# Long-read DNA and RNA sequencing to identify disease-causing genetic variation and streamline testing

> **NIH NIH DP5** · UNIVERSITY OF WASHINGTON · 2024 · $388,750

## Abstract

PROJECT SUMMARY/ABSTRACT
Clinical genetic testing, including exome sequencing, has diagnosed many rare and novel genetic disorders.
These diagnoses have helped guide treatment, suggest novel or precision therapies, and provide long-term
prognostic information for individuals and their families. However, at least 50% of individuals with a suspected
genetic disorder remain undiagnosed after a complete clinical evaluation, which can take years to complete.
There are two major technical reasons for this low solve rate. First, structural variants such as large deletions,
insertions, inversions, and repeat expansions account for a significant fraction of unsolved cases, but they are
challenging to analyze using traditional short-read sequencing technologies. Second, many variants lie in
recently duplicated genomic regions that are difficult to evaluate using short-read sequencing technologies.
Recently, it has become economically feasible to pursue whole-genome long-read sequencing (LRS) of human
genomes with sufficient coverage to analyze these complex genomic regions. This presents an opportunity to
systematically evaluate the incremental diagnostic rate of LRS over current testing approaches and apply LRS
technology to a large cohort of individuals with unsolved genetic disorders. Moreover, LRS is unique in that as a
single test it has the potential to replace nearly all existing clinical genetic testing (microarray, exome, methylation
studies), making it possible to perform a complete clinical genetic evaluation in days to weeks using a single
dataset. The overall goal of this project is to establish a framework for the clinical adoption of long-read DNA and
RNA sequencing by systematic evaluation of individuals with suspected or unsolved genetic disorders. To
achieve this goal, LRS will be performed on 50 critically ill neonates and their parents who had nondiagnostic
trio short-read whole-genome sequencing (WGS) and 25 trios from the same cohort who had diagnostic WGS
(Aim 1). This will help establish the incremental diagnostic rate of LRS over short-read WGS. To evaluate the
technical advantages of LRS over traditional clinical testing, I will sequence 50 individuals with a suspected
genetic disorder who remain unsolved after at least clinical exome sequencing (Aim 2). In up to 20 persons that
remain undiagnosed after LRS, long-read RNA sequencing will be used to identify high-priority regions that
influence gene expression or splicing for further analysis. I will then evaluate the sensitivity of LRS as a single
genetic test by sequencing 50 individuals undergoing a typical outpatient clinical evaluation (Aim 3).
Demonstrating that LRS can be used as a single data source will help streamline the current stepwise approach
to clinical testing, leading to an increase in the diagnostic rate and an overall cost savings to the health system
through reduced testing and clinic visits. Overall, the aims outlined in this proposal will benefit patients and...

## Key facts

- **NIH application ID:** 10928256
- **Project number:** 5DP5OD033357-03
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Danny Erwin Miller
- **Activity code:** DP5 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $388,750
- **Award type:** 5
- **Project period:** 2022-09-13 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10928256

## Citation

> US National Institutes of Health, RePORTER application 10928256, Long-read DNA and RNA sequencing to identify disease-causing genetic variation and streamline testing (5DP5OD033357-03). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10928256. Licensed CC0.

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