A Complementary Role for Immunohistochemistry and NGS for Detection of MTAP Loss in Patients with Non-Small Cell Lung Cancer.

Methylthioadenosine phosphorylase (MTAP) is an enzyme encoded by MTAP gene on chromosome 9p21. MTAP inactivation introduces a metabolic vulnerability with implications for targeted therapy. MTAP loss may be detected at the protein or DNA level, but characterization of clinical assays for detection of this event in non-small cell lung carcinoma (NSCLC) is limited. Clinicopathologic and genomic correlates of MTAP gene deletion were examined via retrospective review of an institutional cohort of 5,233 NSCLC cases with available next generation sequencing (NGS) data for 447 genes, including full coverage of the MTAP coding sequence. A subset of 105 cases were examined to assess the correlation between MTAP deletion by NGS and MTAP expression by immunohistochemistry (IHC). Homozygous deletion of MTAP was detected in 5.6% of NSCLC by NGS and was significantly more common in lung adenocarcinomas from patients with never/light smoking history (34.8%), and concurrent ALK fusions (8.2%) or EGFR mutations (45.9%). Approximately 13% of MTAP "loss" cases showed a heterogenous staining pattern by IHC. Concordance of NGS and IHC for detection of MTAP deficiency in NSCLC was 97.3%, following careful quality control (including recognition of a single case with partial deletion of 3' MTAP) and exclusion of NGS results from tumors with ≤30% tumor content. The remaining two discordant cases included one case with non-diploid genome and multiple copy states resulting in an incorrect NGS interpretation and one case with copy neutral NGS result and complete loss of protein expression by IHC. MTAP protein loss was therefore observed in the absence of a sequencing alteration in <1% of cases. MTAP gene deletion appears enriched in NSCLC with certain molecular drivers. NGS and IHC can show excellent concordance for detection of MTAP loss in NSCLC, with IHC showing superior sensitivity in the context of low tumor content or subclonal events.