CHICAGO – A novel genomic analysis technique known as exome analysis has pinpointed two previously unsuspected genes strongly related to platelet reactivity in patients on clopidogrel.
A hoped-for practical outcome from this finding is development of a rapid test for clopidogrel responsiveness. Before undergoing percutaneous coronary intervention, a swab could be run through a patient’s mouth and a quick analysis of the genetic sample would indicate whether clopidogrel would be an effective antiplatelet agent in that individual. Current assays require patients to already be on clopidogrel, which may or may not be providing them protection.
Dr. Matthew J. Price, director of the cardiac catheterization laboratory at the Scripps Clinic, La Jolla, Calif. presented the findings of the Genotype Information and Functional Testing Exome (GIFT EXOME) study, in which he and his coworkers performed whole exome analysis on genetic material obtained from 192 self-identified white participants in the earlier GRAVITAS (Gauging Responsiveness with A VerifyNow P2Y12 assay – Impact on Thrombosis And Safety) trial. That study, for which Dr. Price served as principal investigator, showed no benefit for double-dose clopidogrel in patients with high on-treatment platelet reactivity after percutaneous coronary intervention (JAMA 2011;305:1097-105).
In GIFT EXOME, three distinct genes were found to be associated with on-treatment platelet reactivity 12-24 hours post-PCI in patients taking clopidogrel. One of them, CYP2C18/9, was already known to be associated with platelet resistance to clopidogrel, although variants in this gene explain only a small portion of the overall variability in clopidogrel response. The finding of the other two genes, ATP2B2 and TIAM2, came as a surprise.
The ATP2B2 gene codes for a plasma membrane calcium transporting ATPase. It exports calcium ions out of the cell, so it plays a critical role in maintaining intracellular calcium homeostasis, thereby influencing platelet activation and aggregation, the cardiologist explained at the annual meeting of the American College of Cardiology.
TIAM2 (T-cell lymphoma invasion and metastasis 2) is the primary mediator of activation of a protein called Rac1, which is involved in platelet aggregation.
"These findings are preliminary, but identification of two genes critical to platelet function among the 21,000 genes we sequenced lends credibility to the validity of the result," Dr. Price observed.
The overall frequency of the ATP2B2 variant linked to platelet activity in the presence of clopidogrel is 27% in the white population, while for the key TIAM2 variant it’s about 13%, he said.
The next step in the GIFT EXOME project is to validate the results in more than 1,000 patients, an effort already underway.
As an aside, eight subjects in GIFT EXOME turned out to have genomes inconsistent with white race and were excluded from the study.
Whole exome analysis entails sequencing the entire protein-coding regions of the human genome. This high-powered technique identifies both single nucleotide polymorphisms and insertion/deletions. Exome analysis is far more likely to identify specific gene mutations that are causative of disease than is the older, widely utilized method of genome-wide association studies, which basically points investigators toward what Dr. Price calls "zip codes" of interest along the genome without zeroing in on specific culprit genes.
He said that the major challenge posed by whole exome analysis is the enormous computational muscle required. More than 400 days of serial supercomputer time went into analyzing the samples from 192 GIFT EXOME participants. In excess of 6.1 million single nucleotide polymorphisms and more than 500,000 insertion/deletions were detected. Computers are getting ever faster, though, and the reagents required for exome sequencing are getting more affordable, he noted.
The GIFT EXOME study was supported by Bristol-Myers Squibb/Sanofi. Dr. Price reported serving as a consultant to those companies and more than half a dozen others. He also holds an equity interest in Iverson Genetics.