Digital Commons Network^™

Implementing Educational And Systems-Level Changes To Improve Cancer Screening Rates Among State Employees In Missouri, Misty A Phillips, Sarah Chavez, Maggie Grotefendt, Xarria Lewis, Melanie Gowdy, Jane A Mcelroy, Jean S Wang, Sandra Hentges

2020-Current year OA Pubs

As of 2022, only 51% of active eligible state employees in Missouri have been screened for colorectal cancer and 67% for breast cancer, despite having state-sponsored health insurance. In fall 2020, the Missouri Department of Health and Senior Services Comprehensive Cancer Program partnered with the Missouri Cancer Consortium to create a strategy to improve cancer screening rates among state employees. The project was designed to include 3 phases: 1) a colorectal cancer education phase, 2) an expanded education phase that included additional cancers, and 3) a proposed intervention phase that will include screening events. In the first phase, in 2020, …

Approaches To Healthcare Personnel Exemption Requests From Coronavirus Disease 2019 (Covid-19) Vaccination: Results Of A National Survey, Thomas R Talbot, Susan E Beekmann, Hilary M Babcock, Philip M Polgreen

2020-Current year OA Pubs

OBJECTIVE: Although a growing number of healthcare facilities are implementing healthcare personnel (HCP) coronavirus disease 2019 (COVID-19) vaccination requirements, vaccine exemption request management as a part of such programs is not well described.

DESIGN: Cross-sectional survey.

PARTICIPANTS: Infectious disease (ID) physician members of the Emerging Infections Network with infection prevention or hospital epidemiology responsibilities.

METHODS: Eligible persons were sent a web-based survey focused on hospital plans and practices around exemption allowances from HCP COVID-19 vaccine requirements.

RESULTS: Of the 695 ID physicians surveyed, 263 (38%) responded. Overall, 160 respondent institutions (92%) allowed medical exemptions, whereas 132 (76%) allowed religious exemptions. …

Changes In Biceps Brachii Muscle Hardness Assessed By A Push-In Meter And Strain Elastography After Eccentric Versus Concentric Contractions, Mitsuyoshi Murayama, Takayuki Inami, Norihiro Shima, Tsugutake Yoneda, Kazunori Nosaka

Research outputs 2022 to 2026

Changes in biceps brachii muscle hardness assessed by a push-in meter (PM) and strain elastography (SE) were compared between eccentric (ECC) and concentric contractions (CON) of the elbow flexors to test the hypothesis that muscle hardness would increase greater after ECC. Ten men performed 5 sets of 10 ECC with their non-dominant arms and 5 sets of 10 CON with their dominant arms using a dumbbell corresponding to 50% of maximum voluntary isometric contraction (MVIC) force at 90º elbow flexion. Before and 1–4 days after the exercise, MVIC force, elbow joint angles, upper-arm circumference, and muscle soreness as muscle damage …

Opensep: A Generalizable Open Source Pipeline For Sofa Score Calculation And Sepsis-3 Classification, Mackenzie R Hofford, Sean C Yu, Alistair E W Johnson, Albert M Lai, Philip R O Payne, Andrew P Michelson

2020-Current year OA Pubs

EHR-based sepsis research often uses heterogeneous definitions of sepsis leading to poor generalizability and difficulty in comparing studies to each other. We have developed OpenSep, an open-source pipeline for sepsis phenotyping according to the Sepsis-3 definition, as well as determination of time of sepsis onset and SOFA scores. The Minimal Sepsis Data Model was developed alongside the pipeline to enable the execution of the pipeline to diverse sources of electronic health record data. The pipeline's accuracy was validated by applying it to the MIMIC-IV version 1.0 data and comparing sepsis onset and SOFA scores to those produced by the pipeline …

Metal Transfer To Sediments, Invertebrates And Fish Following Waterborne Exposure To Silver Nitrate Or Silver Sulfide Nanoparticles In An Indoor Stream Mesocosm, Nathaniel Clark, Joanne Vassallo, Pv Silva, Arr Silva, Marta Baccaro, Neja Medvešček, Magdalena Grgić, Abel Ferreira, Martí Busquets-Fité, Kerstin Jurkschat, Anastasios G. Papadiamantis, Victor Puntes, Iseult Lynch, Claus Svendsen, Den Brink Nw Van, Gestel Cam Van, Susana Loureiro, Richard D. Handy

School of Health Professions

No abstract provided.

