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2023 ACMG Annual Clinical Genetics Meeting Digital ...
Comparing the analytical performance of exome sequ ...
Comparing the analytical performance of exome sequencing and traditional panel testing in a cancer population
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The study assessed the analytical performance of exome sequencing (ES) compared to traditional panel testing in individuals with a history of cancer or polyposis. ES was performed on a research basis using the Agilent SureSelectXT Clinical Research Exome. The concordance rate (CR) for clinically relevant sequence variants was determined for all individuals who underwent both ES and panel testing.<br /><br />The results showed that ES had a high analytical performance compared to panel testing. The concordance rate for all variants, including pathogenic, likely pathogenic, and variants of uncertain significance, was 99.71%. For substitutions and small insertions/deletions, the concordance rates were also high at 99.71% and 100% respectively.<br /><br />In a subset of individuals with additional variant data, the sensitivity and specificity of ES and the panel in overlapping regions were evaluated. The preliminary analysis showed a sensitivity of 99.69% and specificity of 99.99% for all variants.<br /><br />Furthermore, all 110 sequence variants identified by the panel in the region of interest were also detected by ES, resulting in a concordance rate of 100%. There were a few variants that were identified by the panel but not called by the ES pipeline due to low coverage or allelic fraction.<br /><br />Overall, the study demonstrated that ES has a high analytical performance compared to traditional panel testing in a cancer population. These findings support the integration of ES as an analytically valid diagnostic tool in clinical care. The study also highlighted the potential of GS as a diagnostic tool that can be reanalyzed as new genes and evidence emerge.
Asset Subtitle
Co-Author - Emma Reble, MSc; Co-Author - Jordan Sam, MHSc; Co-Author - Rita Kodida, MSc, CCGC; Presenting Author - Marc Clausen, MA; Co-Author - Salma Shickh, MS, CGC; Co-Author - Chloe Mighton, MSc; Co-Author - Jose-Mario Capo-Chichi, PhD, FACMG; Co-Author - Elena Greenfeld, PhD, MD; Co-Author - Abdul Noor, PhD; Co-Author - Raymond H. Kim, MD/PhD; Co-Author - Yvonne Bombard, PhD; Co-Author - Jordan Lerner-Ellis, PhD;
Meta Tag
Genetic Testing
Methodology
NextGen Sequencing
Sequencing
Co-Author
Emma Reble, MSc
Co-Author
Jordan Sam, MHSc
Co-Author
Rita Kodida, MSc, CCGC
Co-Author
Salma Shickh, MS, CGC
Co-Author
Chloe Mighton, MSc
Co-Author
Jose-Mario Capo-Chichi, PhD, FACMG
Co-Author
Elena Greenfeld, PhD, MD
Co-Author
Abdul Noor, PhD
Co-Author
Raymond H. Kim, MD/PhD
Co-Author
Yvonne Bombard, PhD
Co-Author
Jordan Lerner-Ellis, PhD
Presenting Author
Marc Clausen, MA
Keywords
exome sequencing
panel testing
analytical performance
concordance rate
variants of uncertain significance
sensitivity
specificity
overlapping regions
cancer population
diagnostic tool
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