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Testing Indications and Diagnostic Yield of Clinical Exome Sequencing in a US Midwestern Patient Cohort

Laboratory Genetics and Genomics
  • Primary Categories:
    • Clinical- Pediatric
  • Secondary Categories:
    • Clinical- Pediatric
Introduction:
Exome sequencing (ES) is widely used as a first-tier test for various disorders, including developmental delay, intellectual disability, and multiple congenital anomalies. Since September 2022, the Clinical Genomics Laboratory at Washington University in St. Louis, Missouri, has been offering clinical ES primarily to serve internal outpatients from the Department of Pediatrics. In this study, we evaluated the clinical indications and diagnostic yield of ES in a Midwestern cohort of 600 consecutive patients. We also describe our experience with reporting secondary findings and variation in genes with emerging evidence of disease association.

Methods:
Single nucleotide variants (SNVs) and indels were annotated, filtered, and prioritized using a commercial software platform (Franklin by Genoox) for 600 affected individuals (1399 considering comparator samples) to detect disease-causal variants as part of the standard of care evaluation and testing. Variants were classified according to the ACMG/AMP 2015 guidelines. Primary findings, ACMG secondary findings (ACMG SFv3.1 and 3.2) and variants in candidate genes (or genes of unknown significance) were returned.

 

Results:
Clinical ES was performed on 349 (58%) traditional trios (patient and both biological parents), 142 duos (24%) and 109 singletons (18%). The mean age of probands was 10.3 years (range of 0-76 years). Most probands were male (56%) and self-reported European ancestry (81%). Prior to ES, 75% of probands had received at least one clinical genetic test, such as chromosomal microarray analysis (CMA; 21%) or targeted gene panel testing (17%). Notably, 50 patients had undergone three or more genetic tests before ES. Many patients referred for ES (54%) exhibited complex phenotypes involving multiple affected systems, while 32% presented solely with neurological phenotypes. Other less common indications included ophthamology and immunology.



The overall diagnostic yield was 20% (n = 120). Inconclusive results, including variants of uncertain significance in known disease genes or candidate genes, were returned in 47% of cases (n = 283). Diagnostic rates were highest among patients with suspected inborn errors of metabolism (60%, 3/5 patients) and cardiovascular issues (37.5%, 3/8 patients). Of the patients with complex phenotypes, 20.4% (66/323) received a genetic diagnosis. Diagnostic yield did not significantly vary by family structure, sex, ancestry, or prior genetic testing.



Eighty-nine percent of patients and 91% of parents opted to receive secondary findings. Overall, SFs were identified in 7.4% of cases: 4.5% in probands and 2.9% in comparators. Seven (1.3%) patients received both a positive primary and secondary finding, while nine (1.7%) received only a secondary finding. Most SFs were associated with genes linked to breast and/or ovarian cancer and tachycardia phenotypes.



The high rate of inconclusive results (47%) in our clinical ES cohort is partially due to the reporting of candidate gene findings. A candidate gene result alone was provided for 8% of probands. Manhy of these inconclusive findings hold potential for future reclassification to diagnostic status as additional evidence for pathogenicity emerges, including data from segregation analyses, case reports, and functional studies. This potential change in classification may be facilitated through active collaboration between the laboratory and ordering providers or via submission to GeneMatcher to identify phenotypically similar patients who harbor variation within the same gene.

Conclusion:
Our data further supports the utility of comprehensive genetic testing (exome sequencing) as part of the standard of care to reduce diagnostic delays and end the diagnostic odyssey for patients with rare diseases. Furthermore, we present ES findings from a large cohort of patients from the Midwestern US.

 

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