OUR RESEARCH

Alagille syndrome (ALGS), is a rare, pediatric, multi-system disorder that is caused by defective Notch signaling due to pathogenic variants in the JAG1 ligand or the NOTCH2 receptor. Causative mutations can be found in a high percentage of ALGS patients, but many variants can’t be classified as disease-causing, and this uncertainty is problematic for patients and clinicians. We are using cutting-edge sequencing technologies and developing high-throughput assays to solve this uncertainty. Our goal is to develop variant detection strategies and functional assays for ALGS to apply to other genetic diseases for resolution of variant uncertainty.

Biliary atresia (BA) is a rare pediatric cholangiopathy affecting the extrahepatic bile ducts. The etiology of BA is unknown, although it is predicted to involve environmental, inflammatory, infectious, and/or genetic risk factors. We are interested in identifying susceptibility genes for BA and have carried out a GWAS that identified the extracellular matrix protein, EFEMP1, as a putative susceptibility gene. Our goal is to perform functional studies to validate this gene as well as to continue studying patient samples to identify additional susceptibility genes.

Ring chromosomes occur when the ends of chromosomes fuse, forming a ring-shaped chromosome. These fusion events can occur with and without the deletion of genetic material. Ring chromosomes lead to various developmental issues, depending on which chromosome is affected, with many resulting in epileptic phenotypes. Our lab is interested in studying the formation and consequence of ring chromosomes.

We are carrying out rapid genome sequencing for infants in the neonatal intensive care unit (NICU). The diagnostic rate is about 32%, and we aim to understand who should be tested, what diagnoses we are missing using our current platform, and what the effect of a positive or negative diagnosis is on patients, their families, and the physicians who care for them.

Variants in JAG1 cause ALGS through haploinsufficiency and are typically protein-truncating. However, many JAG1 variants are missense, which usually have uncertain associations with disease. We design Multiplexed Assays of Variant Effects (MAVEs) to assess the function of variants. These assays incorporate hundreds of controls in a single experiment, allowing for increased accuracy with functional predictions. Data calibration allows for the assignment of variants as "normal" or "abnormal" in function, which can be applied as a criterion during clinical variant classification. We have a number of ongoing projects in this area to study multiple functional properties of JAG1 and NOTCH2.

We are actively studying how NOTCH2 variants cause ALGS. In addition to correlating these variants with abnormal function using MAVEs, we are also testing the effect of variants on functional processes, such as glycosylation, trafficking, and binding. We are establishing assays both in cell culture as well as using CRISPR-based editing techniques and iPSC differentiation to study changes in a liver organoid model.

While genome sequencing is identifying mutations in 30-35% of patients, we suspect that there are genetic changes underlying the disorders in some of our patients with a normal result. We will carry out RNA-sequencing, investigation of methylation status, and long read sequencing in mutation negative patients, to understand the true rate of genomic changes causing neonatal disorders and improve our diagnostic pipeline.