Variant call concordance between two laboratory-developed, solid tumor targeted genomic profiling assays using distinct workflows and sequencing instruments

Exp Mol Pathol. 2017 Apr;102(2):215-218. doi: 10.1016/j.yexmp.2017.02.002. Epub 2017 Feb 10.


Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes. The validation samples were run on the Illumina MiSeq platform. Clinical specificity and sensitivity were evaluated by testing samples harboring genomic variants previously identified in CLIA-approved, CAP accredited laboratories with clinically validated molecular assays. The Molecular Laboratory at Dartmouth Hitchcock Medical Center (DHMC) provided 11 FFPE specimens that had been analyzed on AmpliSeq Cancer Hotspot Panel version 2 (CHPv2) and run on the Ion Torrent PGM. A Venn diagram of the gene lists from the two institutions is shown. This provided an excellent opportunity to compare the inter-laboratory reliability using two different target sequencing methods and sequencing platforms. Our data demonstrated an exceptionally high level of concordance with respect to the sensitivity and specificity of the analyses. All clinically-actionable SNV and InDel variant calls in genes covered by both panels (n=17) were identified by both laboratories. This data supports the proposal that distinct gene panel designs and sequencing workflows are capable of making consistent variant calls in solid tumor FFPE-derived samples.

Keywords: Amplicon sequencing; Hybrid-capture sequencing; Laboratory developed tests; Massively-parallel DNA sequencing; Solid tumor genomic profiling.

Publication types

  • Validation Study

MeSH terms

  • Alleles
  • DNA, Neoplasm / genetics
  • DNA, Neoplasm / isolation & purification*
  • Exons
  • Gene Expression Profiling
  • Genomics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Introns
  • Neoplasms / diagnosis
  • Neoplasms / genetics*
  • Nucleic Acid Hybridization
  • Polymorphism, Single Nucleotide
  • Sensitivity and Specificity
  • Sequence Analysis, DNA*


  • DNA, Neoplasm