Patients with metastatic esophageal, gastric, and gastroesophageal junction adenocarcinoma receiving therapy at Memorial Sloan Kettering Cancer Center (MSK) were consented to an institutional review board approved protocol for prospective tumor genomic profiling between February 2014 and February 2017. The studies were conducted in accordance with the Declaration of Helsinki, International Ethical Guidelines for Biomedical Research Involving Human Subjects (CIOMS), Belmont Report, or U.S. Common Rule.
All tumors were prospectively reviewed to confirm histologic subtype, Lauren classification, and to estimate tumor content. Of 376 tumors submitted for sequencing, 318 samples were included in the final analysis (see CONSORT diagram in
Supplementary Figure 4). We integrated genomic data with clinical characteristics, treatment history, response, and survival data (as of September 2017). Overall survival (OS) time was measured from the date of diagnosis of Stage IV disease until the date of death or last follow-up. Progression-free survival (PFS) and OS on first-line platinum therapy and first-line chemotherapy with trastuzumab and immune checkpoint inhibitors in chemotherapy-refractory patients was calculated from the date of start of treatment to the date of radiographic disease progression, death or last evaluation. Clinical HER2 status was based on HER2 protein expression by immunohistochemistry (IHC, positive defined as 3+) or
ERBB2 gene amplification by FISH using College of American Pathologists (CAP)/American Society of Clinical Oncology (ASCO) criteria. IHC analysis of mismatch repair (MMR) proteins, and beta 2 microglobulin (B2M), and Epstein-Barr encoding region (EBER)
in situ hybridization analysis was performed on a subset of tumors from patients treated with checkpoint inhibitors.
The MSK-IMPACT assay was performed in a CLIA-certified laboratory, initially using a 341 and more recently 410 and 468 gene panels (
Supplementary Table 5), as previously described, with results reported in the electronic medical record (12 (
link),31 (
link)). The assay is capable of detecting mutations, small insertions and deletions, copy number alterations and select structural rearrangements. In a previously published validation set,
ERBB2 amplification calls on this NGS assay had an overall concordance of 98.4% with the combined IHC/FISH results (20 (
link)). The PPV and NPV of our NGS assay with respect to HER2 IHC/FISH was calculated in this cohort.
Tumors were assigned to consensus TCGA molecular subtypes: CIN, GS, EBV, MSI-H (3 (
link)). We assessed tumors for microsatellite instability (MSI) using the MSI-sensor method, and samples with a score >=10 were classified as MSI-high (MSI-H). Tumors were characterized as genomically stable (GS) if the fraction of the autosomal genome affected by DNA copy number alterations of any kind (FGA) was less than 5%. We classified tumors that were neither EBV-positive, MSI, or GS as CIN (chromosomal instability). The OncoKB Precision Oncology Knowledge Base was used (data from May 2017) (14 ) to infer the oncogenic effect and clinical actionability of individual somatic mutations. Recurrent mutational hotspots were annotated using
cancerhotspots.org (32 (
link)). We inferred allele-specific DNA copy number using FACETS (33 (
link)) to determine the zygosity of key mutant tumor suppressors as well as to generate estimates of tumor purity. We also inferred large-scale state transition (LST) scores (34 (
link)), based on the copy number data, from tumors with an analytically estimated tumor purity greater than 20%. Samples with <20% tumor content were excluded from the analysis.
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