Tyre Particle Exposure Affects The Health Of Two Key Estuarine Invertebrates, S. L. Garrard, J. I. Spicer, R. C. Thompson

School of Biological and Marine Sciences

Tyre wear particles may be the largest source of microplastic to the natural environment, yet information on their biological impacts is inadequate. Two key estuarine invertebrates; the clam Scrobicularia plana and the ragworm Hediste diversicolor were exposed to 10% tyre particles in sediment for three days. Both species consumed the particles, although S. plana consumed 25x more than H. diversicolor (967 compared with 35 particles.g−1 wet weight, respectively). We then investigated the impact of 21 days exposure to different concentrations of tyre particles in estuarine sediments (0.2, 1, and 5% dry weight sediment) on aspects of the health of S. …

Democracy And Schooling: The Paradox Of Co‐Operative Schools In A Neoliberal Age?, Tom Woodin, Cath Gristy

Plymouth Institute of Education

From the first co-operative trust school at Reddish Vale in Manchester in 2006, the following decade would witness a remarkable growth of ‘co-operative schools’ in England, which at one point numbered over 850. This paper outlines the key development of democratic education by the co-operative schools network. It explains the approach to democracy and explores the way values were put into practice. At the heart of co-operativism lay a tension between engaging with technical everyday reforms and utopian transformative visions of an educational future. A new arena of debate and practice was established with considerable importance for our understanding of …

Association Of Visceral Adiposity Index With Incident Nephropathy And Retinopathy: A Cohort Study In The Diabetic Population, Zhiyuan Wu, Siqi Yu, Xiaoping Kang, Yue Liu, Zongkai Xu, Zhiwei Li, Jinqi Wang, Xinlei Miao, Xiangtong Liu, Xia Li, Jingbo Zhang, Wei Wang, Lixin Tao, Xiuhua Guo

Research outputs 2022 to 2026

Background: The association between visceral adiposity index (VAI) and diabetic complications has been reported in cross-sectional studies, while the effect of VAI on complication development remains unclear. This study aims to evaluate the longitudinal association of VAI and Chinese VAI (CVAI) with the incidence of diabetic nephropathy and retinopathy using a Chinese cohort. Methods: A total of 8 948 participants with type 2 diabetes from Beijing Health Management Cohort were enrolled during 2013–2014, and followed until December 31, 2019. Nephropathy was confirmed by urine albumin/creatinine ratio and estimated glomerular filtration rate; retinopathy was diagnosed using fundus photograph. Results: The mean …

Characterizing The Diversity Of Mhc Conserved Extended Haplotypes Using Families From The United Arab Emirates, Halima Alnaqbi, Guan K. Tay, Sarah El Hajj Chehadeh, Habiba Alsafar

Research outputs 2022 to 2026

Aside from its anthropological relevance, the characterization of the allele frequencies of genes in the human Major Histocompatibility Complex (MHC) and the combination of these alleles that make up MHC conserved extended haplotypes (CEHs) is necessary for histocompatibility matching in transplantation as well as mapping disease association loci. The structure and content of the MHC region in Middle Eastern populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. This study was conceived to address a gap of knowledge, aiming to …

The Multifaceted Mechanisms Of Malignant Glioblastoma Progression And Clinical Implications, Rui Sun, Albert H Kim

2020-Current year OA Pubs

With the application of high throughput sequencing technologies at single-cell resolution, studies of the tumor microenvironment in glioblastoma, one of the most aggressive and invasive of all cancers, have revealed immense cellular and tissue heterogeneity. A unique extracellular scaffold system adapts to and supports progressive infiltration and migration of tumor cells, which is characterized by altered composition, effector delivery, and mechanical properties. The spatiotemporal interactions between malignant and immune cells generate an immunosuppressive microenvironment, contributing to the failure of effective anti-tumor immune attack. Among the heterogeneous tumor cell subpopulations of glioblastoma, glioma stem cells (GSCs), which exhibit tumorigenic properties and …

Cortical Bone Relationships Are Maintained Regardless Of Sex And Diet In A Large Population Of Lgxsm Advanced Intercross Mice, Nicole Migotsky, Michael D Brodt, James M Cheverud, Matthew J Silva

2020-Current year OA Pubs

INTRODUCTION: Knowledge of bone structure-function relationships in mice has been based on relatively small sample sets that limit generalizability. We sought to investigate structure-function relationships of long bones from a large population of genetically diverse mice. Therefore, we analyzed previously published data from the femur and radius of male and female mice from the F34 generation of the Large-by-Small advanced intercross line (LGXSM AI), which have over a two-fold continuous spread of bone and body sizes (Silva et al. 2019 JBMR).

