Exploring the Limitations of DNA Microarray Technology A

Exploring the Limitations of DNA Microarray Technology: A Case Study in Quality Control Emily 1, 2 Oldham , A. Malcolm 1 Campbell , Laurie J. Heyer 1 Biology 1 How DNA Microarrays Work 4 Microarray Production 2 & 2 Math Depts. , Davidson College, Davidson, NC 7 Ratios from Alternative Methods Step 1: Spot each gene onto microarray Step 2: c. DNAs from two conditions are labeled red and green Step 3: Hybridize c. DNAs to microarray Step 4: Scan to measure fluorescence A schematic map of the experimental microarray spots. Each colored box represents a different known yeast (or fly) PCR product. Diagonals show a 4096 -fold concentration range. Step 5: Determine red: green ratios 2 Why Microarrays are Exciting 5 Data Collection Theoretical versus actual experimental ratios for three hybridization methods. No method gave 1: 1 ratios consistently. Error bars are 90% confidence intervals. 8 Data Analysis • Genome-wide expression of genes can be determined quickly • Current applications include: - cellular circuitry - drug discovery - mutation and polymorphism detection http: //www. tigr. org/tdb/microarray/images. shtml 3 Research Goals 6 Gene-Specific Ratios 9 Conclusions • Some genes will give unpredictable ratios • Design novel system to evaluate microarray method • Rigorous controls should: • Determine if microarrays detect known 1: 1 ratios a) identify any aberrant genes • Measure gene-specific variation in ratios b) compensate for gene-specific ratios • Document sources of experimental error • Significance for ratio values must be determined for each Theoretical versus actual experimental results. Ratios were filtered for spot morphology and 15% similarity between partner spots. Values for the three highest concentrations and three experimental replicates were pooled. emoldham@davidson. edu Differences between pairwise ratios are gene- and method-dependent. Error bars are 90% confidence intervals. A microarray hybridized for all 10 yeast genes in equal concentrations of both red and green dye. microarray application