Skip to main content

Conference Program

Subpage Hero

Loading

Long-Read Genome Sequencing to Diagnose Rare Disease in a State-Funded Study

Clinical Genetics and Therapeutics
  • Primary Categories:
    • Clinical- Pediatric
  • Secondary Categories:
    • Clinical- Pediatric
Introduction:
The Alabama Genomic Health Initiative (AGHI) is a state-funded, IRB-approved study that since 2017 has prioritized providing access to emerging genomic technologies to a diverse, statewide population. This has included a cohort of children and adults with undiagnosed rare disease. In 2024, the AGHI began offering long-read genome sequencing (lrGS) to this cohort, as evidence from other studies has demonstrated its effectiveness in increasing diagnostic rate in cases refractory to short-read genome sequencing (srGS).

Methods:
Participants referred to the AGHI and determined to have symptoms suspicious of an underlying genetic condition are enrolled at one of three clinical sites: Children’s of Alabama (Birmingham, AL), UAB-Kirklin Clinic (Birmingham, AL), or the Smith Family Clinic for Genomic Medicine (Huntsville, AL). Participant DNA is isolated in a CAP/CLIA laboratory and genome sequencing is performed on a PacBio Revio sequencer. Structural variants are called from genome sequencing data using a variety of software packages and annotated with population frequency and other information. Single nucleotide variants (SNVs) and indels are loaded into a custom software analysis application for interpretation and annotation. Variant pathogenicity is determined by ACMG criteria. When possible, clinical confirmation of variants of interest is performed via Sanger sequencing. Results are returned to participants and their families via a study genetic counselor (a member of the AGHI education working group) and/or their referring provider. When challenging or unusual cases are presented, the AGHI bioethics working group assists in determining whether and how results should be returned to participants.

Results:
Sequencing, analysis, and result return have been completed for 16 participants to date. Ten variants have been returned among nine participants. Of returned variants, five were classified as pathogenic or likely pathogenic and five were classified as variants of uncertain significance. At a participant level, 25% of cases (n=4) were determined to be diagnostic and 31.25% of cases (n=5) were determined to be uncertain. Five of the returned variants were SNVs or indels, three were triplet repeat expansions, one was an insertion, and one was a copy number variant (CNV).  Genes containing reportable variants included ATXN8OS, C2CD3, CADM3, COL3A1, DNMT3A, HTT, SYNE2, and TSC2.

Conclusion:
This early data demonstrates a potential utility for lrGS as a diagnostic tool in the setting of this state-funded research study, particularly in the identification of a wide variety of variant types using a single assay, including variants that would not have been identified via srGS, such as triplet repeat expansions in ATXN8OS and HTT. Additional benefits of this approach are the availability of this emerging technology to eligible participants at no cost and the structure of the AGHI, which benefits from working groups with a variety of professional perspectives. The AGHI bioethics working group is particularly valuable in this regard, as they advise on the return of results that would not have previously been identified via srGS but have ethical implications for returning to participants (triplet repeat expansions in HTT, for example). Limitations to our study include the lack of a direct comparison between lrGS and srGS and the inability to clinically-confirm variants that are not detectable via Sanger sequencing (though downstream commercial clinical testing may be available to participants). Desired future directions for this cohort include increasing enrollment and diagnostic yield, comparison to other ongoing lrGS efforts, and demonstration of a reduced time-to-diagnosis by avoiding a multiple assay, stepwise approach.

Agenda

Sponsors