METHODS: Morphological traits, mechanical properties, and estimated material properties were collected from the femur and radius from 1113 LGXSM …

Defining Terms Commonly Used In Sarcopenia Research: A Glossary Proposed By The Global Leadership In Sarcopenia (Glis) Steering Committee, Peggy M Cawthon, Ellen Binder, Et Al.

2020-Current year OA Pubs

METHODS: The aim of this paper is to define terms commonly related to sarcopenia to enable standardization of these terms in research and clinical settings. The Global Leadership Initiative in Sarcopenia (GLIS) aims to bring together leading investigators in sarcopenia research to develop a single definition that can be utilized worldwide; work on a global definition of sarcopenia is ongoing. The first step of GLIS is to develop the common terminology, or a glossary, that will facilitate agreement on a global definition of sarcopenia as well as interpretation of clinical and research findings.

RESULTS: Several terms that are commonly used …

Western Australian Adolescent Emotional Wellbeing During The Covid-19 Pandemic In 2020, H. M. Thomas, K. C. Runions, L. Lester, K. Lombardi, M. Epstein, J. Mandzufas, T. Barrow, S. Ang, A. Leahy, M. Mullane, A. Whelan, J. Coffin, F. Mitrou, S. R. Zubrick, A. C. Bowen, P. W. Gething, D. Cross

Research outputs 2022 to 2026

Background:

The impacts of the COVID-19 pandemic have been vast and are not limited to physical health. Many adolescents have experienced disruptions to daily life, including changes in their school routine and family’s financial or emotional security, potentially impacting their emotional wellbeing. In low COVID-19 prevalence settings, the impact of isolation has been mitigated for most young people through continued face-to-face schooling, yet there may still be significant impacts on their wellbeing that could be attributed to the pandemic.

Methods:

We report on data from 32,849 surveys from Year 7–12 students in 40 schools over two 2020 survey cycles (June/July: …

Medicines And Vaccines Supply Chains Challenges In Nigeria: A Scoping Review, Victory O. Olutuase, Chinwe J. Iwu-Jaja, Cynthia P. Akuoko, Emmanuel O. Adewuyi, Vishnu Khanal

Research outputs 2022 to 2026

Background:

Medicines and vaccines supply chains represent critical systems for realising one of the major targets of the United Nations’ third Sustainable Development Goals (SDGs)- access to safe, effective, quality, and affordable essential medicines and vaccines, for all. However, evidence suggests the system is confronted with several challenges in many low-medium income countries, including Nigeria. This scoping review aims to summarize the available evidence on the challenges of medicines and vaccines supply chain system in Nigeria.

Results:

We searched relevant databases including Scopus and Web of Science for studies published between January 2005 and August 2020 on the challenges associated …

Geotemporospatial And Causal Inference Epidemiological Analysis Of Us Survey And Overview Of Cannabis, Cannabidiol And Cannabinoid Genotoxicity In Relation To Congenital Anomalies 2001–2015, Albert Stuart Reece, Gary Kenneth Hulse

Research outputs 2022 to 2026

Background:

Cannabinoids including cannabidiol have recognized genotoxic activities but their significance has not been studied broadly epidemiologically across the teratological spectrum. We examined these issues including contextual space-time relationships and formal causal inferential analysis in USA.

Methods:

State congenital anomaly (CA) rate (CAR) data was taken from the annual reports of the National Birth Defects Prevention Network 2001–2005 to 2011–2015. Substance abuse rates were from the National Survey of Drug Use and Health a nationally representative longitudinal survey of the non-institutionalized US population with 74.1% response rate. Drugs examined were cigarettes, monthly and binge alcohol, monthly cannabis and analgesic and …

Effectiveness Of Mobile Apps To Improve Urinary Incontinence: A Systematic Review Of Randomised Controlled Trials, Renee Widdison, Amineh Rashidi, Lisa Whitehead

