Diagnostic yield of long-read sequencing in short-read-negative patients: a systematic review and meta-analysis

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Babazade A., Mulayım M. F., Bahap Y., Ergün M. A., Yirmibeş Karaoğuz M.

HUMAN GENOMICS, cilt.0, sa.0, ss.1, 2026 (SCI-Expanded, Scopus)

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 0 Sayı: 0
  • Basım Tarihi: 2026
  • Doi Numarası: 10.1186/s40246-026-01039-1
  • Dergi Adı: HUMAN GENOMICS
  • Derginin Tarandığı İndeksler: Natural Science Collection (ProQuest), Biological Science Database (ProQuest), Health Research Premium Collection (ProQuest), Scopus, Pharma Collection (ProQuest), Science Citation Index Expanded (SCI-EXPANDED), BIOSIS, EMBASE, MEDLINE, Directory of Open Access Journals
  • Sayfa Sayıları: ss.1
  • Açık Arşiv Koleksiyonu: AVESİS Açık Erişim Koleksiyonu
  • Gazi Üniversitesi Adresli: Evet

Özet

Abstract

Background Long-read sequencing (LRS) is increasingly used for rare disease patients undiagnosed by short-read

sequencing (SRS), but its additional yield has not been synthesized at the individual-patient level or across both

targeted and genome-wide approaches, and the phenotypes and rescue mechanisms driving added diagnoses

remain mostly uncharacterized.

Methods We assessed the LRS contribution across rare diseases by performing a systematic literature search in

PubMed, Scopus, Web of Science, EMBASE and Google Scholar (to 31 October 2025), including studies that applied

LRS to patients with monogenic rare disease undiagnosed after SRS. Studies were categorized into genome-wide

cohort studies (Tier 1), targeted studies (Tier 2), and case reports/series (Tier 3), and random-effects meta-analysis

was performed for Tier 1 studies with prespecified subgroup analyses. Patient phenotypes were encoded as Human

Phenotype Ontology terms and hierarchically aggregated to test phenotype-specific associations with rescue.

Results Across 11 Tier 1 studies (538 patients), the pooled rescue rate combining definitive and possible diagnoses

was 16.4% (95% CI: 6.9–29.0%); restricting to definitive rescue only, the pooled yield was 12.0% (95% CI: 3.3–25.3%).

Across 15 Tier 2 targeted studies (165 SRS-negative patients), the rescue rate was 37.6%, reaching 100% in MUC1-

associated ADTKD (12/12) and Canavan disease (2/2 SRS-negative and 8/8 second-hit cases) but only 3.9% in NF1

(2/51). Across 119 second-hit cases (Tier 1 + Tier 2), 34.5% were rescued. Among SRS-negative patients in the primary

meta-analysis cohort, yield declined as prior testing deepened (ES-only 23.5% vs ES+GS 6.8%). Structural variants

accounted for ~49% of genome-wide rescues, though ~29% of rescues reflected reanalysis findings rather than LRSspecific

capability. In exploratory phenotype analysis, spasticity, microcephaly, and intellectual disability were among

the phenotypes most strongly associated with rescue, a signal that persisted within neurological cases.

Conclusion LRS provides a meaningful rescue for patients with rare diseases undiagnosed after SRS, primarily

through structural variant detection. Re-evaluation of existing SRS data and prioritization of patients directly after

negative ES may optimize diagnostic yield, and phenotype-informed prioritization is a promising direction that

warrants prospective evaluation.