Innovative genomic techniques on display at ARVO 2025 could slam the door shut on some of the biggest challenges in inherited retinal disorders.
Genetic researchers revealed the most sophisticated tools available for tackling some of the greatest challenges in ophthalmology and inherited retinal diseases (IRDs)—and some of them must be seen to be believed.
At a Day 5 ARVO 2025 session in Salt Lake City, five global experts showcased cutting-edge genomic technologies aimed at capturing an array of diagnostic, treatment and analysis blind spots. The Thursday session, An Updated Toolkit for Genetic Analysis: New methods for Heritable Eye Disease, demonstrated how researchers are pushing beyond the limitations of conventional sequencing to reveal truths underlying a wide variety of genetic eye disease culprits.
READ MORE: Advanced Research in Genetic Interpretation at ARVO 2025
The hidden value in “junk” reads
The session opened with Dr. Carlo Rivolta (Switzerland) presenting OFFpeak, a tool that turns sequencing “contamination” into valuable diagnostic information. His approach ingeniously leverages off-target reads—data typically discarded from targeted sequencing and exome analyses—to detect copy number variations (CNVs).
“Pathogenic variants in the human genome, in retinal diseases, in ocular diseases and in any kind of genetic conditions, are not represented by signal-to-signal sequence change, but a fairly large number of pathogenic variations are in fact CNVs,” Dr. Rivolta explained.
His team’s validation studies showed OFFpeak outperformed existing tools for detecting CNVs, which constitute approximately 20% of pathogenic variants in human disease.
“Off-target reads that contaminate exome and panel NGS procedures do contain important information for CNV detection. They are not wanted, but they are useful,” Dr. Rivolta said in conclusion.
READ MORE: Genetics Deep Dive, Adaptive Optics and Award-Winning Regenerative RP Tech
Long-read RNA sequencing revelations
Dr. Bin Guan (USA) followed with research on long-read RNA sequencing, a powerful tool that captures full-length transcripts rather than fragments. He explained how this approach is revealing numerous high-value, previously undocumented transcript variants in eye disease genes.
“The BEST1 gene was identified as the gene with the highest number of novel isoforms, which also has the highest number of reads,” Dr. Guan said, showing session attendees the surprising diversity in transcripts for this gene associated with Best disease.
The clinical relevance of such revelations could be massive—and already within reach of applicability. To illustrate, Dr. Guan described a mysterious patient initially lacking a genetic diagnosis. Long-read RNA sequencing identified a variant in an alternative exon of BEST1 not typically captured in clinical testing, leading to a definitive diagnosis where one would have otherwise been difficult or impossible.
“Long-read RNA sequencing can provide novel insights for gene function,” Dr. Guan said in conclusion. “The hope is that it perhaps could lead to better molecular diagnosis and potentially better therapeutic options.”
READ MORE: Beyond the Genetic Code at ARVO 2025: Breakthrough Approaches to Retinal Repair
Is optical genome mapping the future?
Dr. Elfride De Baere (Belgium) shifted the session’s focus to an intriguing, (relatively) novel technique with profound implications for the field: optical genome mapping (OGM).
Unlike conventional sequencing, OGM creates high-resolution images of fluorescently labeled DNA to detect structural variations.
Dr. De Baere presented a case of Peters anomaly where conventional testing fell short when it identified a simple 2.5 MB deletion that didn’t fully explain the patient’s condition. When her team applied OGM, they uncovered a far more complex scenario.
“Using optical genome mapping, this allowed us to find complex structural variants that were previously missed by molecular karyotyping and to close the diagnostic gap in this family with inherited eye disease,” Dr. De Baere explained.
The technology revealed four separate events, including translocations affecting regulatory elements of the PITX2 gene—a finding that better explained the patient’s phenotype than the initially detected deletion.
Dr. De Baere demonstrated how combining OGM with other approaches could provide game-changing complementary insights. “The combination of optical genome mapping and long-read sequencing is important to advance the understanding of difficult-to-interpret structural variants,” she said.
READ MORE: Seeing the Unseen: Adaptive Optics Enters the Clinical Arena at ARVO 2025
Ultra-long reads for phasing challenges
Session co-chair Dr. Gavin Arno (United Kingdom) presented work using Oxford Nanopore’s ultra-long read sequencing with adaptive sampling to target 309 retinal dystrophy genes. This approach generates reads exceeding 50 kilobases.
This technology could go a long way in overcoming pesky obstacles facing conventional methods.
“A big issue for clinical labs is of course uncertain genotypes,” Dr. Arno explained. “Patients may go through clinical genetic testing and then have a positive result with two mutations. But without phasing, the report is often inconclusive because we don’t know if the variants are in cis or trans,” Dr. Arno explained.
His team successfully resolved molecular diagnoses in previously unsolved cases and accurately characterized the opsin array—a notoriously difficult genomic region containing nearly identical genes responsible for color vision.
“This enables us to phase distant variants in the absence of family members, so crucially being able to achieve a confirmed molecular diagnosis for patients in the absence of parents or family members,” Dr. Arno added.
Epigenetics explains female variability
Dr. Quentin Gouil (Australia) ended the session by addressing a long-standing mystery: why female carriers of X-linked eye diseases show such variable phenotypes. His approach uses nanopore sequencing to simultaneously measure genetic variants and DNA methylation patterns that indicate which X chromosome is active in a given cell.
“Even though this is common and it’s a clear explanatory factor for variability in females, it’s not taken into account systematically. It usually requires another test,” Dr. Gouil noted.
By examining multiple tissues, his team found correlations between X-inactivation skew and disease severity in carriers of choroideremia and X-linked retinitis pigmentosa. In one case, a mother-daughter pair showed opposite skew patterns that explained why the younger patient had a more severe presentation despite her younger age.
“Adding this extra layer of epigenetic information really improves on linking the genotype and phenotype in female carriers,” Dr. Gouil concluded.
Complementary approaches
Together, these five technologies represent a formidable toolkit for tackling the heaps of remaining unsolved or misdiagnosed genetic eye disease cases. They address different challenges: from detecting elusive variants and interpreting their significance, to resolving complex structural rearrangements and explaining variable expressivity.
As these approaches mature and become more accessible, the field is inching closer to a highly sought-after comprehensive genetic diagnosis for all patients with inherited eye diseases—illuminating paths not just to diagnosis but potentially to life-changing treatments as well.
READ MORE: Check out our daily ARVO 2025 coverage here! We’ve covered all.
Editor’s Note: Reporting for this story took place during the annual meeting of The Association for Research in Vision and Ophthalmology (ARVO 2025) held from 4-8 May in Salt Lake City, Utah, United States.
