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Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

Zanfagnin Cordelia D. McGehee Ellen L. Goode Eric C. Polley Paul Haluska S. John Weroha OPEN Published: xx xx xxxx As patient derived xenograft (PDX) models are increasingly used for preclinical drug

Expression signature distinguishing two tumour transcriptome classes associated with progression-free survival among rare histological types of epithelial ovarian cancer

Ellen L Goode 0 Brooke L Fridley 6 0 Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905 , USA 1 Department of Obstetrics , Gynecology and Women's Health , University of Minnesota

Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women’s Cancers

We introduce a novel per-gene measure of intra-gene DNA methylation variability (IGV) based on the Illumina Infinium HumanMethylation450 platform, which is prognostic independently of well-known predictors of clinical outcome. Using IGV, we derive a robust gene-panel prognostic signature for ovarian cancer (OC, n = 221), which validates in two independent data sets from Mayo...

The Ratios of CD8+ T Cells to CD4+CD25+ FOXP3+ and FOXP3- T Cells Correlate with Poor Clinical Outcome in Human Serous Ovarian Cancer

Ovarian cancer is an immune reactive malignancy with a complex immune suppressive network that blunts successful immune eradication. This suppressive microenvironment may be mediated by recruitment or induction of CD4+ regulatory T cells (Tregs). Our study sought to investigate the association of tumor-infiltrating CD4+CD25+FOXP3+ Tregs, and other immune factors, with clinical...

The contribution of deleterious germline mutations in BRCA1, BRCA2 and the mismatch repair genes to ovarian cancer in the population

The aim of this study was to estimate the contribution of deleterious mutations in BRCA1, BRCA2, MLH1, MSH2, MSH6 and PMS2 to invasive epithelial ovarian cancer (EOC) in the population. The coding sequence and splice site boundaries of all six genes were amplified in germline DNA from 2240 invasive EOC cases and 1535 controls. Barcoded fragment libraries were sequenced using the...

A Latent Model for Prioritization of SNPs for Functional Studies

One difficult question facing researchers is how to prioritize SNPs detected from genetic association studies for functional studies. Often a list of the top M SNPs is determined based on solely the p-value from an association analysis, where M is determined by financial/time constraints. For many studies of complex diseases, multiple analyses have been completed and integrating...

Integrative genomic analysis identifies epigenetic marks that mediate genetic risk for epithelial ovarian cancer

Cunningham Sebastian Armasu Melissa C Larson Jeremy Chien Matthew Block Kimberly R Kalli Thomas A Sellers Brooke L Fridley 0 Ellen L Goode 0 Department of Biostatistics, University of Kansas Medical Center

Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome

Stacey J Winham Kimberly R Kalli Devin C Koestler 0 David N Rider Viji Shridhar Janet E Olson Julie M Cunningham Ellen L Goode 0 Department of Biostatistics, University of Kansas, Medical Center , 3901

Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome

Genome-wide interrogation of DNA methylation (DNAm) in blood-derived leukocytes has become feasible with the advent of CpG genotyping arrays. In epithelial ovarian cancer (EOC), one report found substantial DNAm differences between cases and controls; however, many of these disease-associated CpGs were attributed to differences in white blood cell type distributions. We examined...

Prognostic and Therapeutic Relevance of Molecular Subtypes in High-Grade Serous Ovarian Cancer

, He-Jing Wang, Lynn C. Hartmann, Dennis J. Slamon, Ellen L. Goode 3 of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic , Rochester , MN; Department of Biostatistics, David Geffen

Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium

Current genome-wide linkage-mapping single-nucleotide polymorphism (SNP) panels with densities of 0.3 cM are likely to have increased intermarker linkage disequilibrium (LD) compared to 5-cM microsatellite panels. The resulting difference in haplotype frequencies versus that predicted may affect multipoint linkage analysis with ungenotyped founders; a common haplotype may be...

The role of parametric linkage methods in complex trait analyses using microsatellites

Many investigators of complexly inherited familial traits bypass classical segregation analysis to perform model-free genome-wide linkage scans. Because model-based or parametric linkage analysis may be the most powerful means to localize genes when a model can be approximated, model-free statistics may result in a loss of power to detect linkage. We performed limited segregation...

The role of parametric linkage methods in complex trait analyses using microsatellites

Many investigators of complexly inherited familial traits bypass classical segregation analysis to perform model-free genome-wide linkage scans. Because model-based or parametric linkage analysis may be the most powerful means to localize genes when a model can be approximated, model-free statistics may result in a loss of power to detect linkage. We performed limited segregation...

Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium

Current genome-wide linkage-mapping single-nucleotide polymorphism (SNP) panels with densities of 0.3 cM are likely to have increased intermarker linkage disequilibrium (LD) compared to 5-cM microsatellite panels. The resulting difference in haplotype frequencies versus that predicted may affect multipoint linkage analysis with ungenotyped founders; a common haplotype may be...

Kernel canonical correlation analysis for assessing gene–gene interactions and application to ovarian cancer

B Larson, Gregory D Jenkins, Melissa C Larson, Robert A Vierkant, Ellen L Goode & Brooke L FridleyCancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USAThomas A Sellers & Catherine M PhelanDuke ... ScholarSearch for Nicolas Wentzensen in:Nature Research journals • PubMed • Google ScholarSearch for Ellen L Goode in:Nature Research journals • PubMed • Google ScholarSearch for Brooke L Fridley in:Nature

HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer

Fiegl Marie Kalwa Wolfgang Wagner Kantaraja Chindera 0 Iona Evans 0 Louis Dubeau Arturo Orjalo Hugo M. Horlings Lukas Niederreiter Arthur Kaser Winnie Yang Ellen L. Goode Brooke L. Fridley Richard G

European American Stratification in Ovarian Cancer Case Control Data: The Utility of Genome-Wide Data for Inferring Ancestry

We investigated the ability of several principal components analysis (PCA)-based strategies to detect and control for population stratification using data from a multi-center study of epithelial ovarian cancer among women of European-American ethnicity. These include a correction based on an ancestry informative markers (AIMs) panel designed to capture European ancestral...

Single versus multiple imputation for genotypic data

Due to the growing need to combine data across multiple studies and to impute untyped markers based on a reference sample, several analytical tools for imputation and analysis of missing genotypes have been developed. Current imputation methods rely on single imputation, which ignores the variation in estimation due to imputation. An alternative to single imputation is multiple...

Inherited variation in carcinogen-metabolizing enzymes and risk of colorectal polyps

Exposures such as cigarette smoke and meat contain a variety of procarcinogens, which are thought to play a role in elevation of risk for colorectal polyps and/or cancer. These procarcinogens (including heterocyclic amines and polycyclic aromatic hydrocarbons) are metabolized by a variety of polymorphic enzymes including N-acetyltransferases, sulfotransferases, cytochrome P450...

TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer

. Kaufmann 5 Lynn C. Hartmann 5 Viji Shridhar 6 Ellen L. Goode 1 0 Illumina, Inc. , San Diego, CA 92122 , USA 1 Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905 , USA 2 Department of