyskinesia (PCD) is a rare heterogenous condition that causes progressive suppurative lung disease, chronic rhinosinusitis, chronic otitis media, infertility and abnormal situs. 'Better Experimental Approaches to Treat Primary Ciliary Dyskinesia' (BEAT-PCD) is a network of scientists and clinicians coordinating research from basic science through to clinical care with the intention of developing treatments and diagnostics that lead to improved long-term outcomes for patients. BEAT-PCD activities are supported by EU Framework Programme Horizon 2020 funded COST Action (BM1407). Read More

    Transforming Health Care in Remote Communities: report on an international conference.
    BMC Proc 2016 10;10(Suppl 6). Epub 2016 Aug 10.
    John H. Daniels Faculty of Architecture, Landscape and Design, University of Toronto, Toronto, Canada.
    An international conference titled "Transforming Health Care in Remote Communities" was held at the Chateau Lacombe Hotel in Edmonton, Canada, April 28-30, 2016. The event was organized by the University of Alberta's School of Public Health, in partnership with the Institute for Circumpolar Health Research in Yellowknife, Northwest Territories, and the Qaujigiartiit Health Research Centre in Iqaluit, Nunavut. There were 150 registrants from 7 countries: Canada (7 provinces and 3 territories), United States, Denmark, Iceland, Norway, Sweden, and Australia. Read More

    The African cholera surveillance network (Africhol) consortium meeting, 10-11 June 2015, Lomé, Togo.
    BMC Proc 2017 31;11(Suppl 1). Epub 2017 Jan 31.
    Agence de Médecine Préventive, 21 bd Pasteur, 75015 Paris, France.
    The fifth annual meeting of the African cholera surveillance network (Africhol) took place on 10-11 June 2015 in Lomé, Togo. Together with international partners, representatives from the 11 member countries -Cameroon, Côte d'Ivoire, Democratic Republic of Congo, Guinea, Kenya, Mozambique, Nigeria, Tanzania, Togo, Uganda, Zimbabwe- and an invited country (Malawi) shared their experience. The meeting featured three sessions: i) cholera surveillance, prevention and control in participating countries, ii) cholera surveillance methodology, such as cholera mapping, cost-effectiveness studies and the issue of overlapping epidemics from different diseases, iii) cholera laboratory diagnostics tools and capacity building. Read More

    Reflections on 'medical tourism' from the 2016 Global Healthcare Policy and Management Forum.
    BMC Proc 2017 13;11(Suppl 8). Epub 2017 Jul 13.
    Department of Health Administration, Yonsei University, Wonju, South Korea.
    In October 2016, the Global Healthcare Policy and Management Forum was held at Yonsei University, Seoul, South Korea. The goal of the forum was to discuss the role of the state in regulating and supporting the development of medical tourism. Forum attendees came from 10 countries. Read More

    The activity of the Research Investments in Global Health study and ways forward within the global funding and policy landscape.
    BMC Proc 2016 10;10(Suppl 8):59. Epub 2016 Oct 10.
    Global Health Research Institute and Faculty of Medicine, University of Southampton, Southampton, UK.
    The Research Investments in Global Health (ResIn, study analyses funding trends in health research, with a predominant focus on infectious diseases. Read More

    Recommendations for action: a community meeting in preparation for a mass-casualty opioid overdose event in Southeastern Ontario.
    BMC Proc 2017 18;11(Suppl 7). Epub 2017 Jul 18.
    Public Health Ontario, Toronto, M5G 1V2 Canada.
    Given the steady rise of overdose morbidity and mortality in North America, and increasing frequency of sudden clusters of non-fatal and fatal overdoses in other jurisdictions, regional preparedness plans to respond effectively to clusters of overdoses may reduce the impact of such events on the population. On the 27th of February 2017 in Kingston, Ontario, KFL&A Public Health, in collaboration with public health partners, hosted a full-day workshop involving table-top exercises and discussions for service partners on how to prepare for, respond to, and manage a mass-casualty event secondary to opioid overdose in Southeastern Ontario. The workshop assisted in identifying the various challenges faced by service partners, provided an understanding of the roles and responsibilities of partner agencies, and helped to determine next steps in preparation to address a mass opioid overdose situation at the local level. Read More

    Vaccination ecosystem health check: achieving impact today and sustainability for tomorrow.
    BMC Proc 2017 27;11(Suppl 2). Epub 2017 Jan 27.
    Valera, Cambridge, MA 02141 USA.
    Background: Vaccination is a complex ecosystem with several components that interact with one another and with the environment. Today's vaccine ecosystem is defined by the pursuit of polio eradication, the drive to get as many of the new vaccines to as many people as possible and the research and development against immunologically challenging diseases. Despite these successes, vaccine ecosystem is facing keys issues with regard to supply/distribution and cost/profitability asymmetry that risk slowing its global growth. Read More

    Causal effect estimation in sequencing studies: a Bayesian method to account for confounder adjustment uncertainty.
    BMC Proc 2016 18;10(Suppl 7):411-415. Epub 2016 Oct 18.
    Department of Biostatistics, College of Public Health, University of Kentucky, 725 Rose St, Lexington, KY 40536 USA.
    Estimating the causal effect of a single nucleotide variant (SNV) on clinical phenotypes is of interest in many genetic studies. The effect estimation may be confounded by other SNVs as a result of linkage disequilibrium as well as demographic and clinical characteristics. Because a large number of these other variables, which we call potential confounders, are collected, it is challenging to select and adjust for the variables that truly confound the causal effect. Read More

    Comparing performance of non-tree-based and tree-based association mapping methods.
    BMC Proc 2016 18;10(Suppl 7):405-410. Epub 2016 Oct 18.
    Department of Biostatistics, University of Kentucky College of Public Health, Lexington, KY 40536-0003 USA.
    A central goal in the biomedical and biological sciences is to link variation in quantitative traits to locations along the genome (single nucleotide polymorphisms). Sequencing technology has rapidly advanced in recent decades, along with the statistical methodology to analyze genetic data. Two classes of association mapping methods exist: those that account for the evolutionary relatedness among individuals, and those that ignore the evolutionary relationships among individuals. Read More

    Using next-generation DNA sequence data for genetic association tests based on allele counts with and without consideration of zero inflation.
    BMC Proc 2016 18;10(Suppl 7):397-404. Epub 2016 Oct 18.
    Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, 69120 Germany.
    The relationship between genetic variability and individual phenotypes is usually investigated by testing for association relying on called genotypes. Allele counts obtained from next-generation sequence data could be used for this purpose too. Genetic association can be examined by treating alternative allele counts (AACs) as the response variable in negative binomial regression. Read More

    Identification of low frequency and rare variants for hypertension using sparse-data methods.
    BMC Proc 2016 11;10(Suppl 7):389-395. Epub 2016 Oct 11.
    Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, ON M5T 3L9 Canada.
    Availability of genomic sequence data provides opportunities to study the role of low-frequency and rare variants in the etiology of complex disease. In this study, we conduct association analyses of hypertension status in the cohort of 1943 unrelated Mexican Americans provided by Genetic Analysis Workshop 19, focusing on exonic variants in on chromosome 3. Our primary interest is to compare the performance of standard and sparse-data approaches for single-variant tests and variant-collapsing tests for sets of rare and low-frequency variants. Read More

    Type I error rates of rare single nucleotide variants are inflated in tests of association with non-normally distributed traits using simple linear regression methods.
    BMC Proc 2016 18;10(Suppl 7):385-388. Epub 2016 Oct 18.
    Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224 USA.
    In this study, the effects of (a) the minor allele frequency of the single nucleotide variant (SNV), (b) the degree of departure from normality of the trait, and (c) the position of the SNVs on type I error rates were investigated in the Genetic Analysis Workshop (GAW) 19 whole exome sequence data. To test the distribution of the type I error rate, 5 simulated traits were considered: standard normal and gamma distributed traits; 2 transformed versions of the gamma trait (log and rank-based inverse normal transformations); and trait Q1 provided by GAW 19. Each trait was tested with 313,340 SNVs. Read More

