Medicine and Health Sciences Commons^™

Randomized Controlled Trials: Who Fails Run-In?, Judy R. Rees, Leila A. Mott, Elizabeth L. Barry, John A. Baron, Jane C. Figueiredo, Douglas J. Robertson, Robert S. Bresalier, Janet L. Peacock

Dartmouth Scholarship

Background: Early identification of participants at risk of run-in failure (RIF) may present opportunities to improve trial efficiency and generalizability. Methods: We conducted a partial factorial-design, randomized, controlled trial of calcium and vitamin D to prevent colorectal adenoma recurrence at 11 centers in the United States. At baseline, participants completed two self-administered questionnaires (SAQs) and a questionnaire administered by staff. Participants in the full factorial randomization (calcium, vitamin D, both, or neither) received a placebo during a 3-month single-blinded run-in; women electing to take calcium enrolled in a two-group randomization (calcium with vitamin D, or calcium alone) and received calcium …

Phenotypes Associated With Knockouts Of Eight Dense Granule Gene Loci (Gra2-9) In Virulent Toxoplasma Gondii, Leah M. Rommereim, Valeria Bellini, Barbara A. Fox, Graciane Pètre, Camille Rak, Bastien Touquet, Delphine Aldebert, Jean-François Dubremetz, Marie-France Cesbron-Delauw, Corinne Mercier, David J. Bzik

Dartmouth Scholarship

Toxoplasma gondii actively invades host cells and establishes a parasitophorous vacuole (PV) that accumulates many proteins secreted by the dense granules (GRA proteins). To date, at least 23 GRA proteins have been reported, though the function(s) of most of these proteins still remains unknown. We targeted gene knockouts at ten GRA gene loci (GRA1-10) to investigate the cellular roles and essentiality of these classical GRA proteins during acute infection in the virulent type I RH strain. While eight of these genes (GRA2-9) were successfully knocked out, targeted knockouts at the GRA1 and GRA10 loci were not …

Artificial Intelligence And Amikacin Exposures Predictive Of Outcomes In Multidrug-Resistant Tuberculosis Patients, Chawangwa Modongo, Jotam G. Pasipanodya, Shashikant Srivastava, Nicola Zetola, Scott Williams, Giorgio Sirugo, Tawanda Gumbo

Dartmouth Scholarship

Aminoglycosides such as amikacin continue to be part of the backbone of treatment of multidrug-resistant tuberculosis (MDR- TB). We measured amikacin concentrations in 28 MDR-TB patients in Botswana receiving amikacin therapy together with oral levofloxacin, ethionamide, cycloserine, and pyrazinamide and calculated areas under the concentration-time curves from 0 to 24 h (AUC0 –24). The patients were followed monthly for sputum culture conversion based on liquid cultures. The median duration of amikacin therapy was 184 (range, 28 to 866) days, at a median dose of 17.30 (range 11.11 to 19.23) mg/kg. Only 11 (39%) pa- tients had sputum culture conversion during …

Pilot Study Of A Web-Delivered Multicomponent Intervention For Rural Teens With Poorly Controlled Type 1 Diabetes, Amy H. Lansing, Catherine Stanger, Alan Budney, Ann S. Christiano, Samuel Casella

Dartmouth Scholarship

Objective. The purpose of this study was to examine the feasibility and effectiveness of a web-delivered multicomponent behavioral and family-based intervention targeting self-regulation and self-monitoring of blood glucose levels (SMBG) and glycemic control (HbA1c) in teens with type 1 diabetes (T1DM) living in rural US. Methods. 15 teens with poorly controlled T1DM participated in a 25-week web-delivered intervention with two phases, active treatment (weekly treatment sessions and working memory training program) and maintenance treatment (fading of treatment sessions). Results. Almost all (13 of 15) participants completed at least 14 of 15 treatment sessions and at least 20 of 25 working …

Secretion Of Rhoptry And Dense Granule Effector Proteins By Nonreplicating Toxoplasma Gondii Uracil Auxotrophs Controls The Development Of Antitumor Immunity, Barbara A. Fox, Kiah L. Sanders, Leah M. Rommereim, Rebekah B. Guevara, David J. Bzik

