Validation and Clinical Applications of a Comprehensive Next Generation Sequencing System for Molecular Characterization of Solid Cancer Tissues.

Identification of somatic molecular alterations in primary and metastatic solid tumor specimens can provide critical information regarding tumor biology and its heterogeneity, and enables the detection of molecular markers for clinical personalized treatment assignment. However, the optimal methods and target genes for clinical use are still being in development. Toward this end, we validated a targeted amplification-based NGS panel (Oncomine comprehensive assay v1) on a personal genome machine sequencer for molecular profiling of solid tumors. This panel covers 143 genes, and requires low amounts of DNA (20 ng) and RNA (10 ng). We used 27 FFPE tissue specimens, 10 cell lines, and 24 commercial reference materials to evaluate the performance characteristics of this assay. We also evaluated the performance of the assay on 26 OCT-embedded fresh frozen specimens (OEFF). The assay was found to be highly specific (>99%) and sensitive (>99%), with low false-positive and false-negative rates for single-nucleotide variants, indels, copy number alterations, and gene fusions. Our results indicate that this is a reliable method to determine molecular alterations in both fixed and fresh frozen solid tumor samples, including core needle biopsies.

Utility of array CGH in molecular diagnosis of mitochondrial disorders.

Array comparative genomic hybridization (aCGH) is a powerful clinical diagnostic tool that can be used to evaluate copy number changes in the genome. Targeted aCGH provides a much higher resolution in targeted gene regions to detect copy number changes within single gene or single exon. A custom-designed oligonucleotide aCGH platform (MitoMet(®)) has been developed to provide tiled coverage of the entire 16.6-kb mitochondrial genome and high-density coverage of a set of nuclear genes associated with metabolic and mitochondrial related disorders, for quick evaluation of copy number changes in both genomes (1). The high-density probes in mitochondrial genome on the MitoMet(®) array allow estimation of mtDNA deletion breakpoints and deletion heteroplasmy (2). This technology is particularly useful as a complementary diagnostic test to detect large deletions in genes related to mitochondrial disorders.