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. 2024 May;26(5):101076.
doi: 10.1016/j.gim.2024.101076. Epub 2024 Jan 19.

Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort

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Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort

Kerith-Rae Dias et al. Genet Med. 2024 May.

Abstract

Purpose: Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively.

Methods: ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID.

Results: The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis.

Conclusion: Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.

Keywords: Episignature; Exome negative; Genome sequencing; Health economics; Intellectual disability.

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Conflict of interest statement

Conflict of Interest The authors declare no conflicts of interest.

Figures

Figure 1.
Figure 1.. ID Flagship study.
74 trios with molecularly undiagnosed ID investigated using ES (74 trios), GS (32 trios), EpiSign (32 probands) and LRS (16 probands). The overall ES/GS diagnostic yield is 69% (51/74) with 31% (23/74) unresolved. ID, intellectual disability; ES, exome sequencing, GS, genome sequencing; LRS, long read sequencing.
Figure 2.
Figure 2.. Concordance between GS and episignature findings.
A. A Kleefstra syndrome episignature in proband 62 was concordant to the finding of a duplication in EHMT1 using GS. B. A Beckwith-Weidemann syndrome with IC2 episignature in proband 44 and detection of a de novo heterozygous partial out of frame tandem duplication (NM_015335.5, exons 5 – 16 of 31) of MED13L using GS might be related by a yet unknown mechanism.

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