A5089120555- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Diabetes and associated disorders
- Genetic and phenotypic traits in livestock
- Pancreatic function and diabetes
- Bayesian Methods and Mixture Models
- Genomic variations and chromosomal abnormalities
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Statistical Methods and Inference
- Genetic factors in colorectal cancer
- Diabetes Management and Research
- RNA Research and Splicing
- Lung Cancer Treatments and Mutations
- Genomics and Rare Diseases
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Software Testing and Debugging Techniques
- Immune Cell Function and Interaction
- Evolution and Genetic Dynamics
- Vasculitis and related conditions
- T-cell and B-cell Immunology
- Morphological variations and asymmetry
- Advanced Clustering Algorithms Research
Simon Fraser University
2013-2024
BC Cancer Agency
2012-2013
University of British Columbia
2012-2013
Bristol-Myers Squibb (Germany)
2011
University of Washington
1995-2004
Lynn University
2004
National Institute of Statistical Sciences
2000
North Carolina State University
2000
Seattle University
1999
Fred Hutch Cancer Center
1995
We describe the R function LDheatmap() which produces a graphical display, as heat map, of pairwise linkage disequilibrium measurements between single nucleotide polymorphisms within genomic region. uses grid graphics system, an alternative to traditional system. The features and use tools from package modify maps are illustrated by examples.
Age-dependent associations between type 1 diabetes risk genes HLA, INS VNTR, and CTLA-4 autoantibodies to GAD65 (GADAs), ICA512/IA-2, insulin, islet cells were determined by logistic regression analysis in 971 incident patients with 702 control subjects aged 0–34 years. GADAs associated HLA-DQ2 young but not older (P = 0.009). Autoantibodies insulin negatively age < 0.0001) positively DQ8 0.03) VNTR 0.04), supporting possible immune tolerance induction. ICA512/IA-2 DQ2 0.04). Males...
Complex medical disorders, such as heart disease and diabetes, are thought to involve a number of genes which act in conjunction with lifestyle environmental factors increase susceptibility. Associations between complex traits single nucleotide polymorphisms (SNPs) candidate genomic regions can provide useful tool for identifying genetic risk factors. However, analysis trait associations SNPs ignores the potential extra information from haplotypes, combinations variants at multiple along...
Anthracyclines are very effective chemotherapeutic agents; however, their use is hampered by the treatment-induced cardiotoxicity. Genetic variants that help define patient's sensitivity to anthracyclines will greatly improve design of optimal regimens. However, identification such lack analytical approaches address complex, multi-genic character anthracycline induced cardiotoxicity (AIC). Here, using a multi-SNP based approach, we examined 60 genes coding for proteins involved in drug...
Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on structure. Wang et al. developed an approach analysis genomic using penalized multi-task regression with regularization based a novel group l2,1-norm penalty which encourages structured sparsity at both gene level SNP level. While incorporating number useful features, proposed method only furnishes point estimate coefficients; techniques...
Objective Individuals with deficiency of adenosine deaminase 2 ( DADA 2), a recently recognized autosomal recessive disease, present various systemic vascular and inflammatory manifestations, often young age at disease onset or early recurrent strokes. Their clinical features histologic findings overlap those childhood‐onset polyarteritis nodosa PAN ), primary “idiopathic” vasculitis. Despite similar presentation, individuals may respond better to biologic therapy than traditional...
Exact inference is based on the conditional distribution of sufficient statistics for parameters interest given observed values remaining statistics. logistic regression can be problematic when data sets are large and support cannot represented in memory. Additionally, these methods not widely implemented except commercial software packages such as LogXact SAS. Therefore, we have developed elrm, R implementing (approximate) exact binomial models from sets. We provide a description underlying...
HLA‐associated relative risks of type 1 (insulin‐dependent) diabetes mellitus were analysed in population‐based Swedish patients and controls aged 0–34 years. The age dependence was assessed by likelihood ratio tests regression parameters separate logistic models for each HLA category. analyses demonstrated an attenuation with increasing at onset the risk positively associated DQB1*0201‐A1*0502/B1*0302‐A1*0301 (DQ2/8) genotype ( P =0.02) negatively DQB1*0602‐A1*0102 (DQ6.2) haplotype...
HLA‐associated relative risks of type 1 (insulin‐dependent) diabetes mellitus were analysed in population‐based Swedish patients and controls aged 0–34 years. The age dependence was assessed by likelihood ratio tests regression parameters separate logistic models for each HLA category. analyses demonstrated an attenuation with increasing at onset the risk positively associated DQB1*0201‐A1*0502/B1*0302‐A1*0301 (DQ2/8) genotype ( P =0.02) negatively DQB1*0602‐A1*0102 (DQ6.2) haplotype...
