SAN DIEGO—Will acustomized chip called IBC help pinpoint genetic links to vascular disease?Illumina Inc., is providing its iSelect Infinium Custom Genotyping BeadChip toa growing consortium of researchers who hope the collaboration's large scalewill generate information valuable to discovery science.
The name "IBC" recognizes consortium leaders: I for Institute of Translational Medicine andTherapeutics (ITMAT) at the University of Pennsylvania, B for the BroadInstitute of MIT and Harvard, and C for the Candidate-gene Association Resource(CARe) Consortium, supported by the National Heart, Lung, and Blood Instituteof the National Institutes of Health.
The consortium examined a variety of technology platformsfor about a year before choosing Illumina. "We made our choice based on trackrecord of reliability, flexibility—the ability to add on genes—and price," saysGarret FitzGerald, ITMAT's director. The IBC chip, FitzGerald believes, isparticularly relevant to this study because of its density of SNP coverage.Chip content includes CYPs, drug metabolizing enzymes, and genes whose variantsmay influence drug response to cardiovascular disease. FitzGerald says the mostcommon cardiovascular diseases—high blood pressure, heart attack, and heartfailure—are most represented.
IBC will analyze over 55,000 SNPs in more than 2,1
00 genesselected for cardiovascular and other phenotypes. The goal of analyzing 120,000samples from population studies and clinical trials is rapidly expanding,according to FitzGerald. "This reflects the buy in from the academicinvestigators whom we have contacted and who have bought into the program. Thisconsortium continues to grow."
IBC's content came together through the efforts of BrendanKeating, a postdoc in FitzGerald's lab. Stacey Gabriel, director of the geneticanalysis platform at the Broad Institute, who also works under a CARe grant,says Keating identified genes and built a database, then collaborated on SNPselection with Joel Hirschhorn, associate member, and coordinator of metabolisminitiative at the Broad.Although some targeted panels with SNPs haven't beensuccessful because they lacked certain genes, Gabriel sees value in thisproject, which she says is unique in scale and specificity. "This is a verylarge panel, and a lot went into curating the list," she says, adding thatrelevant genes identified later can be added to a second-generation chip. Shenotes that IBC's deep SNP coverage also incorporates blood and sleepingdisorders.
IBC's appeal to researchers is clear. "The idea," saysFitzGerald, "is that everyone who enrolls can use the resource for their ownstudies—to pursue their own discovery science." Many of the studies enlistedare randomized trials of drug effects providing phenotypic information on drugefficacy and adverse effects, says FitzGerald. "In some situations, we will beable to look across these studies at drugs which are distinct members of thesame class," he says.
At Illumina, Carsten Rosenow, senior marketing manager, DNAanalysis, says the IBC chip underlines Illumina's dedication to working withacademic researchers and validating a technology released in 2006. "I think forone, it clearly shows the importance of our iSelect program and thecustomizable subcontent, and this emphasizes the flexibility of our Infiniumassay," says Rosenow. The project is one of the largest ever undertaken withiSelect.
Illumina expects thecollaboration will last several years. "We are essentially in design process,"says Rosenow, with a goal of commercializing IBC by year end.
