Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort
- PMID: 38258669
- PMCID: PMC11786952
- DOI: 10.1016/j.gim.2024.101076
Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort
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.
Copyright © 2024 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.
Conflict of interest statement
Conflict of Interest The authors declare no conflicts of interest.
Figures


Similar articles
-
The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing.BMC Med Genomics. 2020 May 19;13(1):70. doi: 10.1186/s12920-020-0726-x. BMC Med Genomics. 2020. PMID: 32429945 Free PMC article.
-
Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: A prospective study.Hum Mutat. 2022 May;43(5):568-581. doi: 10.1002/humu.24347. Epub 2022 Mar 1. Hum Mutat. 2022. PMID: 35143101
-
Proband-Only Exome Sequencing for Intellectual Disability in Iran: Diagnostic Yield and Genetic Insights.Am J Med Genet A. 2025 Apr;197(4):e63915. doi: 10.1002/ajmg.a.63915. Epub 2024 Dec 10. Am J Med Genet A. 2025. PMID: 39655768
-
Systematic evidence-based review: outcomes from exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability.Genet Med. 2020 Jun;22(6):986-1004. doi: 10.1038/s41436-020-0771-z. Epub 2020 Mar 23. Genet Med. 2020. PMID: 32203227 Free PMC article.
-
Making headway with genetic diagnostics of intellectual disabilities.Clin Genet. 2014 Feb;85(2):101-10. doi: 10.1111/cge.12244. Epub 2013 Aug 26. Clin Genet. 2014. PMID: 23895455 Review.
Cited by
-
Phenotypic compatibility and specificity in genomic variant classification.Eur J Hum Genet. 2024 May;32(5):471-473. doi: 10.1038/s41431-024-01554-6. Epub 2024 Feb 13. Eur J Hum Genet. 2024. PMID: 38351291 Free PMC article. No abstract available.
-
Clinician-Driven Reanalysis of Exome Sequencing Data From Patients With Inherited Retinal Diseases.JAMA Netw Open. 2024 May 1;7(5):e2414198. doi: 10.1001/jamanetworkopen.2024.14198. JAMA Netw Open. 2024. PMID: 38819824 Free PMC article.
-
Considerations for reporting variants in novel candidate genes identified during clinical genomic testing.bioRxiv [Preprint]. 2024 Jun 21:2024.02.05.579012. doi: 10.1101/2024.02.05.579012. bioRxiv. 2024. Update in: Genet Med. 2024 Oct;26(10):101199. doi: 10.1016/j.gim.2024.101199. PMID: 38370830 Free PMC article. Updated. Preprint.
-
Considerations for reporting variants in novel candidate genes identified during clinical genomic testing.Genet Med. 2024 Oct;26(10):101199. doi: 10.1016/j.gim.2024.101199. Epub 2024 Jun 26. Genet Med. 2024. PMID: 38944749
-
GREGoR: Accelerating Genomics for Rare Diseases.ArXiv [Preprint]. 2024 Dec 18:arXiv:2412.14338v1. ArXiv. 2024. PMID: 39764392 Free PMC article. Preprint.
References
-
- Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L, et al. (2019). Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genetics in Medicine. 10.1038/s41436-019-0554-6. - DOI - PMC - PubMed
-
- Marshall CR, Chowdhury S, Taft RJ, Lebo MS, Buchan JG, Harrison SM, Rowsey R, Klee EW, Liu P, Worthey EA, et al. (2020). Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease. NPJ Genom Med 5. 10.1038/s41525-020-00154-9. - DOI - PMC - PubMed
-
- Ewans LJ, Schofield D, Shrestha R, Zhu Y, Gayevskiy V, Ying K, Walsh C, Lee E, Kirk EP, Colley A, et al. (2018). Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders. Genetics in Medicine 20, 1564–1574. 10.1038/gim.2018.39. - DOI - PubMed
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Miscellaneous