DNA microarray analysis has become a widely used genetic tool; however, its massive scale creates quality control and analysis problems for most laboratories wishing to use it. The purpose of this proposal is to facilitate the application of this technology to fundamental hypothesis-driven research through the identification and resolution of the sources of cDNA microarray data variability. Since the array itself is a considerable source of variability we have developed a three-color array platform that allows prehybridization array visualization. Our direct labeling approach separates assessment of slide coating, printing and blocking from hybridization, enabling evaluation of element/array morphology, surface DNA deposition/retention, and background levels prior to hybridization. We have also developed Matarray, a software package for hybridized image processing and data acquisition that provides quantitative QC for each array element as well as the entire slide. Combined, these efforts provide the basis for an integrated quality control (QC) approach to effectively manage microarray technical and systematic variability. For this application we will build upon these initial efforts through the following specific aims 1) We will study the relationship between measurable prehybridization image quality parameters and data quality/reproducibility, including the influence of background, spot morphology, and bound probe. Data compression caused by limiting bound probe will be quantified using the third dye so that data derived from sub-optimal spots can either be normalized or filtered. 2) We will develop pre-hybridization array qualification software based upon parameters identified in aim 1, which will encompass probe plate tracking, quantification of probe available for hybridization, and array/element morphology. Post-hybridization algorithms will be developed that utilize third dye information for data normalization and filtering. 3) Our improved microarray and analysis platforms will be validated by expression profiling disease development in an animal system. The commercial oligonucleotide and cDNA arrays will be used as reference platforms to assess cost effectiveness and value of our approach. Our success will provide an accurate, flexible, lower cost alternative to commercial arrays for laboratories wishing to conduct gene expression studies.

Agency
National Institute of Health (NIH)
Institute
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Type
Research Project (R01)
Project #
5R01EB001421-03
Application #
6916304
Study Section
Special Emphasis Panel (ZRG1-GEN (90))
Program Officer
Korte, Brenda
Project Start
2003-08-01
Project End
2007-06-30
Budget Start
2005-07-01
Budget End
2006-06-30
Support Year
3
Fiscal Year
2005
Total Cost
$375,000
Indirect Cost
Name
Medical College of Wisconsin
Department
Pediatrics
Type
Schools of Medicine
DUNS #
937639060
City
Milwaukee
State
WI
Country
United States
Zip Code
53226
Cohen, Eric P; Lenarczyk, Marek; Fish, Brian L et al. (2013) Evaluation of Genomic Evidence for Oxidative Stress in Experimental Radiation Nephropathy. J Genet Disord Genet Rep 2:
Schulteis, Ryan D; Chu, Haiyan; Dai, Xuezhi et al. (2008) Impaired survival of peripheral T cells, disrupted NK/NKT cell development, and liver failure in mice lacking Gimap5. Blood 112:4905-14
Heiden, Tisha C King; Struble, Craig A; Rise, Matthew L et al. (2008) Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. Reprod Toxicol 25:47-57
Gao, Shouguo; Jia, Shuang; Hessner, Martin et al. (2008) Quality Weighted Mean and T-test in Microarray Analysis Lead to Improved Accuracy in Gene Expression Measurements and Reduced Type I and II Errors in Differential Expression Detection. J Comput Sci Syst Biol 1:41
Wang, Xujing; Jia, Shuang; Geoffrey, Rhonda et al. (2008) Identification of a molecular signature in human type 1 diabetes mellitus using serum and functional genomics. J Immunol 180:1929-37
Wang, Xujing; Jia, Shuang; Meyer, Lisa et al. (2007) Quantitative measurement of pathogen-specific human memory T cell repertoire diversity using a CDR3 beta-specific microarray. BMC Genomics 8:329
Hessner, Martin J; Liang, Mingyu; Kwitek, Anne E (2006) The application of microarray analysis to pediatric diseases. Pediatr Clin North Am 53:579-90
Wang, Xujing; Jia, Shuang; Meyer, Lisa et al. (2006) Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays. BMC Bioinformatics 7:378
Hessner, Martin J; Xiang, Bixia; Jia, Shuang et al. (2006) Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms. Physiol Genomics 25:166-78
Hessner, Martin J; Meyer, Lisa; Tackes, Jennifer et al. (2004) Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics 5:53

Showing the most recent 10 out of 13 publications