    Identifying rare and common variants with Bayesian variable selection.
    BMC Proc 2016 18;10(Suppl 7):379-384. Epub 2016 Oct 18.
    Biostatistics, Department of Population Health, New York University, New York, NY 10016 USA.
    Background: Recent advances in next-generation sequencing technologies have made it possible to generate large amounts of sequence data with rare variants in a cost-effective way. Yet, the statistical aspect of testing disease association of rare variants is quite challenging as the typical assumptions fail to hold owing to low minor allele frequency (<0.5 or 1 %). Read More

    Comparison of 2 models for gene-environment interactions: an example of simulated gene-medication interactions on systolic blood pressure in family-based data.
    BMC Proc 2016 18;10(Suppl 7):371-377. Epub 2016 Oct 18.
    Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514 USA.
    Background: Nearly half of adults in the United States who are diagnosed with hypertension use blood-pressure-lowering medications. Yet there is a large interindividual variability in the response to these medications. Two complementary gene-environment interaction methods have been published and incorporated into publicly available software packages to examine interaction effects, including whether genetic variants modify the association between medication use and blood pressure. Read More

    Association of rare haplotypes on and genes with hypertension.
    BMC Proc 2016 15;10(Suppl 7):363-369. Epub 2016 Nov 15.
    Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX USA.
    Several variants have been implicated earlier on and genes on chromosome 3 to be associated with hypertension. As a natural follow-up step, we explore association of haplotypes in those genes. We consider the Genetic Analysis Workshop 19 real data on unrelated individuals and analyze haplotype blocks of 5 single-nucleotide polymorphisms through a sliding window approach. Read More

    Estimating relationships between phenotypes and subjects drawn from admixed families.
    BMC Proc 2016 18;10(Suppl 7):357-362. Epub 2016 Oct 18.
    Department of Biostatistics, University of Washington, Seattle, WA 98195 USA.
    Background: Estimating relationships among subjects in a sample, within family structures or caused by population substructure, is complicated in admixed populations. Inaccurate allele frequencies can bias both kinship estimates and tests for association between subjects and a phenotype. We analyzed the simulated and real family data from Genetic Analysis Workshop 19, and were aware of the simulation model. Read More

    A multistep approach to single nucleotide polymorphism-set analysis: an evaluation of power and type I error of gene-based tests of association after pathway-based association tests.
    BMC Proc 2016 18;10(Suppl 7):349-355. Epub 2016 Oct 18.
    Department of Mathematics, Statistics and Computer Science, Dordt College, 498 4th Ave. NE, Dordt College, Sioux Center, IA 51250 USA.
    The aggregation of functionally associated variants given a priori biological information can aid in the discovery of rare variants associated with complex diseases. Many methods exist that aggregate rare variants into a set and compute a single value summarizing association between the set of rare variants and a phenotype of interest. These methods are often called gene-based, rare variant tests of association because the variants in the set are often all contained within the same gene. Read More

    Association of polymorphisms in the aldosterone-regulated sodium reabsorption pathway with blood pressure among Hispanics.
    BMC Proc 2016 18;10(Suppl 7):343-348. Epub 2016 Oct 18.
    Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153 USA.
    Background: Whereas genome-wide association study (GWAS) has proven to be an important tool for discovery of variants influencing many human diseases and traits, unfortunately its performance has not been much of all-around success for some complex conditions, for example, hypertension. Because some of the existing effective pharmacotherapeutic agents act by targeting known biological pathways, pathway-based analytical approaches could lead to more success in discovery of disease-associated variants. The objective of the present study was to identify functional variants associated with blood pressure in the aldosterone-regulated sodium reabsorption pathway using the simulated and real blood pressure phenotypes provided for Genetic Analysis Workshop 19. Read More

