HiFi sequencing accurately identifies clinically relevant variants in paralogous genes.

PacBio HiFi sequencing with Paraphase caller for segmental duplication gene-pseudogene regions

PacBio HiFi long-read sequencing is prospectively evaluated for identifying pathogenic variants in paralogous genes—regions with high homology to pseudogenes that remain inaccessible to standard short-read sequencing. 125 clinically confirmed variants in 86 individuals are tested across loci including SMN1, CYP2D6, HBA1/2, and PMS2. The integrated Paraphase caller detects SNVs, indels, CNVs, SVs, and gene conversions with superior accuracy compared to conventional approaches. The authors propose a workflow directly deployable in first-tier clinical diagnostics.

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This work confirms that long-read sequencing is now mature enough for paralogous regions—a persistent blind spot in short-read NGS diagnostics. The prospective validation on 86 individuals with known variants is methodologically sound, and integration into a first-tier diagnostic pipeline appears immediately feasible for PacBio-equipped laboratories.

Clinical impact: 3/3 · Evidence strength: 3/3 · Novelty: 1/2 · Sample size: 1/1 · Publication status: 1/1 → Total: 9/10