Journal article
Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays
The Journal of molecular diagnostics : JMD, Vol.19(1), pp.43-56
01/2017
DOI: 10.1016/j.jmoldx.2016.07.012
PMID: 27836695
Abstract
Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations. Using a sample set of 104 normal, solid tumor, and hematopoietic malignancy specimens, head-to-head NGS data analyses allowed for 6.8 million individual clinical base call comparisons, including 2729 previously confirmed variants, with 100% sensitivity and specificity. University of Chicago Medicine OncoPlus showed excellent performance for detection of single-nucleotide variants, insertions/deletions up to 52 bp, and FLT3 internal tandem duplications of up to 102 bp or larger. Highly concordant copy number variant and ALK/RET/ROS1 gene fusion detection were also observed. In addition to underlining the efficiency of NGS validation via full-data benchmarking against existing clinical NGS assays, this study also highlights the degree of performance similarity between hybrid capture and amplicon assays that is attainable with the application of strict quality control parameters and optimized computational analytics.
Details
- Title: Subtitle
- Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays
- Creators
- Sabah Kadri - University of ChicagoBradley C Long - University of ChicagoIbro Mujacic - University of ChicagoChao J Zhen - University of ChicagoMichelle N Wurst - University of ChicagoShruti Sharma - University of ChicagoNadia McDonald - University of ChicagoNifang Niu - University of ChicagoSonia Benhamed - University of ChicagoJigyasa H Tuteja - University of ChicagoTanguy Y Seiwert - University of ChicagoKevin P White - University of ChicagoMegan E McNerney - University of ChicagoCarrie Fitzpatrick - University of ChicagoY Lynn Wang - University of ChicagoLarissa V Furtado - University of ChicagoJeremy P Segal - University of Chicago
- Resource Type
- Journal article
- Publication Details
- The Journal of molecular diagnostics : JMD, Vol.19(1), pp.43-56
- DOI
- 10.1016/j.jmoldx.2016.07.012
- PMID
- 27836695
- ISSN
- 1525-1578
- eISSN
- 1943-7811
- Language
- English
- Date published
- 01/2017
- Academic Unit
- Stead Family Department of Pediatrics; Medical Genetics and Genomics
- Record Identifier
- 9984701547702771
Metrics
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