Clinical Impact and Cost-Effectiveness of Whole Exome Sequencing as a Diagnostic Tool: A Pediatric Center's Experience.
BACKGROUND
There are limited reports of the use of whole exome sequencing (WES) as a clinical diagnostic tool. Moreover, there are no reports addressing the cost burden associated with genetic tests performed prior to WES.


OBJECTIVE
We demonstrate the performance characteristics of WES in a pediatric setting by describing our patient cohort, calculating the diagnostic yield, and detailing the patients for whom clinical management was altered. Moreover, we examined the potential cost-effectiveness of WES by examining the cost burden of diagnostic workups.


METHODS
To determine the clinical utility of our hospital's clinical WES, we performed a retrospective review of the first 40 cases. We utilized dual bioinformatics analyses pipelines based on commercially available software and in-house tools.


RESULTS
Of the first 40 clinical cases, we identified genetic defects in 12 (30%) patients, of which 47% of the mutations were previously unreported in the literature. Among the 12 patients with positive findings, seven have autosomal dominant disease and five have autosomal recessive disease. Ninety percent of the cohort opted to receive secondary findings and of those, secondary medical actionable results were returned in three cases. Among these positive cases, there are a number of novel mutations that are being reported here. The diagnostic workup included a significant number of genetic tests with microarray and single-gene sequencing being the most popular tests. Significantly, genetic diagnosis from WES led to altered patient medical management in positive cases.


CONCLUSIONS
We demonstrate the clinical utility of WES by establishing the clinical diagnostic rate and its impact on medical management in a large pediatric center. The cost-effectiveness of WES was demonstrated by ending the diagnostic odyssey in positive cases. Also, in some cases it may be most cost-effective to directly perform WES. WES provides a unique glimpse into the complexity of genetic disorders.
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
C Alexander
CA
Valencia
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Ammar
A
Husami
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Jennifer
J
Holle
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Judith A
JA
Johnson
Myriad Genetics Laboratories, Inc. , Salt Lake City, UT , USA.
Yaping
Y
Qian
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Abhinav
A
Mathur
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Chao
C
Wei
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Subba Rao
SR
Indugula
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Fanggeng
F
Zou
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Haiying
H
Meng
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Lijun
L
Wang
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Xia
X
Li
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Rachel
R
Fisher
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Tony
T
Tan
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Amber
A
Hogart Begtrup
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Kathleen
K
Collins
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Katie A
KA
Wusik
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Derek
D
Neilson
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Thomas
T
Burrow
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Elizabeth
E
Schorry
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Robert
R
Hopkin
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Mehdi
M
Keddache
Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA ; US Department of Veterans Affairs Medical Center , Cincinnati, OH , USA.
John Barker
JB
Harley
Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA ; US Department of Veterans Affairs Medical Center , Cincinnati, OH , USA.
Kenneth M
KM
Kaufman
Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH , USA.
Kejian
K
Zhang
children; clinical utility; diagnosis; next generation sequencing; pediatrics; whole exome sequencing