Jaundice Chip: Diagnostic tool for cholestatic liver dis

DESCRIPTION (provided by applicant): Cholestasis (or pathologic jaundice) is the most common sign of liver disease in children, and results from genetic defects in genes that play a critical role in bile formation and transport. In adults, mutations in the same genes also cause debilitating liver diseases or increase susceptibility to common biliary diseases, such as gallstones. Despite the remarkable progress in understanding how these genes cause liver disease in humans, the new knowledge has so far failed to result in a practical method of diagnosis or improved treatment of these diseases. In this Phase I application, our long-term aim is to develop a diagnostic gene chip that accurately identifies genetic mutations in patients with chronic cholestatic syndromes. To this end, we developed the prototype of a resequencing gene chip to diagnose mutations in the five genes that cause the most common forms of cholestatic liver disease, and named it the "Jaundice Chip". Here, we propose to determine the precision of the Jaundice Chip to sequence the target genes. To this end, we will test two hypotheses: 1) Hybridization of amplicons with the Jaundice Chip generates complete nucleotide sequences of target genes, and 2) the Jaundice Chip sequences target genes at >99% accuracy. To test both hypotheses, we will amplify DNA fragments ("amplicons") from blood of human subjects, followed by labeling and hybridization of amplicons with the chip. This will be followed by an analysis of the chip readout with bioinformatics software to determine whether the chip readout fully matches the target gene sequence tiled on the chip. Lastly, the accuracy of the chip will be determined by a direct comparison with the sequence readout using the standard capillary sequencing methodology. The proposed experiments will establish the technical merit and feasibility of the Jaundice Chip as a precise diagnostic tool with a high potential for commercial value. The full potential for commercialization will be explored in a future Phase II application that will benchtest the chip against a large patient population to establish a genotype-phenotype relationship, sensitivity, and specificity. We envision that this product will provide a rapid means to diagnose the genetic defects in patients with chronic cholestasis and to expedite patient-based research in the field of cholestasis.