Research outputs 2022 to 2026

Introduction: Pelvic floor exercises are effective in the treatment of urinary incontinence (UI) and are routinely prescribed, along with bladder training, by primary healthcare providers as first line conservative management. Mobile phone applications are increasingly popular within the healthcare setting and can provide opportunities for patients to complete treatments at home. To date, there has not been a systematic review examining outcomes from randomised controlled trials on the effectiveness of mobile applications to improve UI. Methods: A systematic review of randomized controlled trials evaluating the effectiveness of mobile applications to improve UI was carried out according to the PRISMA reporting …

Nursing Practicum Equity For A Changing Nurse Student Demographic: A Qualitative Study, Lesley Andrew, Julie Dare, Ken Robinson, Leesa Costello

Research outputs 2022 to 2026

Background: The nursing practicum (clinical practice) is an essential but often highly stressful aspect of the nursing degree. A review of the published literature reveals a strong focus on the stressors that originate within the practicum environment, rather than the student’s life outside the university and practice setting. This article reports on an Australian study, completed before the COVID-19 pandemic, of the university experiences of undergraduate women nurse students with family responsibilities. The findings reveal the importance of factors outside the university on the women students’ practicum experience and their ability to engage and achieve. Methods: The study was qualitative, …

Physical And Technical Demands Of Australian Football: An Analysis Of Maximum Ball In Play Periods, Christopher Wing, Nicolas H. Hart, Fadi Ma’Ayah, Kazunori Nosaka

Research outputs 2022 to 2026

Background: This study compares ball in play (BiP) analyses and both whole game (WG) and quarter averaged data for physical and technical demands of sub-elite Australian football (AF) players competing in the West Australian Football League across playing positions. Methods: Microsensor data were collected from 33 male AF players in one club over 19 games of the 2019 season. BiP time periods and technical performance data (e.g., kicks) were acquired from the Champion Data timeline of statistics, and time matched to the microsensor data. Linear mixed modelling was utilised to establish differences between maximum BiP periods and averaged data. Results: …

The Production And Destiny Of Public Space In An American City: Examining The Emergence And Disruption Of Brooklyn City Hall Square, Jason Montgomery

Publications and Research

Urban form should reflect collective value for place in communities. Urban squares in particular have the potential to serve as the nucleus of communities, urban artefacts that link place to memory and heritage while serving basic needs for everyday life in the city. Civic squares, those linked to governmental institutions, have further potential to facilitate community gatherings for memorialisation, commemoration, celebration and political action. Despite these important functions and potential, the incremental planning of Brooklyn in the early nineteenth century placed little emphasis on squares of any kind, despite the community’s expressed desires. Brooklyn’s first civic square, here referred to …

Designing Of X-Ray Beams To Assess Mineral Loss In Dehydrated Fruits – Radiology Readiness During Climate Change, Angela Moore, Katie Tam

Publications and Research

Key minerals such as iron, manganese and copper are necessary for optimal health and vitality of human beings. These minerals are within the biomolecules of food, particularly in fruits and are not detectable without destroying their natural biochemical roles. A compilation was done on average mineral compositions for multiple apple varieties from USDA and academic horticulture research labs to design the x-ray beams in the low energy ranges in our mammography system that provide “soft” x-rays for imaging light-weight atoms. In this project homemade external filters like Aluminum sheets, Iodine and Gadolinium contrast media were developed to modify low energy …

How Will Climate Change Affect The Future, Ashanti K. Belone, Farrukh Zia

Publications and Research

Climate Change has played a massive role in the habitat of us earth dwellers and the animals that co-exists with us. I believe that essentially climate change plays a massive role because this can dictate whether or not the earth is habitable and if a need for evacuation is necessary. Many might believe that climate change only refers to the rising temperature but that’s just the icing on the cake. Earth is a system that is very much connected, this means that changes in one area will set off a chain reaction allowing these changes to happen in many other …

Studying Factors Of Environmental Injustice And Ways To Achieve Equity, Arham Hussain, Reginald Metellus

Publications and Research

In today's day of age, the biggest concern for current and future generations: the environment. The urban heat island (UHi) with its significant energy, health, and societal impacts is among the major environmental issues in urban regions, especially in historically underserved and socially vulnerable communities (HUSVCs). In the 1930s, the former federal agency, Homeowners' Loan Corporation (H0Lq, created ''Residential Security" maps of major cities, known today as "redlined" areas. These neighborhoods were often designated as "hazardous" due to the high percentages of people of color living there, leading to systematic disinvestment based on race. While the program ended in 1968, …

Business Information Security Officer (Biso) Responsibilities And Role Development, Kaung Myat Thu, Hudda Siddique

Publications and Research

In today's interconnected world, the success of enterprises heavily relies on network connectivity and technology. To safeguard sensitive information from cyber threats and ensure business success, the role of Information Security has become critical. This research project focuses on the Business Information Security Officer (BISO) role, studying their responsibilities, strategies, and how they handle threats. We explore the knowledge and skills required for BISOs, including certifications such as ISC² CISSP, ISACA CRISC, CISM, and CompTIA Security+. By contributing to the maturity of the BISO role, this study aims to enhance information security in organizations.

Fulminant Lung Fibrosis In Non-Resolvable Covid-19 Requiring Transplantation, Soma S K Jyothula, Andrew Peters, Yafen Liang, Weizhen Bi, Pooja Shivshankar, Simon Yau, Puneet S Garcha, Xiaoyi Yuan, Bindu Akkanti, Scott Collum, Nancy Wareing, Rajarajan A Thandavarayan, Fernando Poli De Frias, Ivan O Rosas, Bihong Zhao, L Maximilian Buja, Holger K Eltzschig, Howard J Huang, Harry Karmouty-Quintana

Faculty, Staff and Student Publications

BACKGROUND: Coronavirus Disease 2019 (COVID-19) can lead to the development of acute respiratory distress syndrome (ARDS). In some patients with non-resolvable (NR) COVID-19, lung injury can progress rapidly to the point that lung transplantation is the only viable option for survival. This fatal progression of lung injury involves a rapid fibroproliferative response and takes on average 15 weeks from initial symptom presentation. Little is known about the mechanisms that lead to this fulminant lung fibrosis (FLF) in NR-COVID-19.

METHODS: Using a pre-designed unbiased PCR array for fibrotic markers, we analyzed the fibrotic signature in a subset of NR-COVID-19 lungs. We …

Tceal1 Loss-Of-Function Results In An X-Linked Dominant Neurodevelopmental Syndrome And Drives The Neurological Disease Trait In Xq222 Deletions, Hadia Hijazi, Linda M Reis, Davut Pehlivan, Jonathan A Bernstein, Michael Muriello, Erin Syverson, Devon Bonner, Mehrdad A Estiar, Ziv Gan-Or, Guy A Rouleau, Ekaterina Lyulcheva, Lynn Greenhalgh, Marine Tessarech, Estelle Colin, Agnès Guichet, Dominique Bonneau, R H Van Jaarsveld, A M A Lachmeijer, Lyse Ruaud, Jonathan Levy, Anne-Claude Tabet, Rafal Ploski, Małgorzata Rydzanicz, Łukasz Kępczyński, Katarzyna Połatyńska, Yidan Li, Jawid M Fatih, Dana Marafi, Jill A Rosenfeld, Zeynep Coban-Akdemir, Weimin Bi, Richard A Gibbs, Grace M Hobson, Jill V Hunter, Claudia M B Carvalho, Jennifer E Posey, Elena V Semina, James R Lupski

Faculty, Staff and Student Publications

An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving …

Early Systemic Glycolytic Shift After Aneurysmal Subarachnoid Hemorrhage Is Associated With Functional Outcomes, Aaron M Gusdon, Chenlian Fu, Vasanta Putluri, Atzhiry S Paz, Hua Chen, Xuefang Ren, Mohammed Khurshidul Hassan, Pramod Dash, Cristian Coarfa, Nagireddy Putluri, Huimahn A Choi, Jude P J Savarraj

Faculty, Staff and Student Publications

BACKGROUND: Aneurysmal subarachnoid hemorrhage (aSAH) leads to a robust systemic inflammatory response. We hypothesized that an early systemic glycolytic shift occurs after aSAH, resulting in a unique metabolic signature and affecting systemic inflammation.

