Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

By Hane Lee, Joshua L. Deignan, N. Dorrani, Samuel P. Strom, S. Kantarci, F. Quintero-Rivera, Kingshuk Das, Traci Toy, B. Harry, Michael Yourshaw and 11 more. Journal of the American Medical Association (JAMA), 2014

985 citations recorded by the source corpus.

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% (2of 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.

Subfields: Cellular and Molecular Neuroscience, Genetics

View Paper: https://www.semanticscholar.org/paper/2a0689437fccc420ae5b9bb5dca2806edbcb516e

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Citations in the corpus

Predicting Splicing from Primary Sequence with Deep Learning. (2019, background): “However, the diagnostic yield of exome sequencing is 25%–30% in rare genetic disease cohorts, leaving the majority of patients without a diagnosis even after combined exome and microarray testing (Lee et al., 2014; Yang et al., 2014).”
EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay (2017, methodology): “For P3, WES was performed at the University of California, Los Angeles Clinical Genomics Center, as described previously (Lee et al., 2014).”
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity (2016, positive): “Whole-exome sequencing for the diagnosis of Mendelian diseases is now a routine part of medical genetics clinical practice 1–3 , but variant interpretation remains a serious challenge 4,5 .”