Dartmouth Scholarship

Nonreplicating type I uracil auxotrophic mutants of Toxoplasma gondii possess a potent ability to activate therapeutic immunity to established solid tumors by reversing immune suppression in the tumor microenvironment. Here we engineered targeted deletions of parasite secreted effector proteins using a genetically tractable Δku80 vaccine strain to show that the secretion of specific rhoptry (ROP) and dense granule (GRA) proteins by uracil auxotrophic mutants of T. gondii in conjunction with host cell invasion activates antitumor immunity through host responses involving CD8α⁺ dendritic cells, the IL-12/interferon-gamma (IFN-γ) T_H1 axis, as well as CD4⁺ and CD8 …

Patient‐Defined Goals For The Treatment Of Severe Aortic Stenosis: A Qualitative Analysis, Megan Coylewright, Roseanne Palmer, Elizabeth S. O'Neill, John F. Robb, Terri Fried

Dartmouth Scholarship

Patients with severe aortic stenosis (AS) at high risk for aortic valve replacement are a unique population with multiple treatment options, including medical therapy, surgical aortic valve replacement and transcatheter aortic valve replacement (TAVR). Traditionally, in elderly populations, goals of treatment may favour quality of life over survival. Professional guidelines recommend that clinicians engage patients in shared decision making, a process that may lead to decisions more aligned with patient-defined goals of care. Goals of care for high-risk patients with AS are not well defined in the literature, and patient-reported barriers to shared decision making highlight the need for explicit …

Design Of Nanoparticle-Based Carriers For Targeted Drug Delivery, Xiaojiao Yu, Ian Trase, Muqing Ren, Kayla Duval, Xing Guo, Zi Chen

Dartmouth Scholarship

Nanoparticles have shown promise as both drug delivery vehicles and direct antitumor systems, but they must be properly designed in order to maximize efficacy. Computational modeling is often used both to design new nanoparticles and to better understand existing ones. Modeled processes include the release of drugs at the tumor site and the physical interaction between the nanoparticle and cancer cells. In this paper, we provide an overview of three different targeted drug delivery methods (passive targeting, active targeting, and physical targeting) and compare methods of action, advantages, limitations, and the current stages of research. For the most commonly used …

Methylation Of The Leukocyte Glucocorticoid Receptor Gene Promoter In Adults: Associations With Early Adversity And Depressive, Anxiety And Substance-Use Disorders, A. R. Tyrka, S H. Parade, E S. Welch, K. K. Ridout, L Price, C Marsit, L Carpenter

Dartmouth Scholarship

Early adversity increases risk for developing psychopathology. Epigenetic modification of stress reactivity genes is a likely mechanism contributing to this risk. The glucocorticoid receptor (GR) gene is of particular interest because of the regulatory role of the GR in hypothalamic–pituitary–adrenal (HPA) axis function. Mounting evidence suggests that early adversity is associated with GR promoter methylation and gene expression. Few studies have examined links between GR promoter methylation and psychopathology, and findings to date have been mixed. Healthy adult participants (N = 340) who were free of psychotropic medications reported on their childhood experiences of maltreatment and parental death and desertion. …

Physical Activity And Risk Of Breast Cancer, Colon Cancer, Diabetes, Ischemic Heart Disease, And Ischemic Stroke Events: Systematic Review And Dose-Response Meta-Analysis For The Global Burden Of Disease Study 2013, Hmwe H. Kyu, Victoria F. Bachman, Lily T. Alexander, John E. Mumford, Ashkan Afshin, Kara Estep, J. Lennert Veerman, Kristen Delwiche

Dartmouth Scholarship

Objective: To quantify the dose-response associations between total physical activity and risk of breast cancer, colon cancer, diabetes, ischemic heart disease, and ischemic stroke events.

Ethics In Community-Based Research With Vulnerable Children: Perspectives From Rwanda, Theresa Betancourt, Mary C. Smith Fawzi, Anne Stevenson, Fredrick Kanyanganzi, Catherine Kirk, Lauren Ng, Christina Mushashi, Justin I. Bizimana, William Beardslee, Guiseppe Raviola, Stephanie Smith, Yvonne Kayiteshonga, Agnes Binagwaho

Dartmouth Scholarship

A “risk of harm” protocol to identify youth in need of immediate emergency assistance in a study on mental health and HIV in Rwanda among 680 youth ages 10–17 is described. Cases are presented that describe the experience in using this protocol to ensure safety of participants, with ethical and logistical challenges considered. Among the population of the study, 3.2% were deemed "risk of harm.” The most prevalent presenting problem was non-fatal suicidal behavior (91% of risk of harm cases), with 36% having a history of a reported previous attempt. Challenges included: acute food insecurity/significant poverty; lack of support/adequate supervision …

Microrna Mir-155 Is Necessary For Efficient Gammaherpesvirus Reactivation From Latency, But Not For Establishment Of Latency, Rebecca L. Crepeau, Peisheng Zhang, Edward J. Usherwood

Dartmouth Scholarship

MicroRNA-155 (miR-155) has been shown to play significant roles in the immune response, including in the formation of germinal centers (GC) and the development and maturation of T follicular helper (Tfh) cells. There is in vitro evidence to support a critical role for cellular miR-155 and viral miR-155 homologs in the establishment of gammaherpesvirus latency in B cells. We sought to determine the contribution of miR-155 to the establishment and maintenance of latency in vivousing murine gammaherpesvirus (MHV-68) infection. MHV-68-infected mice deficient in miR-155 exhibited decreases in GC B cells and Tfh cells. However, the frequencies of spleen cells …

Cyclic Di-Gmp-Regulated Periplasmic Proteolysis Of A Pseudomonas Aeruginosa Type Vb Secretion System Substrate, Richard B. Cooley, T. Jarrod Smith, Wilfred Leung, Valerie Tierney, Bradley Borlee, George A. O'Toole, Holger Sondermann

Dartmouth Scholarship

We previously identified a second-messenger-regulated signaling system in the environmental bacterium Pseudomonas fluorescens which controls biofilm formation in response to levels of environmental inorganic phosphate. This system contains the transmembrane cyclic di-GMP (c-di-GMP) receptor LapD and the periplasmic protease LapG. LapD regulates LapG and controls the ability of this protease to process a large cell surface adhesin protein, LapA. While LapDG orthologs can be identified in diverse

The Brain Imaging Data Structure, A Format For Organizing And Describing Outputs Of Neuroimaging Experiments, Krzysztof Gorgolewski, Tibor Auer, Vince Calhoun, R Cameron Craddock, Samir Das, Eugene Duff, Guillaume Flandin, Tristan Glatard, Yaroslav Halchenko

Dartmouth Scholarship

The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this …

Consistency Of Hemoglobin A1c Testing And Cardiovascular Outcomes In Medicare Patients With Diabetes, Philip P. Goodney, Karina A. Newhall, Kimon Bekelis, Daniel Gottlieb, Richard Comi, Sushela Chaudrain, Adrienne E. Faerber, Todd A. Mackenzie, Jonathan S. Skinner

Dartmouth Scholarship

Background:

Annual hemoglobin A1c testing is recommended for patients with diabetes mellitus. However, it is unknown how consistently patients with diabetes mellitus receive hemoglobin A1c testing over time, or whether testing consistency is associated with adverse cardiovascular outcomes.

Methods and Results:

We identified 1 574 415 Medicare patients (2002–2012) with diabetes mellitus over the age of 65. We followed each patient for a minimum of 3 years to determine their consistency in hemoglobin A1C testing, using 3 categories: low (testing in 0 or 1 of 3 years), medium (testing in 2 of 3 years), and high (testing in all 3 …

Female Chromosome X Mosaicism Is Age-Related And Preferentially Affects The Inactivated X Chromosome, Mitchell J. Machiela, Weiyin Zhou, Eric Karlins, Joshua N. Sampson, Neal D. Freedman, Qi Yang, Belynda Hicks, Casey Dagnall, Christopher Hautman, Kevin B. Jacobs, Christian C. Abnet, Melinda C. Aldrich, Christopher Amos, Laufey T. Amundadottir, Alan A. Arslan, Laura E. Beane-Freeman, Sonja I. Berndt, Amanda Black, William J. Blot, Cathryn H. Bock, Paige M. Bracci, Louise A. Brinton, H Bas Bueno-De-Mesquita, Laurie Burdett, Julie E. Buring, Mary A. Butler, Federico Canzian, Tania Carreon, Kari G. Chaffee, I-Shou Chang, Nilanjan Chatterjee, Chu Chen, Constance Chen, Kexin Chen, Charles C. Chung, Linda S. Cook, Marta Crous Bou, Michael Cullen, Faith G. Davis, Immaculata De Vivo, Ti Ding, Jennifer Doherty

Dartmouth Scholarship

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events 4 2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses …

The Pseudomonas Aeruginosa Efflux Pump Mexghi-Opmd Transports A Natural Phenazine That Controls Gene Expression And Biofilm Development, Hassan Sakhtah, Leslie Koyama, Yihan Zhang, Diana K. Morales, Blanche Fields, Alexa Price-Whelan, Deborah Hogan

Dartmouth Scholarship

Redox-cycling compounds, including endogenously produced phenazine antibiotics, induce expression of the efflux pump MexGHI-OpmD in the opportunistic pathogen Pseudomonas aeruginosa Previous studies of P. aeruginosa virulence, physiology, and biofilm development have focused on the blue phenazine pyocyanin and the yellow phenazine-1-carboxylic acid (PCA). In P. aeruginosa phenazine biosynthesis, conversion of PCA to pyocyanin is presumed to proceed through the intermediate 5-methylphenazine-1-carboxylate (5-Me-PCA), a reactive compound that has eluded detection in most laboratory samples. Here, we apply electrochemical methods to directly detect 5-Me-PCA and find that it is transported by MexGHI-OpmD in P. aeruginosa strain PA14 planktonic and biofilm cells. We …

Methylation Of The Glucocorticoid Receptor (Nr3c1) In Placenta Is Associated With Infant Cry Acoustics, Stephen J. Sheinkopf, Giulia Righi, Carmen J. Marsit, Barry M. Lester

Dartmouth Scholarship

Epigenetic mechanisms regulating expression of the glucocorticoid receptor gene (NR3C1) promoter may influence behavioral and biological aspects of stress response in human infants. Acoustic features of infant crying are an indicator of neurobehavioral and neurological status not yet investigated in relation to epigenetic mechanisms. We examined NR3C1 methylation in placental tissue from a series of 120 healthy newborn infants in relation to a detailed set of acoustic features extracted from newborn infant cries. We identified significant associations of NR3C1 methylation with energy variation in infants' cries as well as with the presence of very high fundamental frequency in …

Privacy And Security In Mobile Health – A Research Agenda, David Kotz, Carl A. Gunter, Santosh Kumar, Jonathan P. Weiner

Dartmouth Scholarship

Mobile health technology has great potential to increase healthcare quality, expand access to services, reduce costs, and improve personal wellness and public health. However, mHealth also raises significant privacy and security challenges.

Portable, Parallel 9-Wavelength Near-Infrared Spectral Tomography (Nirst) System For Efficient Characterization Of Breast Cancer Within The Clinical Oncology Infusion Suite, Yan Zhao, Brian W. Pogue, Steffen J. Haider, Jiang Gui, Roberta Diflorio-Alexander, Keith Paulsen, Shudong Jiang

Dartmouth Scholarship

A portable near-infrared spectral tomography (NIRST) system was developed with simultaneous frequency domain (FD) and continuous-wave (CW) optical measurements for efficient characterization of breast cancer in a clinical oncology setting. Simultaneous FD and CW recordings were implemented to speed up acquisition to 3 minutes for all 9 wavelengths, spanning a range from 661nm to 1064nm. An adjustable interface was designed to fit various breast sizes and shapes. Spatial images of oxy- and deoxy-hemoglobin, water, lipid, and scattering components were reconstructed using a 2D FEM approach. The system was tested on a group of 10 normal subjects, who were examined bilaterally …

Elevated Mtss1 Expression Associated With Metastasis And Poor Prognosis Of Residual Hepatitis B-Related Hepatocellular Carcinoma, Xiu-Yan Huang, Zi-Li Huang, Bin Xu, Zi Chen

Dartmouth Scholarship

Background: Hepatectomy generally offers the best chance of long-term survival for patients with hepatocellular carcinoma (HCC). Many studies have shown that hepatectomy accelerates tumor metastasis, but the mechanism remains unclear.