Recently, Lake et al. [Human Heredity 2003;55:56–65] have proposed an approach based on the EM algorithm for maximum-likelihood inference of trait associations with haplotypes and environmental cofactors in generalized linear models. In this short report, we describe extension to accommodate missing SNP genotype information. We also discuss differences calculation standard errors between their implementation our own. Finally, present results indicating that is robust low levels dependence...
The purpose of this study was to test the hypothesis that glutamate cysteine ligase catalytic subunit (GCLC) promoter polymorphisms are susceptibility factors for type 1 diabetes (T1D), T1D age-at-onset and autoantibodies. patients control subjects from Swedish Childhood Diabetes Registry Incidence Study registry were genotyped two GCLC polymorphisms; -129 C T single nucleotide polymorphism (GCLC SNP) GAG trinucleotide repeat TNR). Glutamate decarboxylase antibody (GAD65Ab) positive with SNP...
Background Non-Hodgkin lymphomas are a heterogeneous group of solid tumours that constitute the 5th highest cause cancer mortality in United States and Canada. Poor control cell death lymphocytes can lead to autoimmune disease or cancer, making genes involved programmed logical candidate for lymphoma susceptibility. Materials Methods We tested genetic association with NHL subtypes, SNPs lymphocyte using an established population-based study. 17 were chosen based on biological function, 123...
DNA methylation patterns are often poorly conserved through cell culturing. To determine the effect of immortalization and culture on profiles, we analyzed in differentially methylated regions (DMR) five imprinted domains: intergenic (IG) DMR chromosome 14q32; potassium voltage-gated channel, KQT-like subfamily, member 1, (KCNQ1); small nuclear ribonucleoprotein polypeptide N (SNRPN), mesoderm specific transcript homolog (MEST); H19 lymphoblastoid lines (LCLs). In IG found an aberrant...
Abstract Background: Evidence suggests that interpatient variability in anthracycline metabolic rate may contribute to the cardiotoxicity associated with anthracycline-based chemotherapy. Therefore, polymorphisms metabolizing enzymes have been proposed as potential biomarkers of anthracycline-induced (AIC). Methods: We previously shown 13 naturally occurring nonsynonymous single-nucleotide (nsSNP) aldo–keto reductases (AKR) and carbonyl (CBR) reduce vitro. Here, we test these SNPs...
Platelet-activating factor (PAF) has been implicated in the development of type 1 diabetes. Our previous studies have suggested that PAF inhibitors reduce insulitis and frequency diabetes BB rats. In this study, serum levels were reduced to address hypothesis is important for insulitis. From age 35 days on, DP-BB rats treated with human recombinant acetylhydrolase (rPAF-AH), which efficiently inactivates PAF. data indicate intraperitoneal injections rPAF-AH incidence rat. Daily 6.0 mg/kg...
Type 1 diabetes is a complex disease where numerous genes are involved in the pathogenesis. Genes that account for approximately 50% of familial clustering located within or vicinity HLA on chromosome 6. Some DRB1, DQA1 and DQB1 known to be involved, addition as yet unidentified HLA‐linked genes. The DR4‐DQ8 DR3‐DQ2 haplotypes confer high risk developing disease, particularly when occurring together. Approximately 10% patients, however, do not carry any these high‐risk class II haplotypes....
Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2-5 bases. In the absence genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is match probability. The probability conditional that random person would have interest given suspect has it and these people different members same subpopulation. One issue in population differentiation, which can induce coancestry among subpopulation members. Forensic assessments...
Objectives. Chronic primary systemic vasculitidies (CPV) are a collection of rare diseases involving inflammation in blood vessels, often multiple organs. CPV can affect adults and children may be life- or organ-threatening. Treatments for adult CPV, although effective, have known severe potential toxicities; safety efficacy these drugs pediatric patients is not fully understood. There an unmet need biologic measures to assess the level disease activity and, turn, inform treatment choices...
CTLA-4 is important to down-regulating T cell responses and has been implicated in type 1 (insulin dependent) diabetes mellitus both linkage association studies. The aim of our study was relate the polymorphic (AT)n microsatellite 3′ untranslated sequence gene risk. We studied 616 consecutively diagnosed 0-34 year-old Swedish patients 502 matched controls by PCR-based genotyping determine length 3′-end repeat region categorizing alleles as predominantly monomorphic short (S) or highly (in...
We propose a stepwise approach to identify recombination breakpoints in sequence alignment. The can be applied any detection method that uses permutation test and provides estimates of breakpoints.We illustrate the by analyses simulated dataset alignments real data from HIV-1 human chromosome 7. presented simulation results compare statistical properties one-step two-step procedures. More are found with procedure than single application given method, particularly for higher rates. At rates,...