Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors.

DNA methylation is an essential molecular assay for central nervous system (CNS) tumor diagnostics. While some fusions define specific brain tumors, others occur across many different diagnoses. We performed a retrospective analysis of 219 primary CNS tumors with whole genome DNA methylation and RNA next-generation sequencing. DNA methylation profiling results were compared with RNAseq detected gene fusions. We detected 105 rare fusions involving 31 driver genes, including 23 fusions previously not implicated in brain tumors. In addition, we identified 6 multi-fusion tumors. Rare fusions and multi-fusion events can impact the diagnostic accuracy of DNA methylation by decreasing confidence in the result, such as BRAF, RAF, or FGFR1 fusions, or result in a complete mismatch, such as NTRK, EWSR1, FGFR, and ALK fusions. IMPLICATIONS: DNA methylation signatures need to be interpreted in the context of pathology and discordant results warrant testing for novel and rare gene fusions.

Prevalence, clinicopathologic associations, and molecular spectrum of ERBB2 (HER2) tyrosine kinase mutations in lung adenocarcinomas.

PURPOSE: Activating mutations in the tyrosine kinase domain of HER2 (ERBB2) have been described in a subset of lung adenocarcinomas (ADCs) and are mutually exclusive with EGFR and KRAS mutations. The prevalence, clinicopathologic characteristics, prognostic implications, and molecular heterogeneity of HER2-mutated lung ADCs are not well established in U.S. patients. EXPERIMENTAL DESIGN: Lung ADC samples (N = 1,478) were first screened for mutations in EGFR (exons 19 and 21) and KRAS (exon 2), and negative cases were then assessed for HER2 mutations (exons 19-20) using a sizing assay and mass spectrometry. Testing for additional recurrent point mutations in EGFR, KRAS, BRAF, NRAS, PIK3CA, MEK1, and AKT was conducted by mass spectrometry. ALK rearrangements and HER2 amplification were assessed by FISH. RESULTS: We identified 25 cases with HER2 mutations, representing 6% of EGFR/KRAS/ALK-negative specimens. Small insertions in exon 20 accounted for 96% (24/25) of the cases. Compared with insertions in EGFR exon 20, there was less variability, with 83% (20/24) being a 12 bp insertion causing duplication of amino acids YVMA at codon 775. Morphologically, 92% (23/25) were moderately or poorly differentiated ADC. HER2 mutation was not associated with concurrent HER2 amplification in 11 cases tested for both. HER2 mutations were more frequent among never-smokers (P < 0.0001) but there were no associations with sex, race, or stage. CONCLUSIONS: HER2 mutations identify a distinct subset of lung ADCs. Given the high prevalence of lung cancer worldwide and the availability of standard and investigational therapies targeting HER2, routine clinical genotyping of lung ADC should include HER2.

Human epidermal growth factor receptor 2 testing in gastroesophageal cancer: correlation between immunohistochemistry and fluorescence in situ hybridization.

CONTEXT: Patients with advanced gastroesophageal cancer have poor survival with current therapy. Human epidermal growth factor receptor 2 (HER2) represents a promising therapeutic target, but the optimal HER2 testing strategy is not yet defined. OBJECTIVES: To evaluate the concordance between immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) and to determine if the American Society of Clinical Oncology/College of American Pathologists HER2 scoring system is applicable to gastroesophageal carcinomas. DESIGN: Formalin-fixed paraffin-embedded tumor samples from patients with advanced stage gastroesophageal cancer were tested by IHC and FISH and scored according to the American Society of Clinical Oncology/College of American Pathologists criteria for breast cancer. Concordance between IHC and FISH was evaluated. A subset of cases was subjected to array comparative genomic hybridization to verify the positive and negative HER2 results. RESULTS: A total of 135 cases with paired IHC and FISH results were evaluated. The majority of samples (84%) were biopsies. HER2 amplification was detected in 20 tumors (15%). Using the American Society of Clinical Oncology/College of American Pathologists scoring system, IHC-FISH concordance was 97% for IHC 0, 93% for IHC 1+, and 100% for IHC 3+. Human epidermal growth factor receptor 2 positivity was strongly associated with tumor grade (moderately differentiated > poorly differentiated, P < .001) and histologic subtype (intestinal > diffuse, P  =  .007). Array comparative genomic hybridization analysis was successful in 31 tumors (14 FISH+ and 17 FISH-). Fluorescence in situ hybridization and array comparative genomic hybridization results were highly concordant in both HER2-positive and HER2-negative groups (93% and 100% concordance, respectively). CONCLUSIONS: Human epidermal growth factor receptor 2 testing in gastroesophageal cancer can be performed using standard breast cancer procedures and the American Society of Clinical Oncology/College of American Pathologists scoring criteria. Although IHC 0 and IHC 3+ provide clear stratification, reliable separation of IHC 1+ and IHC 2+ may be difficult, especially in biopsy samples. The latter 2 groups are best referred to FISH for definitive classification.