Methods: An orthotopic nude mice model with palliative HCC hepatectomy was performed in this study. Metastasis-related genes in tumor following resection were screened; HCC invasion, metastasis, and some molecular alterations were examined in vivo and in vitro. Clinical significance of key gene mRNA expression was also analyzed.

Human Papillomavirus Infection In Rwanda At The Moment Of Implementation Of A National Hpv Vaccination Programme, Fidele Ngabo, Silvia Franceschi, Iacopo Baussano, M. Chantal Umulisa, Peter Snijders, Anne Uyterlinde, Fulvio Lazzarato, Vanessa Tenet, Maurice Gatera, Agnes Binagwaho, Gary Clifford

Dartmouth Scholarship

Cervical cancer is the most common female cancer in Rwanda that, in 2011, became the first African country to implement a national vaccination programme against human papillomavirus (HPV). To provide a robust baseline for future evaluations of vaccine effectiveness, cervical cell specimens were obtained from 2508 women aged 18–69 years from the general population in Kigali, Rwanda, during 2013/14. 20 % of women were HIV-positive. Samples were used for liquid-based cytology and HPV testing (44 types) with GP5+/6+ PC.

Validation Of The Kinyarwanda-Version Short-Form Leeds Dyspepsia Questionnaire And Short-Form Nepean Dyspepsia Index To Assess Dyspepsia Prevalence And Quality-Of-Life Impact In Rwanda, Arcade Nkurunziza, Vincent Dusabejambo, Kelly Everhart, Steve Bensen, Tim Walker

Dartmouth Scholarship

We aimed to develop and validate Kinyarwanda versions of Short-Form Leeds Dyspepsia Questionnaire (SF-LDQ) and Short-Form Nepean Dyspepsia Index (SF-NDI) to measure the frequency and severity of dyspepsia and associated quality-of-life impact in Rwanda.

A Qualitative Analysis Of Virtual Patient Descriptions In Healthcare Education Based On A Systematic Literature Review, Inga Hege, Andrzej A. Kononowicz, Daniel Tolks, Samuel Edelbring

Dartmouth Scholarship

Background: Virtual Patients (VPs) have been in the focus of research in healthcare education for many years. The aim of our study was to analyze how virtual patients are described in the healthcare education literature, and how the identified concepts relate to each other.

Methods: We performed a literature review and extracted 185 descriptions of virtual patients from the articles. In a qualitative content analysis approach we inductively-deductively developed categories and deducted subcategories. We constructed a concept map to illustrate these concepts and their interrelations.

Results: We developed the following five main categories: Patient, Teacher, Virtual Patient, Curriculum, and Learner. …

Signaling In Effector Lymphocytes: Insights Toward Safer Immunotherapy, Kamalakannan Rajasekaran, Matthew J. Riese, Sridhar Rao, Li Wang, Monica Thakar, Charles Sentman, Subramaniam Malarkannan

Dartmouth Scholarship

Receptors on T and NK cells systematically propagate highly complex signaling cascades that direct immune effector functions, leading to protective immunity. While extensive studies have delineated hundreds of signaling events that take place upon receptor engagement, the precise molecular mechanism that differentially regulates the induction or repression of a unique effector function is yet to be fully defined. Such knowledge can potentiate the tailoring of signal transductions and transform cancer immunotherapies. Targeted manipulations of signaling cascades can augment one effector function such as antitumor cytotoxicity while contain the overt generation of pro-inflammatory cytokines that contribute to treatment-related toxicity such as …

Hospital Mortality In The United States Following Acute Kidney Injury, Jeremiah. R. Brown, Michael E. Rezaee, Emily J. Marshall, Michael E. Matheny

Dartmouth Scholarship

Acute kidney injury (AKI) is a common reason for hospital admission and complication of many inpatient procedures. The temporal incidence of AKI and the association of AKI admissions with in-hospital mortality are a growing problem in the world today. In this review, we discuss the epidemiology of AKI and its association with in-hospital mortality in the United States. AKI has been growing at a rate of 14% per year since 2001. However, the in-hospital mortality associated with AKI has been on the decline starting with 21.9% in 2001 to 9.1 in 2011, even though the number of AKI-related in-hospital deaths …