METHODS: Control patients and patients with aSAH were analyzed. Samples from patients with aSAH were collected within 24 h of aneurysmal rupture. Mass spectrometry-based metabolomics was performed to assess relative abundance of 16 metabolites involved in the tricarboxylic acid cycle, glycolysis, and pentose phosphate pathway. Principal component analysis was used to segregate control patients from patients with aSAH. Dendrograms were developed to depict correlations between metabolites and …

Characterizing Treatment Resistance In Muscle Invasive Bladder Cancer Using The Chicken Egg Chorioallantoic Membrane Patient-Derived Xenograft Model, Hugo Villanueva, Gabrielle A Wells, Malachi T Miller, Mariana Villanueva, Ravi Pathak, Patricia Castro, Michael M Ittmann, Andrew G Sikora, Seth P Lerner

Faculty, Staff and Student Publications

BACKGROUND: Non-metastatic muscle invasive urothelial bladder cancer (MIBC) has a poor prognosis and standard of care (SOC) includes neoadjuvant cisplatin-based chemotherapy (NAC) combined with cystectomy. Patients receiving NAC have at best

METHODS: We optimized engraftment conditions for primary MIBC tumors using the CAM-PDX model and tested concordance between cisplatin-based chemotherapy response of patients to matching PDX tumors using tumor growth coupled with immunohistochemistry markers of proliferation and apoptosis. We also tested select kinase inhibitor response on chemotherapy-resistant bladder cancers on the CAM-PDX using tumor growth measurements and immuno-detection of proliferation marker, Ki-67.

RESULTS: Our results show primary, NAC-resistant, MIBC tumors …

Luspatercept In Low-Risk Myelodysplastic Syndrome: A Real-World Single Institution Case Series, Shamis Khan, Sara Taveras Alam, Rosa Torres Ramos, John Etumbani Mbue, Effrosyni Apostolidou, Gustavo A Rivero, Sarvari Venkata Yellapragada

Faculty, Staff and Student Publications

No abstract provided.

Single-Cell Crispr Immune Screens Reveal Immunological Roles Of Tumor Intrinsic Factors, Jiakai Hou, Shaoheng Liang, Chunyu Xu, Yanjun Wei, Yunfei Wang, Yukun Tan, Nidhi Sahni, Daniel J Mcgrail, Chantale Bernatchez, Michael Davies, Yumei Li, Rui Chen, S Stephen Yi, Yiwen Chen, Cassian Yee, Ken Chen, Weiyi Peng

Faculty, Staff and Student Publications

Genetic screens are widely exploited to develop novel therapeutic approaches for cancer treatment. With recent advances in single-cell technology, single-cell CRISPR screen (scCRISPR) platforms provide opportunities for target validation and mechanistic studies in a high-throughput manner. Here, we aim to establish scCRISPR platforms which are suitable for immune-related screens involving multiple cell types. We integrated two scCRISPR platforms, namely Perturb-seq and CROP-seq, with both in vitro and in vivo immune screens. By leveraging previously generated resources, we optimized experimental conditions and data analysis pipelines to achieve better consistency between results from high-throughput and individual validations. Furthermore, we evaluated the performance …

A Framework For Detecting Noncoding Rare-Variant Associations Of Large-Scale Whole-Genome Sequencing Studies, Zilin Li, Xihao Li, Hufeng Zhou, Sheila M Gaynor, Margaret Sunitha Selvaraj, Theodore Arapoglou, Corbin Quick, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K Arnett, Paul L Auer, Lawrence F Bielak, Joshua C Bis, Thomas W Blackwell, John Blangero, Eric Boerwinkle, Donald W Bowden, Jennifer A Brody, Brian E Cade, Matthew P Conomos, Adolfo Correa, L Adrienne Cupples, Joanne E Curran, Paul S De Vries, Ravindranath Duggirala, Nora Franceschini, Barry I Freedman, Harald H H Göring, Xiuqing Guo, Rita R Kalyani, Charles Kooperberg, Brian G Kral, Leslie A Lange, Bridget M Lin, Ani Manichaikul, Alisa K Manning, Lisa W Martin, Rasika A Mathias, James B Meigs, Braxton D Mitchell, May E Montasser, Alanna C Morrison, Take Naseri, Jeffrey R O'Connell, Nicholette D Palmer, Patricia A Peyser, Bruce M Psaty, Laura M Raffield, Susan Redline, Alexander P Reiner, Muagututi'a Sefuiva Reupena, Kenneth M Rice, Stephen S Rich, Jennifer A Smith, Kent D Taylor, Margaret A Taub, Ramachandran S Vasan, Daniel E Weeks, James G Wilson, Lisa R Yanek, Wei Zhao, Jerome I Rotter, Cristen J Willer, Pradeep Natarajan, Gina M Peloso, Xihong Lin

Faculty, Staff and Student Publications

Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate …