The Loyola Genomics Facility has a number of external and internal collaborations in both basic and clinical research.

Human Disease Gene Discovery with Exome Sequencing 
In collaboration with Dr. Eric Pierce at Massachusetts Eye and Ear Infirmary and Dr. Marni Falk at the Children’s Hospital of Philadelphia, we have developed a suite of bioinformatics tools and resources for variant detection and analysis using the Next-Generation Sequencing data. Using these tools to analyze family-based whole exome sequences, we have successfully identified a number of pathogenic variants leading to inherited retinal degeneration and mitochondrial diseases.

Copy Number Variations in Genomic Disorders 
A longtime interest of Dr. Gai’s is understanding of chromosome copy number variations (CNVs) associate with many human pathologies. We have developed bioinformatic tools and databases for CNV detection, analysis, and interpretation. Using these tools, we have gained significant understanding of the genetic mechanisms behind a number of diseases, including ADHD and autism. We hope to expand our understanding of CNVs in human diseases using high-throughput technologies, especially the Next-Generation Sequencing technologies.

Human Mitochondrial Variations and Inheritance Patterns. 
Although distinct mitochondrial DNA variation patterns, or haplogroups have been linked to different demographic and ethnic groups, it is likely that additional alterations are present and have yet to be identified and characterized. We are interested in identifying novel mtDNA variants, understanding their inheritance patterns and relationship to germline bottlenecks, aging, Muller’s ratchet, tissue-specific variations, and human pathologies. This project builds on long-time collaborations with Dr. Marni Falk and Dr. Douglas Wallace at the Children’s Hospital of Philadelphia, and Dr. Theodore Schurr at University of Pennsylvania.

Human Bladder Microbiome and Overactive Bladder Syndrome 
Together with Drs. Alan Wolfe, Linda Brubaker, Cynthia Fok, and others at the Loyola University Chicago Stritch School of Medicine, we are embarking on a challenging yet groundbreaking research project, to identify the microbiota of human bladder. This knowledge will facilitate our understanding of many urinary tract diseases including overactive bladder syndrome.

Human Gut Microbiota Changes in Patients Treated for Severe Burns 
Bowel management is crucial for successfully treating patients with severe lower body burns. It is unclear how continuous bowel management can disrupt gut microbiota of these patients, inhibit recovery and lead to potential pathogen “invasion”. As part of a collective effort with Drs. Richard Kennedy, David Hecht, Richard Gamelli, others at Loyola and the University of Norte Dame, we aim to understand how the gut microbiota of these patients changes throughout their treatment.

Genetic Mechanisms of Hypertension, Sick Cell Disease, and Skin Tone 
In partnership with Drs. Richard Cooper and Bamidele Tayo at the Loyola University Chicago Stritch School of Medicine, we are fine-mapping loci previously known to be associated with hypertension, sick cell disease, and skin tone & Vitamin D level using semiconductor sequencing technology. The goal is to identify functional and causal genetic variants directly related to the phenotypes and disease outcomes.

Sequence-based Cancer Diagnostics and Prognostics
In association with Drs. Eva Wojcik, Marcus Quek, and Guliz Barkan at the Loyola University Chicago Stritch School of Medicine, we hope to develop both sequence-based molecular diagnostic and prognostic tests for bladder cancer. The overall goal of this highly translational project is to not only improve our knowledge of the genetic heterogeneity of bladder cancer, but also develop a cost-effective and highly accurate method to diagnose bladder cancer and stratify its response to treatment.