Yield of Long-Read Genome Sequencing for Rare Disease Diagnosis in Short-Read Genome Negative Cases
- 1Institute for Clinical and Translational Science, University of California Irvine, Ambry Genetics, Aliso Viejo, CA, USA
Abstract
BackgroundA growing body of work has highlighted advantages of long-read genome sequencing (LR-GS) over short-read genome sequencing (SR-GS) with regards to the detection and interpretation of pathogenic variants. However, the incremental diagnostic yield of LR-GS over SR-GS for patients with suspected Mendelian conditions has not been systematically characterized.
MethodsWe performed LR-GS on 144 cases that previously had undergone SR-GS through the Pediatric Mendelian Genomics Research Center at the University of California, Irvine (PMGRC-UCI, a founding center of the GREGoR Consortium), of which 107 remained undiagnosed after SR-GS.
ResultsWe identified new molecular diagnoses in 13 cases, five of which could not have been detected with SR-GS, corresponding to an incremental diagnostic yield of 4.7%. These five diagnoses leveraged distinct capabilities of LR-GS: the detection of variants in short-read "dark" regions, the detection of structural variants and tandem repeat expansions, and the identification of de novo variants using only one biological parent. In two of these five cases, confirmation of the diagnosis also relied critically on identifying aberrant transcript production via RNA-seq, while in one other case LR-GS-based CpG methylation profiling further supported the diagnosis through detection of abnormal methylation at episignature-associated CpGs.
ConclusionsIn this paired comparison of LR-GS and SR-GS, LR-GS provided an incremental diagnostic yield of 4.7% among cases that remained undiagnosed after SR-GS. Together, our findings demonstrate that LR-GS can resolve a meaningful subset of cases beyond the reach of SR-GS while simultaneously expanding the range of genomic and epigenomic mechanisms accessible to a single sequencing assay.
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BibTeX
@misc{pitsava2026yield,
title = {{Yield of Long-Read Genome Sequencing for Rare Disease Diagnosis in Short-Read Genome Negative Cases}},
author = {G. Pitsava and K. Bluske and R. Barrick and I. De Dios and C. Duong and K. Blanco and S. Belhadj and N. Karra and S. L. Stenton and A. Garcia and E. Smith and M. Almalvez and A. Ko and J. Harting and S. Joshi and K. Chen and C. H. King and J. E. LoTempio and J. Albert and K. M. Bujakowska and L. Boukas and UCI-GREGoR Consortium and R. Karam and S. I. Berger and E. C. Delot and C. Xiao and E. Vilain},
howpublished = {medRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.09.26362331},
url = {https://www.medrxiv.org/content/10.64898/2026.09.09.26362331v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Yield of Long-Read Genome Sequencing for Rare Disease Diagnosis in Short-Read Genome Negative Cases
AU - G. Pitsava
AU - K. Bluske
AU - R. Barrick
AU - I. De Dios
AU - C. Duong
AU - K. Blanco
AU - S. Belhadj
AU - N. Karra
AU - S. L. Stenton
AU - A. Garcia
AU - E. Smith
AU - M. Almalvez
AU - A. Ko
AU - J. Harting
AU - S. Joshi
AU - K. Chen
AU - C. H. King
AU - J. E. LoTempio
AU - J. Albert
AU - K. M. Bujakowska
AU - L. Boukas
AU - UCI-GREGoR Consortium
AU - R. Karam
AU - S. I. Berger
AU - E. C. Delot
AU - C. Xiao
AU - E. Vilain
PY - 2026
DA - 2026/09/09
PB - medRxiv
DO - 10.64898/2026.09.09.26362331
UR - https://www.medrxiv.org/content/10.64898/2026.09.09.26362331v1
AB - BackgroundA growing body of work has highlighted advantages of long-read genome sequencing (LR-GS) over short-read genome sequencing (SR-GS) with regards to the detection and interpretation of pathogenic variants. However, the incremental diagnostic yield of LR-GS over SR-GS for patients with suspected Mendelian conditions has not been systematically characterized. MethodsWe performed LR-GS on 144 cases that previously had undergone SR-GS through the Pediatric Mendelian Genomics Research Center at the University of California, Irvine (PMGRC-UCI, a founding center of the GREGoR Consortium), of which 107 remained undiagnosed after SR-GS. ResultsWe identified new molecular diagnoses in 13 cases, five of which could not have been detected with SR-GS, corresponding to an incremental diagnostic yield of 4.7%. These five diagnoses leveraged distinct capabilities of LR-GS: the detection of variants in short-read "dark" regions, the detection of structural variants and tandem repeat expansions, and the identification of de novo variants using only one biological parent. In two of these five cases, confirmation of the diagnosis also relied critically on identifying aberrant transcript production via RNA-seq, while in one other case LR-GS-based CpG methylation profiling further supported the diagnosis through detection of abnormal methylation at episignature-associated CpGs. ConclusionsIn this paired comparison of LR-GS and SR-GS, LR-GS provided an incremental diagnostic yield of 4.7% among cases that remained undiagnosed after SR-GS. Together, our findings demonstrate that LR-GS can resolve a meaningful subset of cases beyond the reach of SR-GS while simultaneously expanding the range of genomic and epigenomic mechanisms accessible to a single sequencing assay.
ER -