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2002 Progress Report: Environmental Factors in the Etiology of Autism; Molecular Biomakers Core
EPA Grant Number: R829388C003Subproject: this is subproject number 003 , established and managed by the Center Director under grant R829388
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
Center: CECEHDPR - University of California at Davis Center for the Study of Environmental Factors in the Etiology of Autism
Center Director: Pessah, Isaac N.
Title: Environmental Factors in the Etiology of Autism; Molecular Biomakers Core
Investigators: Hagerman, Paul , Denison, Michael , Gregg, Jeffrey , Rocke, David
Current Investigators: Hagerman, Paul , Gregg, Jeffrey , Sharp, Frank
Institution: University of California - Davis
EPA Project Officer: Saint, Chris
Project Period: September 30, 2001 through September 29, 2002
Project Period Covered by this Report: September 30, 2001 through September 29, 2002
RFA: Centers for Children's Environmental Health and Disease Prevention Research (2001)
Research Category: Children's Health , Health Effects
Description:
Objective:The principal objective of the Molecular Biomarkers Core is to identify patterns of altered gene expression that form a significant association with autism in human populations, or which are coupled to specific environmental factors in animal models. During this period the core has established a microarray facility that utilizes Affymetrix GeneChip technology. An essential component of the Core’s current efforts are to develop methods of analysis for microarray data in an effort to both better define, and reduce, the errors associated with the interpretation of microarray results (Geller et al 2002, in preparation).
Progress Summary:One of the central problems in the analysis of expression microarrays (cDNA arrays, oligonucleotide arrays) is the run-to-run variability of the expression patterns. In many cases, this variability has not been assessed independently, since the cost of the arrays themselves, coupled with the limited amount of blood per sample precludes the use of multiple replicates. We have therefore decided to use lymphoblastoid cell lines from patients with autism and/or normal controls to establish parameters for reproducibility of the expression profiles. At issue is whether the variability in growth/culture conditions for a given sample will produce a larger variation in expression than the intrinsic difference that is being sought between an autistic individual and a non-autistic control (e.g., sib). In a set of experiments using lymphoblastoid lines from an autistic (HI0489) and non-autistic (HI0487) individual, Dr. Gregg demonstrated that despite clear variations in expression profile with growth conditions including stimulation with pokeweed mitogen (PWM), the autistic and non-autistic lines clearly remained as distinct clusters. These experiments are continuing to define optimal conditions for sampling and obtaining expression profiles from patients.
Our approach to microarray analysis has been systematic, beginning with studies of repeatability and reproducibility. Beginning with an initial experiment with four replicates from the same cell culture, we have developed a method of data transformation and normalization that is more effective than previous procedures. After normalization, it appears that the reproducibility is about 10% for highly expressed genes, and an equivalent amount on a transformed scale for genes that are less highly expressed, which is much less variable than is commonly believed. The next step is to analyze samples from multiple individuals to investigate issues of statistical power and uncertainty; however it appears that with the new technology we have developed, neither variation in laboratory procedures nor variation between gene chips will significantly impede the studies we are conducting. [Geller, S..C., Gregg, J.P., Hagerman, P.J., and Rocke, D.M. (2002) Transformation and Normalization of Affymetrix Microarray Data, in preparation]. These studies have also formed the basis for two abstracts that have been presented at meetings.
Future Activities:The short-term plan is for the further development of the analytical tools for analyzing the microarray data, and for the initiation of studies on blood samples from patients and controls. We will not be able to perform detailed expression profiles for all patients; thus, we are developing a strategy for selecting clinical subgroups of the autistic patients.
Journal Articles:No journal articles submitted with this report: View all 4 publications for this subproject
Supplemental Keywords:Autism, GeneChip, genomics, microarray, variance stabilization, power calculations,
,
ENVIRONMENTAL MANAGEMENT, Scientific Discipline, Health, RFA, PHYSICAL ASPECTS, Susceptibility/Sensitive Population/Genetic Susceptibility, Risk Assessment, Biology, Risk Assessments, Disease & Cumulative Effects, genetic susceptability, Health Risk Assessment, Physical Processes, Chemistry, Children's Health, biomarkers, exposure assessment, xenobiotics, neurological development, autism, synergistic interactions, mechanisms, human health risk, susceptibility, halogenated aromatics, etiology, gene-environment interaction, neurotoxic, biological markers, children, neurobehavioral, pesticides, chemical exposure, exposure, biomarker, neurobehavioral effects, human exposure, neurodevelopmental, neurotoxicity
Progress and Final Reports:
Original Abstract
2003 Progress Report
2004 Progress Report
2005 Progress Report
Main Center Abstract and Reports:
R829388 CECEHDPR - University of California at Davis Center for the Study of Environmental Factors in the Etiology of Autism
Subprojects under this Center:
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R829388C001 Environmental Factors in the Etiology of Autism; Analytic Biomakers (xenobiotic) Core
R829388C002 Environmental Factors in the Etiology of Autism; Cell Activation/Signaling Core
R829388C003 Environmental Factors in the Etiology of Autism; Molecular Biomakers Core
R829388C004 Environmental Factors in the Etiology of Autism; Childhood Autism Risks from Genetics and the Environment (The CHARGE Study)
R829388C005 Environmental Factors in the Etiology of Autism; Animal Models of Autism
R829388C006 Environmental Factors in the Etiology of Autism; Molecular and Cellular Mechanisms of Autism