BIOMED PhD Research Proposal
Title:
Improving Molecular Diagnostics for Rare Mendelian Disorders Using Long Read Sequencing
Speaker:
Tanaya Jadhav, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University
Advisors:
Ahmet Sacan, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University
Ramakrishnan Rajagopalan, PhD
Senior Principal Scientist
Division of Genomic Diagnostics
Children's Hospital of Philadelphia (CHOP)
Details:
Rare Mendelian disorders, while individually rare, collectively affect 25–30 million Americans. Despite the implementation of short-read sequencing (SRS) as the standard of care, approximately 50–60% of patients remain without a definitive molecular diagnosis. This diagnostic gap is in part driven by the inherent technical limitations of SRS, including the inability to resolve variants in "dark" genomic regions, determine phase, or capture DNA methylation without fragmented, multi-tiered testing. While Long-Read Sequencing (LRS) offers a transformative solution by consolidating structural variant detection, phasing, and methylation into a single assay, its adoption in research and clinical settings is hindered by a lack of standardized, validated bioinformatics infrastructure.
This work aims to bridge this gap through the development of two integrated workflows: WAFL (Workflow for Annotation, Filtering, and Prioritization of LRS variants) and MitoPac. WAFL provides a comprehensive, platform-agnostic framework for prioritizing the expanded variant spectrum of the nuclear genome, enabling the identification of compound heterozygous variants, tandem repeat expansions, and imprinting disorders through native methylation and phasing data. MitoPac addresses the critical shortcomings of standard-of-care mitochondrial diagnostics by enabling precise characterization of multiple mitochondrial deletions, SNV calling, and accurate heteroplasmy quantification from LRS without the amplification biases inherent in traditional SRS-based assays.
Without specialized annotation workflows, the expanded variant spectrum provided by LRS, including large SVs, tandem repeats, phased haplotypes, and differential methylation, remains largely overlooked and underutilized. The objective of this work is to bridge this gap by developing integrated variant analysis workflows designed specifically for LRS data. These pipelines will provide a comprehensive solution for filtering, annotating, and prioritizing variants across both nuclear and mitochondrial genomes. We hypothesize that integrating multi-omic data from long-read sequencing in a streamlined variant analysis workflow will provide additional diagnostic yield for rare Mendelian disorders.