Exome sequencing covers >98% of mutations identified on targeted next generation sequencing panels.
BACKGROUND
With the expanded availability of next generation sequencing (NGS)-based clinical genetic tests, clinicians seeking to test patients with Mendelian diseases must weigh the superior coverage of targeted gene panels with the greater number of genes included in whole exome sequencing (WES) when considering their first-tier testing approach. Here, we use an in silico analysis to predict the analytic sensitivity of WES using pathogenic variants identified on targeted NGS panels as a reference.


METHODS
Corresponding nucleotide positions for 1533 different alterations classified as pathogenic or likely pathogenic identified on targeted NGS multi-gene panel tests in our laboratory were interrogated in data from 100 randomly-selected clinical WES samples to quantify the sequence coverage at each position. Pathogenic variants represented 91 genes implicated in hereditary cancer, X-linked intellectual disability, primary ciliary dyskinesia, Marfan syndrome/aortic aneurysms, cardiomyopathies and arrhythmias.


RESULTS
When assessing coverage among 100 individual WES samples for each pathogenic variant (153,300 individual assessments), 99.7% (n = 152,798) would likely have been detected on WES. All pathogenic variants had at least some coverage on exome sequencing, with a total of 97.3% (n = 1491) detectable across all 100 individuals. For the remaining 42 pathogenic variants, the number of WES samples with adequate coverage ranged from 35 to 99. Factors such as location in GC-rich, repetitive, or homologous regions likely explain why some of these alterations were not detected across all samples. To validate study findings, a similar analysis was performed against coverage data from 60,706 exomes available through the Exome Aggregation Consortium (ExAC). Results from this validation confirmed that 98.6% (91,743,296/93,062,298) of pathogenic variants demonstrated adequate depth for detection.


CONCLUSIONS
Results from this in silico analysis suggest that exome sequencing may achieve a diagnostic yield similar to panel-based testing for Mendelian diseases.
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Holly
H
LaDuca
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Kelly D
KD
Farwell
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Huy
H
Vuong
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Hsiao-Mei
HM
Lu
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Wenbo
W
Mu
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Layla
L
Shahmirzadi
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Sha
S
Tang
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Jefferey
J
Chen
Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, United States of America.
Shruti
S
Bhide
Department of Pediatrics, Division of Genetics and Genomic Medicine, University of California Irvine, Irvine, California, United States of America.
Elizabeth C
EC
Chao
D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods / Q000706:statistics & numerical data; D059472:Exome; D005260:Female; D030342:Genetic Diseases, Inborn / Q000175:diagnosis* / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods* / Q000706:statistics & numerical data; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000706:statistics & numerical data; D006801:Humans; D008297:Male; D009154:Mutation; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data