Acth Prevents Deficits In Fear Extinction Associated With Early Life Seizures, Andrew T. Massey, David K. Lerner, Gregory L. Holmes, Rod C. Scott, Amanda Hernan

Dartmouth Scholarship

Objective: Early life seizures (ELS) are often associated with cognitive and psychiatric comorbidities that are detrimental to quality of life. In a rat model of ELS, we explored long-term cognitive outcomes in adult rats. Using ACTH, an endogeneous HPA-axis hormone given to children with severe epilepsy, we sought to prevent cognitive deficits. Through comparisons with dexamethasone, we sought to dissociate the corticosteroid effects of ACTH from other potential mechanisms of action.

Results: Although rats with a history of ELS were able to acquire a conditioned fear learning paradigm and controls, these rats had significant deficits in their ability to extinguish …

Friendly Fire: Biological Functions And Consequences Of Chromosomal Targeting By Crispr-Cas Systems, Gary E. Heussler, George A. O'Toole

Dartmouth Scholarship

Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) systems in bacteria and archaea target foreign elements, such as bacteriophages and conjugative plasmids, through the incorporation of short sequences (termed spacers) from the foreign element into the CRISPR array, thereby allowing sequence-specific targeting of the invader. Thus, CRISPR-Cas systems are typically considered a microbial adaptive immune system. While many of these incorporated spacers match targets on bacteriophages and plasmids, a noticeable number are derived from chromosomal DNA. While usually lethal to the self-targeting bacteria, in certain circumstances, these self-targeting spacers can have profound effects in regard to microbial biology, including functions …

Secreted Herpes Simplex Virus-2 Glycoprotein G Alters Thermal Pain Sensitivity By Modifying Ngf Effects On Trpv1, Jorge Rubén Cabrera, Abel Viejo-Borbolla, Antonio Alcamí, Francisco Wandosell

Dartmouth Scholarship

Genital herpes is a painful disease frequently caused by the neurotropic pathogen herpes simplex virus type 2 (HSV-2). We have recently shown that HSV-2-secreted glycoprotein G (SgG2) interacts with and modulates the activity of the neurotrophin nerve growth factor (NGF). This interaction modifies the response of the NGF receptor TrkA, increasing NGF-dependent axonal growth. NGF is not only an axonal growth modulator but also an important mediator of pain and inflammation regulating the amount, localization, and activation of the thermal pain receptor transient receptor potential vanilloid 1 (TRPV1). In this work, we addressed whether SgG2 could contribute to HSV-2-induced pain. …

Pilz Domain Protein Flgz Mediates Cyclic Di-Gmp-Dependent Swarming Motility Control In Pseudomonas Aeruginosa, Amy Baker, Andreas Diepold, Sherry Kuchma, Jessie Scott, Dae Gon Ha, Giulia Orazi, Judith Armitage, George A. O'Toole

Dartmouth Scholarship

The second messenger cyclic diguanylate (c-di-GMP) is an important regulator of motility in many bacterial species. In Pseudomonas aeruginosa, elevated levels of c-di-GMP promote biofilm formation and repress flagellum-driven swarming motility. The rotation of P. aeruginosa's polar flagellum is controlled by two distinct stator complexes, MotAB, which cannot support swarming motility, and MotCD, which promotes swarming motility. Here we show that when c-di-GMP levels are elevated, swarming motility is repressed by the PilZ domain-containing protein FlgZ and by Pel polysaccharide production. We demonstrate that FlgZ interacts specifically with the motility-promoting stator protein MotC in a c-di-GMP-dependent manner and that a …

Detecting Gene-Gene Interactions Using A Permutation-Based Random Forest Method, Jing Li, James D. Malley, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore

Dartmouth Scholarship

Identifying gene-gene interactions is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Here, we aimed at developing a permutation-based methodology relying on a machine learning method, random forest (RF), to detect gene-gene interactions. Our approach called permuted random forest (pRF) which identified the top interacting single nucleotide polymorphism (SNP) pairs by estimating how much the power of a random forest classification model is influenced by removing pairwise interactions.