Cholestasis (or pathologic jaundice) is the most common sign of liver disease in children and often results from mutations in genes that play a critical role in bile formation and transport. In adults, mutations in the same genes also cause chronic cholestasis that may manifest as non-specific portal fibrosis, intrahepatic cholestasis of pregnancy, and low-phospholipid-associated cholelithiasis. Using recent knowledge of the genetic basis of these disorders, we developed a high-throughput gene chip that identifies mutations in the genes that cause the most common forms of inherited syndromes of chronic cholestasis. The chip is now a clinical test that is increasingly used by physicians as part of diagnostic algorithms in symptomatic patients. Although the chip remarkably facilitates specific diagnoses, its accuracy is limited by the inability to reliably detect insertions or deletions, whih account for 10-20% of the disease-causing mutations, thus decreasing the sensitivity of the chip. In this application, we propose to solve this technological gap by developing the next version of a mutation-screening tool that we are naming """"""""JAUNDICENEXT"""""""". This tool customizes NextGen sequencing to accurately survey the nucleotide composition of target genes to diagnose disease-causing mutations.
Our Specific Aim i s """"""""to determine the accuracy of JAUNDICENEXT to sequence the target genes."""""""" To test Hypothesis-1 that """"""""JAUNDICENEXT sequences the target genes at >99% accuracy,"""""""" we will compare the nucleotide sequence produced by the JaundiceNext with the sequence produced by standard sequencing methodology. To test Hypothesis-2 that """"""""JAUNDICENEXT identifies insertion and deletion mutations in patients with cholestasis,"""""""" we will examine whether the sequence output produced by JAUNDICENEXT detects insertions, deletions, or indels in DNA known to carry these mutations. Collectively, these experiments will validate the technical merits of JAUNDICENEXT and position us for future experiments to further bench-test the assay and develop an automated detection algorithm to in a future Phase-II application.
Jaundice is a clinical sign that is common to several types of chronic liver diseases in children and adults. In a previous STTR, we developed a gene chip to identify mutations in the genes that cause the most common forms of inherited syndromes of persistent jaundice (also known as cholestasis). The chip is now a clinical test that is increasingly used by physicians as part of diagnostic algorithms in symptomatic patients. Although the chip remarkably facilitates specific diagnoses, its accuracy is limited by the inabiliy to reliably detect insertions or deletions, which account for 10-20% of the disease-causing mutations, thus decreasing the sensitivity of the chip. We propose to solve this technological gap by developing the next version of a mutation-screening tool that we are naming """"""""JAUNDICENEXT"""""""". This new tool customizes NextGen, a powerful sequencing technology, to accurately detect the wider spectrum of mutations in four genes simultaneously. These studies will improve the sensitivity and accuracy of a non-invasive diagnostic tool that significantly improves the diagnostic algorithm in patients with liver disease.
| Bezerra, Jorge A (2016) MDR3 mutation analysis: A step closer to precision medicine. Hepatology 63:1421-3 |
| Goldschmidt, Monique L; Mourya, Reena; Connor, Jessica et al. (2016) Increased frequency of double and triple heterozygous gene variants in children with intrahepatic cholestasis. Hepatol Res 46:306-11 |
