The Jaundice Chip: A diagnostic tool for cholestatic liver disease

DESCRIPTION (provided by applicant): Cholestasis (pathologic jaundice) is a very common sign of liver disease in children and adults, and results from genetic defects that play a critical role in bile formation and transport. In adults, mutations in the same genes also cause debilitating liver diseases or increased susceptibility to common biliary diseases, such as gallstones. Because many of the clinical signs and symptoms are shared among these disorders, many laboratory studies and liver biopsies are necessary before specific diagnosis is made. Despite remarkable progress 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 patients. To translate this knowledge into the clinical arena, we developed a gene chip to identify mutations in the five genes that cause the most common forms of inherited syndromes of chronic cholestasis: The Jaundice Chip. The Chip uses a state-of- the-art "resequencing" platform that enables the readout of several thousand nucleotides in one reaction. In a Phase I award that now nears completion, we tested the technical merit of the Jaundice Chip. We found that the Chip efficiently reads the sequence of target genes efficiently and with 99.99% accuracy. We also found that it surveys for >95% of all mutations caused by single nucleotide changes. In this Phase II application, we propose to bench-test the Jaundice Chip against a larger patient population to demonstrate its clinical application as a reliable, high-throughput diagnostic tool for patients with chronic liver disease. In Aim 1, we will determine the ability of the Jaundice Chip to identify insertion and deletion mutations by directly analyzing the sequence readout from patients known to have inherited forms of intrahepatic cholestasis due to these types of mutations. In Aim 2, we will bench-test the Chip as a biomarker of disease by performing a prospective genotype-phenotype relationship in subjects with chronic cholestasis, and by determining whether the Chip can identify genetic markers of clinical response to treatment. And in Aim 3, we will develop an informatics-based analytical tool that optimizes mutation detection by the Jaundice Chip. To assure completion of these aims in a timely fashion, P2D Inc. has assembled a suitable investigative team that combines expertise in the field with a business infrastructure to transform the highly innovative features of the Chip into a non-invasive diagnostic tool that significantly improves the diagnostic algorithm in patients with liver disease. Jaundice is a clinical sign that is common to several types of chronic liver diseases in children and adults. Despite the significant advances in understanding the genetic basis of jaundice in humans, the new knowledge has so far failed to result in a practical method of diagnosis or improved treatment of these patients. To translate this knowledge into practical medial applications in the clinical arena, we developed a gene chip to identify mutations in the five genes that cause the most common forms of inherited syndromes of persistent jaundice (also known as cholestasis). The chip, named "Jaundice Chip," uses a state-of-the-art technology that enables the detection of mutations of selected genes. In the Phase I award that now nears completion, we demonstrated the technical merit of the Jaundice Chip as a efficient and highly accurate gene sequencing tool. In this Phase II application, we propose to bench-test the Jaundice Chip against a larger patient population to demonstrate its clinical application as a reliable, high-throughput diagnostic tool for patients with chronic liver disease. These studies will lead to opportunities to transform the highly innovative features of the Chip into a non-invasive diagnostic tool that significantly improves the diagnostic algorithm in patients with liver disease.