1GG01928001S
A9D9A84B3E59 SCOPE OF WORK UNIVERSITY OF BRITISH COLUMBIA Â SUBAWARD (COLUMBIA PRIME) EPIGENETIC ANALYIS THE FOLLOWING DETAILS THE EPIGENETIC ANALYSIS TO BE UNDERTAKEN IN THE LABORATORIES OF DR. KOBOR PERTAINING TO THIS APPLICATION. DNA METHYLATION RESEARCH METHOD: THE ANALYSIS WILL FOCUS PRIMARILY ON INTERROGATING DNA METHYLATION IN THE CONTEXT OF CPG DINUCLEOTIDES AS A KEY EPIGENETIC MECHANISM MEDIATING BETWEEN ENVIRONMENT AND GENOME, AS IT CURRENTLY REPRESENTS THE MOST ACCESSIBLE AND RELIABLE MARK FOR QUANTITATIVE EPIGENETIC MEASUREMENTS. DNA METHYLATION STUDIES TAKE ADVANTAGE OF BISULFITE TREATMENT OF GENOMIC DNA THAT SELECTIVELY DEAMINATES CYTOSINE RESIDUES THAT ARE NOT METHYLATED, WHILE LEAVING METHYLATED CYTOSINES INTACT. THUS, THIS APPROACH CONVERTS EPIGENETIC INFORMATION TO SEQUENCE-BASED INFORMATION THAT WILL BE MEASURED IN AN UNBIASED GENOME-WIDE ASSAY, USING THE ILLUMINA INFINIUM METHYLATIONEPIC BEADCHIP ARRAY. THIS ENABLES THE QUANTITATIVE INTERROGATION OF MORE THAN 850,000 CPG METHYLATION LOCI PER SAMPLE, WITH A THROUGHPUT OF BETWEEN 96-192 SAMPLES PER WEEK. THE ARRAY COVERS ALL DESIGNABLE REFSEQ GENES, WITH CPG ISLAND SHORES, NON-ISLAND CPGS, CPG ISLANDS OUTSIDE OF CODING REGIONS AND MIRNA PROMOTER REGIONS REPRESENTED. IN ADDITION, NON-CPG SITES FOUND TO BE DIFFERENTIALLY METHYLATED IN HUMAN STEM CELLS ARE INCLUDED, AS WELL AS REGIONS IDENTIFIED IN GWAS STUDIES TO BE DISEASE-ASSOCIATED AND SITES IDENTIFIED AS DIFFERENTIALLY METHYLATED IN TUMOR VS. NORMAL TISSUES. ADDITIONALLY, THE EXTRACTED DNA, BEFORE BISULFATE CONVERSION, CAN BE SIMILARLY RUN ON ARRAYS TO CATEGORIZE 665,608 HUMAN GENOMIC SNPS. PREVIOUS STUDIES HAVE SHOWN THAT ILLUMINAÂ S DNA METHYLATION PRODUCTS THAT WERE DESIGNED FOR HUMAN DNA CAN ALSO READILY AND ACCURATELY MEASURE DNA METHYLATION IN SIMIAN DNA (PMID: 24815017). EPIGENETICS WORK IN THIS PROJECT IS FOCUSED ON 3 CONNECTED PROCEDURES: DNA EXTRACTION, BISULFITE CONVERSION, AND DNA METHYLATION ARRAYS. QUALITY-TESTED COMMERCIAL KITS WILL BE UTILIZED FOR ALL THESE STEPS AND PROCEDURES TO SUPPORT THE ESTABLISHED EXPERIMENTAL PIPELINE IN THE KOBOR LABORATORY. THE LATTER IS FULLY EQUIPPED TO PERFORM ALL PROCEDURES IN HOUSE, INCLUDING THE SAMPLE PREPARATION AND SPECIFIC ASPECTS OF DNA METHYLATION ARRAY EXPERIMENTS. PERFORMING THE DNA METHYLATION ARRAY ASSAYS INCLUDES THE FOLLOWING INDIVIDUAL COMPONENTS: 1. EXTRACTION OF