Introduction Inflammatory bowel disease (IBD) consists of ulcerative colitis (UC), Crohn disease (CD), and indeterminate colitis. While sharing many clinical features, ulcerative colitis and Crohn disease are considered separate entities with unique characteristics. Due to the chronic nature of these diseases, frequent and repeated imaging is often necessary for diagnosis and therapeutic planni...

Data errors and marker allele frequency misspecification can lead to incorrect inference in linkage analysis. Here we demonstrate the effect of each on an allele-sharing statistic in a sample of sib pairs. In the context of relationship testing, we propose a new test that compares the sample genome-wide sib-pair allele sharing to its expectation and show that this test can detect the presence o...

Inflammatory bowel diseases (IBDs) are complex, multifactorial disorders characterized by chronic relapsing intestinal inflammation. Although etiology remains largely unknown, recent research has suggested that genetic factors, environment, microbiota, and immune response are involved in the pathogenesis. Epidemiological evidence for a genetic contribution is defined: 15% of patients with Crohn...

Inflammatory bowel disease (IBD) is a chronic condition which is characterized by recurrent immune-mediated inflammation of the gastrointestinal system. IBD is frequently associated with extraintestinal manifestations (EIM) characterized by involvement of multiple organs. EIM occur in 21% to 47% of IBD patients (Navaneethan & Shen, 2010). While some extraintestinal manifestations are encountere...

Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism data sets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of information about genealogical relationships. We hop...

Background The ARTFL-LEFFTDS Longitudinal Frontotemporal Lobar Degeneration (ALLFTD) research consortium is actively enrolling participants across 23 North American centers to characterize sporadic and familial frontotemporal dementia (FTD) prepare for disease-modifying clinical trials. ability identify, otherwise unknown, relatives among these critical rigorously build family structures downst...

MOTIVATION With the knowledge of large number of SNPs in human genome and the fast development in high-throughput genotyping technologies, identification of linked regions in linkage analysis through allele sharing status determination will play an ever important role, while consideration of recombination fractions becomes unnecessary. RESULTS In this study, we have developed a rule-based pro...

Linkage analysis is often followed by association mapping to localize disease variants. In this paper, we evaluate approaches to determine how much of the observed linkage evidence, namely the identity-by-descent (IBD) sharing at the linkage peak, is explained by associated SNPs. We study several methods: Homozygote Sharing Tests (HST), Genotype Identity-by-Descent Sharing Test (GIST), and a pe...

BACKGROUND/AIM Multidrug resistance 1 (MDR1) gene encodes for P-glycoprotein (P-gp), a transmembrane efflux pump transferring both exogenous and endogenous substrate from the cells. In the human gastrointestinal tract, P-gp is found in high concentrations on the epithelial cells of the colon and small intestine. It is hypothesized that the expression level of MDR1 gene is related to susceptibil...

I introduce a novel approach to derive the distribution of disease affectional status given alleles identical by descent (IBD) sharing through ITO method. My approach tremendously simplifies the calculation of the affectional status distribution compared to the conventional method, which requires the parental mating information, and could be applied to disease with both dichotomous trait and qu...