GeneChip Essentials - How Affymetrix GeneChip® DNA Microarrays Work Before we can understand how Affymetrix GeneChip® DNA Microarrays work, let's first review the fundamentals of Genotyping DNA.

Genotyping DNA
	The Human Genome Project documented our genetic sequence and discovered everyone's DNA...
Understanding Disease
	For simplicity sake, let's use a hypothetical disease to illustrate a common way that...
Genes and Disease
	To find a treatment, researchers first have to find a cause, a mutation or malfunction in...
Finding a disease gene
	Before the advent of microarrays, scientists would have searched previous academic research...
How Affymetrix genotyping microarrays work
	All GeneChip microarrays take advantage of the natural chemical attraction between DNA molecules....
A good match sticks, a bad match doesn't
	When a single strand of DNA (ATCATG) matches a complementary strand of DNA (TAGTAC), the...
The Basic Principle
	Affymetrix microarrays use this base pairing attraction ??? a property known as hybridization...
Features and Probes
	The surface of the Affymetrix array is like a giant checkerboard. The 10K array, which is...
More information
	Quick math will tell you that if we are looking for 10,000 SNPs and there are over 400,000...
Extract DNA
	Now that we have a probe designed to genotype a SNP in a DNA sample, we have to extract...
Getting the DNA ready to be genotyped
	Before you can analyze the SNPs from the DNA you extracted, you need to make millions of...
Chop up the DNA
	Once we've made copies of all the SNPs that will be analyzed on the microarray, we use...
Making Sticky DNA
	After the DNA is chopped up, a chemical called biotin (purple cups) are attached to each...
Wash Sample Over the Array
	All of the prepared DNA sample is washed over the array for 14 to 16 hours. The number...
A Committed Relationship
	But somewhere, in the tagged sample of DNA washing over the array, a match will be made....
Determining a Match
	Let's assume that we have a match and that the SNP genotype in the sample DNA matched...
A Genotype is Determined
	Researchers wash the fluorescent stain over the array, and the glow in the dark molecules...
Measuring Multiple SNP Genotypes at Once
	So far we've been looking at just one possible genotype — C/G — for the SNP....