Long-read sequencing-based diagnosis for complex genomic and DNA methylation changes

PROJECT SUMMARY
Structural changes in the genome and alterations of DNA methylation contribute to many diseases.
Properly assessing these types of changes can be challenging using current technologies. One of the focuses
of D4Z4 Medicine, Inc., is to provide long-read sequencing-based assays that can be used to determine
structural variations and DNA methylation in one assay. In this proposal, we focus on a molecular diagnostic
assay for facioscapulohumeral muscular dystrophy (FSHD). In addition to assay optimization, we will develop a
user friendly and scalable data analysis tool, which will allow fast and accurate diagnostic report generation. In
aim 1, we will standardize and validate the long-read sequencing assay. We will increase the capacity of the
assay by adding additional target regions. We will also validate the assay using clinical samples. In aim 2, we
will optimize a bioinformatics pipeline for analyzing long-read sequencing data containing D4Z4 repeat
sequences and create a user-friendly interface. This approach developed here will provide a novel genetic
diagnostic tool for FSHD which does not have an effective diagnostic tool. In addition, the assay and analysis
tool will be expanded to cover additional genes and diseases.

Grant Number: 1R41TR005388-01
NIH Institute/Center: NIH
Principal Investigator: YI-WEN CHEN