    A variance component method for integrated pathway analysis of gene expression data.
    BMC Proc 2016 18;10(Suppl 7):337-342. Epub 2016 Oct 18.
    South Texas Diabetes and Obesity Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229 USA.
    Background: The application of pathway and gene-set based analyses to high-throughput data is increasingly common and represents an effort to understand underlying biology where single-gene or single-marker analyses have failed. Many such analyses rely on the a priori identification of genes associated with the trait of interest. In contrast, this variance-component-based approach creates a similarity matrix of individuals based on the expression of genes in each pathway. Read More

    Network-guided interaction mining for the blood pressure phenotype of unrelated individuals in genetic analysis workshop 19.
    BMC Proc 2016 18;10(Suppl 7):333-336. Epub 2016 Oct 18.
    Department of Statistics, Columbia University, New York, 10027 USA.
    Interactions between genes are an important part of the genetic architecture of complex diseases. In this paper, we use literature-guided individual genes known to be associated with type 2 diabetes (referred to as "seed genes") to create a larger list of genes that share implied or direct networks with these seed genes. This larger list of genes are known to interact with each other, but whether they interact in ways to influence hypertension in individuals presents an interesting question. Read More

    Constrained multivariate association with longitudinal phenotypes.
    BMC Proc 2016 18;10(Suppl 7):329-332. Epub 2016 Oct 18.
    South Texas Diabetes and Obesity Institute, University of Texas Health Science Center, San Antonio, TX 78229 USA ; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA ; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.
    Background: The incorporation of longitudinal data into genetic epidemiological studies has the potential to provide valuable information regarding the effect of time on complex disease etiology. Yet, the majority of research focuses on variables collected from a single time point. This aim of this study was to test for main effects on a quantitative trait across time points using a constrained maximum-likelihood measured genotype approach. Read More

    Genome-wide association of trajectories of systolic blood pressure change.
    BMC Proc 2016 18;10(Suppl 7):321-327. Epub 2016 Oct 18.
    Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514 USA.
    Background: There is great interindividual variation in systolic blood pressure (SBP) as a result of the influences of several factors, including sex, ancestry, smoking status, medication use, and, especially, age. The majority of genetic studies have examined SBP measured cross-sectionally; however, SBP changes over time, and not necessarily in a linear fashion. Therefore, this study conducted a genome-wide association (GWA) study of SBP change trajectories using data available through the Genetic Analysis Workshop 19 (GAW19) of 959 individuals from 20 extended Mexican American families from the San Antonio Family Studies with up to 4 measures of SBP. Read More

    Multipoint association mapping for longitudinal family data: an application to hypertension phenotypes.
    BMC Proc 2016 18;10(Suppl 7):315-320. Epub 2016 Oct 18.
    Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, 27157 USA.
    It is essential to develop adequate statistical methods to fully utilize information from longitudinal family studies. We extend our previous multipoint linkage disequilibrium approach-simultaneously accounting for correlations between markers and repeat measurements within subjects, and the correlations between subjects in families-to detect loci relevant to disease through gene-based analysis. Estimates of disease loci and their genetic effects along with their 95 % confidence intervals (or significance levels) are reported. Read More

    Joint analysis of multiple blood pressure phenotypes in GAW19 data by using a multivariate rare-variant association test.
    BMC Proc 2016 18;10(Suppl 7):309-313. Epub 2016 Oct 18.
    Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 1A2 Canada ; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2 Canada ; Department of Oncology, McGill University, Montreal, QC H2W 1S6 Canada ; Department of Human Genetics, McGill University, Montreal, QC H3A 1B1 Canada.
    Introduction: Large-scale sequencing studies often measure many related phenotypes in addition to the genetic variants. Joint analysis of multiple phenotypes in genetic association studies may increase power to detect disease-associated loci.

