Finding and interpreting genetic variations that are important to ophthalmologists

Abstract

Purpose: To explore two approaches for making the human genome more accessible and useful to practicing ophthalmologists.

Methods: DNA samples were obtained from patients with inherited eye diseases, and these samples were screened for sequence variations in known disease genes with a combination of single-strand conformational polymorphism analysis and automated DNA sequencing. Data from this screening were then used to evaluate strategies for productively narrowing the sample space as well as for estimating the pathogenic potential of variations that were discovered in individual patients. For the latter purpose, a universal nomenclature for pathogenic potential was proposed based upon the segregation of disease alleles and the evolutionary conservation of specific residues as reflected by a substitution matrix known as blosum 62.

Results: Sequence variations were found to be unevenly distributed among disease-associated genes, such that screening strategies could be refined to discover more than 50% of clinically important sequence variations with only 10% of the effort. The use of the blosum 62 matrix was more statistically powerful than our previous method of estimating pathogenic probability.

Conclusions: The size of the human genome requires that clinical questions be very carefully focused if they are to be meaningfully answered in a reasonable amount of time and with a reasonable amount of resources. By examining the behavior of known disease genes, one can design strategies for significantly focusing the sample space and for more effectively interpreting the variations that are found.