Whole Genome Association

Special techniques are used for screening each individual’s genome for millions of different SNPs. This kind of comparison is referred to as a genome-wide association study.

Special techniques are used for screening each individual’s genome for millions of different SNPs. This kind of comparison is referred to as a genome-wide association study.

Association studies: SNPs and copy number variants each account for approximately 1 difference, on average, in every 1,000 nucleotides. Only a tiny fraction of this naturally occurring variation has an affect on your risk of disease, therefore finding genetic causes of disease is very much like finding a needle in a haystack. To find SNPs that are associated with disease, DNA samples are selected from thousands of patients and thousands of healthy individuals. Special techniques are used for screening each individual’s genome for millions of different SNPs. This kind of comparison is referred to as a genome-wide association study. An association means that a SNP is significantly more frequent in patients compared to controls. Finding an association with a SNP is a way of pinpointing the location of a gene that increases your risk of disease. A special technique called comparative genomic hybridization, or microarray analysis, is used to screen the patient’s genome at a very high resolution identify deletions or duplications of genes. A microarray is a glass microchip. On the surface of the array are million of tiny probes. Each probe is complementary to a specific location in the genome. Genomic DNAs from a patient and a healthy control are labeled with fluorescent dyes. The patient is labeled in red, and the control is labeled in green. Then the two samples are mixed together, and the solution is poured over the surface of the array. The fluorescent DNAs are allowed to bind to the probes on the microarray surface. The unbound is washed away. Now, show a test-tune of blue liquid pouring onto the microarray, with the unbound colored dye washing away. The array is illuminated with a laser away. And the fluorescence of each probe is measured. Where the patient and the control have the same number of genes, the green and red signals are equal. If the gene is deleted in the patient’s genome, this will be indicated by a green spot. If a gene is duplicated in the patient’s genome, this will be indicated by a red spot. We represent this information graphically. The peaks in the figure represent regions where the copy number in the patient differs from the control. If a copy number variant causes disease, it may be significantly more frequent in patients compared to controls. Or, the copy number variant may be something extremely rare, meaning it is not present in any other patients or controls. But it could be highly associated with diseases in an individual family. The CNV may be passed, along with the disease, across multiple generations in a family. Or, a copy number variant may almost always occur as a spontaneous mutation, meaning a copy number variant that is present in the child, but was not inherited from a parent.