GENOMIC DNA FROM DRIED BLOOD SPOT SAMPLES 2. BISULFITE CONVERSION OF EXTRACTED DNA USING A ZYMO EZDNA METHYLATION KIT 3 BISULFITE-CONVERTED SAMPLES WILL BE WHOLE-GENOME AMPLIFIED BEFORE BEING HYBRIDIZED TO THE LLLUMINA METHYLATIONEPIC ARRAY (850K ARRAY) MICROARRAY CHIPS 4. FINALLY, 850K ARRAY CHIPS WILL BE SCANNED BY A HISCAN 2000 (ILLUMINA) STATISTICAL ANALYSIS: WE HAVE PREVIOUSLY PUBLISHED BIOINFORMATICS APPROACHES FOR THE INFINIUM METHYLATION ARRAYS (PMIDS: 21883162, 28673994, 26126446, 24709820) AND OUR LAB INCLUDES EXPERIENCED BIOINFORMATICIANS, ENSURING THAT DATA QUALITY CONTROL AND NORMALIZATION PIPELINES ARE UP TO DATE WITH THE LATEST TECHNIQUES. WE WILL TAKE ADVANTAGE OF THE HIGH-DIMENSIONAL NATURE OF THE ILLUMINA EPIC ARRAYS TO DISCOVER PATTERNS OF DNAM ASSOCIATED WITH EARLY LIFE ADVERSITY, INTER-GENERATIONAL TRANSMISSION OF ADVERSITY, AND LONG-TERM HEALTH OUTCOMES, USING APPROACHES SUCH AS MULTIPLE LINEAR REGRESSION, MACHINE LEARNING, AND REGION-BASED ANALYSES SUCH AS DMRCATE (PMID: 25972926) AND COMEBACK.
The University Of British Columbia
Project Grant R01AG087158
$279.3k 12/3/24 2GG01928001S
TOTAL BUDGET: $402,693 UNC WILL PROVIDE SUPPORT TO COLUMBIA UNIVERSITY IN SAMPLE PREPARATION AND TRANSPORTATION, PULL LIST DEVELOPMENT, DATA ANALYSIS, AND DISSEMINATION. THIS SUPPORT WILL FOCUS ON DATA PREPARATION, CONTEXTUALIZATION, AND DISSEMINATION OF FINDINGS. SPECIFICALLY, UNC WILL PROVIDE BLOOD SPOT SAMPLES AND QUESTIONNAIRE DATA FOR THIS PROJECT. UNC WILL ALSO PROVIDE TECHNICAL SUPPORT, EXPERTISE, AND FIRSTHAND KNOWLEDGE OF THE ORIGINAL DATA COLLECTION TO ENSURE QUALITY DE-IDENTIFIED DATA SHARING AND ANALYSIS ACROSS INSTITUTIONS TO AID IN THE CREATION OF HIGH-QUALITY RESEARCH PRODUCTS. DELIVERABLES: Â ¢ PREPARE BIOLOGICAL SAMPLES FOR TRANSPORTATION TO TESTING AND STORAGE AT FACILITIES. Â ¢ PREPARE BIOLOGICAL SAMPLES FOR LONG-TERM STORAGE. Â ¢ CONTEXTUALIZE THE FINDINGS WITHIN MALAWIÂ S SOCIOECONOMIC AND POLITICAL CONDITIONS, AS WELL AS THE WIDER RESEARCH LANDSCAPE. Â ¢ AID IN THE DEVELOPMENT OF RESEARCH AND REVIEW PRODUCTS, SUCH AS ACADEMIC PAPERS FOR JOURNAL SUBMISSION, PUBLIC PRESENTATIONS, INFOGRAPHICS, AND DIGITAL DISSEMINATION MATERIALS. Â ¢ PARTICIPATE IN DISSEMINATION EVENTS AS NEEDED. Â ¢ CONTRIBUTE TO ANNUAL NIH REPORTING AND ANY FINAL IMPACT REPORTS (YEAR 5).
University Of North Carolina At Chapel Hill
Project Grant R01AG087158
$99.3k 11/26/24