Blood-Informative Transcripts Define Nine Common Axes of Peripheral Blood Gene Expression
Ontology highlight
ABSTRACT: Whole peripheral blood samples collected into Tempus tubes from 189 adult participants in the Center for Health Discovery and Well Being study of Emory University and Georgia Tech, in Midtown Atlanta. The sample is of mixed ethnicity, and is part of a survey of the impact of genetics and lifestyle on gene expression and clinical attributes. Sample annotations include gender, self-reported ethnicity, zipcode of current address, and percent body fat, as well as technical features of the study (Sentrix plate ID, date of hybridization, and RNA quality RIN score. 189 individuals in the Center for Health Discovery and Well Being study of Emory University and Georgia Tech, in Midtown Atlanta., 65 men and 124 women. The age of individulas were between 26 and 79 (mean 51). 140 Caucasian (CAU), 37 African American (AFR), 11 Asian (ASN), 1 American Indian (AMI).
Project description:Whole peripheral blood samples collected into Tempus tubes from 189 adult participants in the Center for Health Discovery and Well Being study of Emory University and Georgia Tech, in Midtown Atlanta. The sample is of mixed ethnicity, and is part of a survey of the impact of genetics and lifestyle on gene expression and clinical attributes. Sample annotations include gender, self-reported ethnicity, zipcode of current address, and percent body fat, as well as technical features of the study (Sentrix plate ID, date of hybridization, and RNA quality RIN score.
Project description:Whole peripheral blood samples collected into Paxgene tubes from 338 adult participants in the Emory University Cardiovascular Biobank, in Midtown Atlanta. The sample is of mixed cardiovascular function diversity, and is part of a survey of the impact of status of cardiovascular disease on gene expression and clinical attributes. Sample annotations only include gender and proofed ethnicity for purposes of IRB, as well as technical features of the study (plate, phase of study, and RNA quality RIN score). 338 individuals in the Emory Cardiovascular Biobank in Midtown Atlanta., 219 men and 119 women. The age of individulas were between 26 and 85 (mean 62). 333 Caucasian (CAU), 4 African American (AFA), 1 South Asian (SAS).
Project description:Whole peripheral blood samples collected into Paxgene tubes from 338 adult participants in the Emory University Cardiovascular Biobank, in Midtown Atlanta. The sample is of mixed cardiovascular function diversity, and is part of a survey of the impact of status of cardiovascular disease on gene expression and clinical attributes. Sample annotations only include gender and proofed ethnicity for purposes of IRB, as well as technical features of the study (plate, phase of study, and RNA quality RIN score).
Project description:Array CGH analysis of Helicobacter pylori strains isolated from a North American cohort of symptomatic pediatric patients. Keywords: genotyping_design A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Patients enrolled under Benjamin Gold's Emory IRB protocol. Initial strain isolation from antral biopsies performed at Emory and culture sweeps sent to FHCRC (Seattle) for analysis. Single colony isolates (4) from each patient antral biopsy were isolated and profiled using RAPD. A single clone of each RAPD type detected in each patient (1-2) were analyzed on duplicate arrays. For analysis 500 ng of genomic DNA of each test strain was labeled with Cy5 and 500 ng of genomic DNA of a reference sample (equimolar mix of 26695 and J99) was labeled with Cy3. Strains identified as Em-patient#-clone#.
Project description:Newborn screening blood spots were obtained for neonates born to women enrolled in the Emory University African American Microbiome in Pregnacy Cohort
Project description:In the United States, African-American (AA) women are more likely to develop early-onset breast cancer and have historically poorer outcomes due to this disease compared to European-American (EA) women. Here, we analyzed genomic profiles of breast tumors from young women (<50 years old), matched by tumor subtype, histological grade, and ethnicity (African-American, AA, compared to European-American, EA). DNA copy number alterations (CNAs) were analyzed using a 32K BAC tiling path array. The study provides insight into the genetic component of ethnicity-related breast cancer health disparities.
Project description:In the United States, African-American (AA) women are more likely to develop early-onset breast cancer and have historically poorer outcomes due to this disease compared to European-American (EA) women. Here, we analyzed genomic profiles of breast tumors from young women (<50 years old), matched by tumor subtype, histological grade, and ethnicity (African-American, AA, compared to European-American, EA). DNA copy number alterations (CNAs) were analyzed on the Affymetrix Human SNP Array v 6.0 platform. The study provides insight into the genetic component of ethnicity-related breast cancer health disparities.
Project description:<p>In order to evaluate whether rare regulatory variants in the vicinity of promoters are likely to impact gene expression, we conducted a novel burden test for rare variants at the extreme of expression. After targeted sequencing of 2kb promoter regions of 472 genes in 410 healthy adults, burden tests were performed by calculating the summed rare allele counts in ranked expression level bins using Illumina whole blood microarray gene expression data. The results clearly show an enrichment of rare variants at both extremes of gene expression. The rare regulatory variant effects were also partitioned into subsets of genes based on their regulatory functions, positions relative to transcription start sites, disease relatedness, with some intriguing biases. The enrichment of rare regulatory variants in extremely expressed genes was replicated in an independent sample of 75 individuals with RNASeq and whole genome sequence information. Participants were from the Emory-Georgia Tech Center for Health Discovery and Well Being (CHDWB) longitudinal cohort study, but only baseline gene expression data was used.</p>
Project description:Expression profiling was used to identify genes differentially expressed in MSS (microsatellite stable) and MSI (microsatellite unstable) colon cancer cell lines. Data submitted in support of manuscript entitled Villin expression is frequently lost in poorly differentiated colon cancer, Diego Arango, Sheren Al-Obaidi, David S. Williams, Jose Dopeso, Rocco Mazzolini, Georgia Corner, Do-Sun Byun, Carmel Murone, Lars Tögel, Nikolajs Zeps, Lauri A. Aaltonen, Barry Iacopetta and John M. Mariadason, American Journal of Pathology, 2012.
Project description:In the United States, African-American (AA) women are more likely to develop early-onset breast cancer and have historically poorer outcomes due to this disease compared to European-American (EA) women. Here, we analyzed genomic profiles of breast tumors from young women (<50 years old), matched by tumor subtype, histological grade, and ethnicity (African-American, AA, compared to European-American, EA). DNA copy number alterations (CNAs) were analyzed using a 32K BAC tiling path array. The study provides insight into the genetic component of ethnicity-related breast cancer health disparities. Breast tumor samples from young women (< 50 years old) were matched as follows: a matched pair consists of one AA and one EA sample, matched for tumor grade and tumor subtype (based on immunohistochemical analysis of ER, PR, and HER2 status). 44 experiments; each experiment is tumor DNA versus reference control DNA (AF) isolated from the blood of a 25-year-old African-American female with no familial or personal history of breast cancer. Additional control experiments included the AF reference versus the well-characterized F1 reference, and 3 self-self hybridization controls (AF versus AF).