    Methods: We apply a recently developed multivariate rare-variant association test to the Genetic Analysis Workshop 19 data in order to test associations between genetic variants and multiple blood pressure phenotypes simultaneously. Read More

    Structural equation modeling with latent variables for longitudinal blood pressure traits using general pedigrees.
    BMC Proc 2016 18;10(Suppl 7):303-307. Epub 2016 Oct 18.
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA ; Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106 USA.
    Structural equation modeling (SEM) has been used in a wide range of applied sciences including genetic analysis. The recently developed R package, implements a framework for SEM for general pedigree data. We explored different SEM techniques using to analyze the multivariate longitudinal data and to ultimately test the association of genotypes on blood pressure traits. Read More

    Identity-by-descent estimation with population- and pedigree-based imputation in admixed family data.
    BMC Proc 2016 18;10(Suppl 7):295-301. Epub 2016 Oct 18.
    Department of Biostatistics, University of Washington, Seattle, WA USA ; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA USA ; Department of Genome Sciences, University of Washington, Seattle, WA USA.
    Background: In the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, although both family- and population-based imputation methods have been proposed. With the recent surge of family-based designs, family-based imputation has become more important. Imputation methods for both designs are based on identity-by-descent (IBD) information. Read More

    Genetic association analysis based on a joint model of gene expression and blood pressure.
    BMC Proc 2016 18;10(Suppl 7):289-294. Epub 2016 Oct 18.
    Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
    Recent work on genetic association studies suggests that much of the heritable variation in complex traits is unexplained, which indicates a need for using more biologically meaningful modeling approaches and appropriate statistical methods. In this study, we propose a biological framework and a corresponding statistical model incorporating multilevel biological measures, and illustrate it in the analysis of the real data provided by the Genetic Analysis Workshop (GAW) 19, which contains whole genome sequence (WGS), gene expression (GE), and blood pressure (BP) data. We investigate the direct effect of single-nucleotide variants (SNVs) on BP and GE, while considering the non-directional dependence between BP and GE, by using copula functions to jointly model BP and GE conditional on SNVs. Read More

    Integrating multiple genomic data: sparse representation based biomarker selection for blood pressure.
    BMC Proc 2016 18;10(Suppl 7):283-288. Epub 2016 Oct 18.
    Unit on Statistical Genomics, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Building 35, Room 3A 1000, 35 Convent Drive, Bethesda, MD 20892 USA.
    Background: Although many genes have been implicated as hypertension candidates, to date, few studies have integrated different types of genomic data for the purpose of biomarker selection.

    Methods: Applying a newly proposed sparse representation based variable selection (SRVS) method to the Genetic Analysis Workshop19 data, we analyzed a combined data set consisting of 11522 gene expressions and 354893 single-nucleotide polymorphisms (SNPs) from 397 subjects (case/control: 151/246), with the aim to identify potential biomarkers for blood pressure using both gene expression measures and SNP data.

    Results: Among the top 1000 variables (SNPs/gene expressions = 575/425) selected, the bioinformatics analysis showed that 302 were plausibly associated with blood pressure. Read More

    Incorporation of protein binding effects into likelihood ratio test for exome sequencing data.
    BMC Proc 2016 18;10(Suppl 7):275-281. Epub 2016 Oct 18.
    Mathematics Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609-2280 USA.
    Statistical association studies are an important tool in detecting novel disease genes. However, for sequencing data, association studies confront the challenge of low power because of relatively small data sample size and rare variants. Incorporating biological information that reflects disease mechanism is likely to strengthen the association evidence of disease genes, and thus increase the power of association studies. Read More

    Comparing strategies for combined testing of rare and common variants in whole sequence and genome-wide genotype data.
    BMC Proc 2016 18;10(Suppl 7):269-273. Epub 2016 Oct 18.
    Department of Genetic Epidemiology, University Medical Center, Georg-August University Göttingen, Humboldtallee 32, 37073 Göttingen, Germany.
    We used our extension of the kernel score test to family data to analyze real and simulated baseline systolic blood pressure in extended pedigrees. We compared the power for different kernels and for different weightings of genetic markers. Moreover, we compared the power of rare and common markers with 3 strategies for joint testing and on marker panels with different densities. Read More

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