Yield of Long-Read Genome Sequencing for Rare Disease Diagnosis in Short-Read Genome Negative Cases

Background A 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. Methods We 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. Results We 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. Conclusions In 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.