Clinical exome sequencing for genetic identification of rare Mendelian disorders
- PMID: 25326637
- PMCID: PMC4278636
- DOI: 10.1001/jama.2014.14604
Clinical exome sequencing for genetic identification of rare Mendelian disorders
Abstract
Importance: Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders.
Objective: To report on initial clinical indications for CES referrals and molecular diagnostic rates for different indications and for different test types.
Design, setting, and participants: Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available.
Main outcomes and measures: Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES.
Results: Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 [95% CI, 1.6-33.1]) of trio-CES was due to the identification of de novo and compound heterozygous variants.
Conclusions and relevance: In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
Conflict of interest statement
Comment in
-
Genome-scale sequencing in clinical care: establishing molecular diagnoses and measuring value.JAMA. 2014 Nov 12;312(18):1865-7. doi: 10.1001/jama.2014.14665. JAMA. 2014. PMID: 25326641 No abstract available.
Similar articles
-
Molecular findings among patients referred for clinical whole-exome sequencing.JAMA. 2014 Nov 12;312(18):1870-9. doi: 10.1001/jama.2014.14601. JAMA. 2014. PMID: 25326635 Free PMC article.
-
Clinical exome sequencing in 509 Middle Eastern families with suspected Mendelian diseases: The Qatari experience.Am J Med Genet A. 2019 Jun;179(6):927-935. doi: 10.1002/ajmg.a.61126. Epub 2019 Mar 27. Am J Med Genet A. 2019. PMID: 30919572 Free PMC article.
-
Diagnostic utility of transcriptome sequencing for rare Mendelian diseases.Genet Med. 2020 Mar;22(3):490-499. doi: 10.1038/s41436-019-0672-1. Epub 2019 Oct 14. Genet Med. 2020. PMID: 31607746 Free PMC article.
-
Proband only exome sequencing in 403 Indian children with neurodevelopmental disorders: Diagnostic yield, utility and challenges in a resource-limited setting.Eur J Med Genet. 2023 May;66(5):104730. doi: 10.1016/j.ejmg.2023.104730. Epub 2023 Feb 15. Eur J Med Genet. 2023. PMID: 36801247 Review.
-
Case for genome sequencing in infants and children with rare, undiagnosed or genetic diseases.J Med Genet. 2019 Dec;56(12):783-791. doi: 10.1136/jmedgenet-2019-106111. Epub 2019 Apr 25. J Med Genet. 2019. PMID: 31023718 Free PMC article. Review.
Cited by
-
CRPD frontiers in movement disorders Therapeutics: From evidence to treatment and applications: Addressing Patients' Needs in the Management of the Ataxias.Clin Park Relat Disord. 2024 May 10;10:100255. doi: 10.1016/j.prdoa.2024.100255. eCollection 2024. Clin Park Relat Disord. 2024. PMID: 38798918 Free PMC article.
-
The Approach to a Child with Dysmorphic Features: What the Pediatrician Should Know.Children (Basel). 2024 May 10;11(5):578. doi: 10.3390/children11050578. Children (Basel). 2024. PMID: 38790573 Free PMC article. Review.
-
Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN.Mol Genet Genomics. 2024 May 21;299(1):55. doi: 10.1007/s00438-024-02149-y. Mol Genet Genomics. 2024. PMID: 38771357
-
Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci.Genome Biol. 2024 May 17;25(1):123. doi: 10.1186/s13059-024-03250-6. Genome Biol. 2024. PMID: 38760655 Free PMC article.
-
Evaluating the utility of multi-gene, multi-disease population-based panel testing accounting for uncertainty in penetrance estimates.NPJ Genom Med. 2024 May 17;9(1):30. doi: 10.1038/s41525-024-00414-y. NPJ Genom Med. 2024. PMID: 38760335 Free PMC article.
References
-
- Rehder CW, David KL, Hirsch B, Toriello HV, Wilson CM, Kearney HM. American College of Medical Genetics and Genomics: standards and guidelines for documenting suspected consanguinity as an incidental finding of genomic testing. Genet Med. 2013;15(2):150–152. - PubMed
-
- Papenhausen P, Schwartz S, Risheg H, et al. UPD detection using homozygosity profiling with a SNP genotyping microarray. Am J Med Genet A. 2011;155A(4):757–768. - PubMed
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical