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Variant call concordance between two laboratory-developed, solid tumor targeted genomic profiling assays using
Ken J Hampel1, Francine B de Abreu2, Nikoletta Sidiropoulos1
1Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, 111 Colchester Avenue, Burlington, VT 05401, United States.
Experimental and Molecular Pathology
|February 14, 2017
Summary
Targeted genomic profiling (TGP) for solid tumors shows high reliability between different labs and sequencing platforms. This consistency in detecting somatic variants is crucial for clinical applications.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Targeted genomic profiling (TGP) is essential for detecting somatic variants in solid tumors.
- Variability in laboratory-developed tests (LDTs) poses challenges for inter-laboratory reliability.
- Standardization is needed for consistent clinical TGP results.
Purpose of the Study:
- To validate a TGP assay for solid tumors at the University of Vermont Medical Center (UVMMC).
- To assess the inter-laboratory reliability of TGP using different sequencing methods and platforms.
- To compare the sensitivity and specificity of TGP assays between two institutions.
Main Methods:
- UVMMC validated a TGP assay using DNA hybridization capture and sequencing of 29 genes on the Illumina MiSeq platform.
- Validation involved testing samples with known genomic variants from CLIA-approved, CAP-accredited laboratories.
- Dartmouth Hitchcock Medical Center (DHMC) provided FFPE specimens analyzed using AmpliSeq Cancer Hotspot Panel v2 on an Ion Torrent PGM.
Main Results:
- High concordance was observed in sensitivity and specificity between the two laboratories.
- All clinically actionable single nucleotide variants (SNVs) and insertions/deletions (InDels) in 17 shared genes were identified by both labs.
- The study demonstrated consistent variant calling across different TGP methodologies and sequencing platforms.
Conclusions:
- Distinct gene panel designs and sequencing workflows can achieve consistent variant calls in solid tumor FFPE samples.
- The findings support the reliability of TGP for clinical use in solid tumor diagnostics.
- Inter-laboratory concordance validates TGP as a robust method for somatic variant detection.
