LIVERCHIP - A diagnostic tool for genetic liver diseases

DESCRIPTION provided by applicant Genetic mutations are known to cause acute and chronic liver diseases and are being increasingly recognized as drivers of phenotype severity As a group these diseases represent a substantial disease burden in the United States and constitute a diagnostic challenge in the clinical evaluation of affected patients In a Phase I Award we developed the JAUNDICENEXT a sequencing platform that combines short and long range PCRs to produce amplicons of target genes the generation of patient specific libraries and sequencing by next generation technologies to successfully identify mutations in subjects with inherited syndromes of intrahepatic cholestasis Then we began experiments to further improve the efficacy and scope of the sequencing platform to better meet the diagnostic needs of patients with genetic liver diseases In preliminary studies for this application we performed proof of principle experiments that demonstrated the feasibility and technical merit of an innovative sequencing platform using a simplified step protocol that combines specific multiplexing chemistry coded for individual patients with an immediate sequencing by next generation technology Having demonstrated the technological merit of this newer platform we propose to expand the gene coverage by creating the LIVERCHIP a high throughput sequencing platform that screens for mutations in genes that manifest as pathologic jaundice chronic liver injury and cystic diseases of the liver thus meeting the needs of a broader population To this end we propose three complementary aims to transition the JAUNDICENEXT to the LIVERCHIP as an expanded diagnostic tool bench test the LIVERCHIP in patients with chronic inheritable liver diseases and to develop an analytical tool that optimizes mutation detection by the LIVERCHIP Our experimental strategy will begin with the development and validation of a TruSeq multiplexing chemistry that enables the sequencing of liver genes accurately in a step assay This will be followed by bench testing the assay against a group of well phenotype patients for each one of the target diseases Last we will develop a browser that will decrease the time required for the analysis of the nucleotide readout thus decreasing the time to diagnosis Our ultimate goal is to positively impact liver based diagnostics by producing an assay that is accurate requires short analytical time and at much lower cost than currently available tests These features will make the end product user friendly in the clinical setting and increase its marketability PUBLIC HEALTH RELEVANCE We propose to develop and validate the LIVERCHIP as a diagnostic tool to screen for mutations in patients with genetic liver diseases While distinct at the molecular level these diseases share many clinical features that make the arrival at specific diagnosis challenging for the practicing physician In order to improve diagnostics P D Inc conducted experiments proposed in a Phase I award to validate the technical merit of the JAUNDICENEXT a sequencing test to screen for genetic mutations in children with pathologic jaundice Here P D Inc proposes to develop a much improved new sequencing chip that customizes a powerful high throughput sequencing technology to meet the diagnostic needs of patients with pathologic jaundice as well as those with other genetic diseases Due to the broader diagnostic scope the name of the sequencing platform will change to LIVERCHIP This new mutation screening tool combines state of the art multiplexing chemistry with next generation sequencing platforms to accurately detect a wider spectrum of mutations in an expanded number of genes simultaneously When fully developed the LIVERCHIP will represent a non invasive tool that will significantly improve the diagnostic algorithms for patient with liver diseases