How%20DNA%20Microarrays%20Work

1

• Exploring the Limitations of DNA Microarray
  Technology A Case Study in Quality Control
• Emily Oldham1, 2, A. Malcolm Campbell1, Laurie J.
  Heyer 2

1Biology 2Math Depts., Davidson College,
Davidson, NC
7
4
1
How DNA Microarrays Work
Microarray Production
Ratios from Alternative Methods
Step 1 Spot each gene onto microarray Step 2
cDNAs from two conditions are labeled red and
green Step 3 Hybridize cDNAs to
microarray Step 4 Scan to measure
fluorescence Step 5 Determine redgreen ratios
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.
Theoretical versus actual experimental ratios for
three hybridization methods. No method gave 11
ratios consistently. Error bars are 90
confidence intervals.
2
5
8
Why Microarrays are Exciting
Data Analysis
Data Collection

• Genome-wide expression of genes can be determined
  quickly
• Current applications include
• - cellular circuitry
• - drug discovery
• - mutation and polymorphism detection

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.
http//www.tigr.org/tdb/microarray/images.shtml
6
3
9
Research Goals
Gene-Specific Ratios
Conclusions

• Some genes will give unpredictable ratios
• Rigorous controls should
• a) identify any aberrant genes
• b) compensate for gene-specific ratios
• Significance for ratio values must be determined
  for each microarray application

• Design novel system to evaluate microarray
  method
• Determine if microarrays detect known 11 ratios
• Measure gene-specific variation in ratios
• Document sources of experimental error

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_at_davidson.edu
Helping Students Discover Genomics, Proteomics
Bioinformatics A. Malcolm Campbell, Laurie J.
Heyer, Adam Abele, Brian Akin, Danielle Choi,
Parul Karnik, Peter Lowry, David Moskowitz, Emily
Oldham, Jennifer Madden