Genotyping Colorectal Tumors for EGFR Pathway

Patients with CRC have their tumor tested for downstream activators of the EGFR signaling pathway at our institution as part of standard of care. Tumor specimens were obtained via primary site specimen (17/40), liver biopsy (20/40), lymph node biopsy (2/40), or lung metastasis biopsy (1/40). After microscopic examination confirmed the diagnosis of adenocarcinoma, tissue was sent to a molecular diagnostic laboratory in the Department of Pathology for extraction of genomic DNA. All samples were determined to have adequate DNA quality prior to testing. Tumors were genotyped using (a) the Sequenom Mass Array system (Sequenom, Inc.), where samples are tested in duplicate using multiplexed assays to interrogate mutations in hotspots of KRAS, BRAF, NRAS, MEK1, PIK3CA, and AKT1[36 (link)] or (b) a previously reported hybridization capture-based next generation sequencing assay for targeted deep sequencing of all exons and selected introns of key cancer genes [37 (link)]. For the next generation sequencing assay that includes 8/40 (20%) of samples, we only include data related to the hotspot mutations tested in the Sequenom assay.

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Ziv E., Bergen M., Yarmohammadi H., Boas F.E., Petre E.N., Sofocleous C.T., Yaeger R., Solit D.B., Solomon S.B, & Erinjeri J.P. (2017). PI3K pathway mutations are associated with longer time to local progression after radioembolization of colorectal liver metastases. Oncotarget, 8(14), 23529-23538.

Publication 2017

Sequenom Mass Array system

Adenocarcinoma Akt1 Assay Biopsy Braf Cancer genes Diagnosis Egfr Exons Genomic Hybridization Introns Kras Liver Lung Lymph node Mek1 Metastasis Microscopic examination Molecular diagnostic Mutations Nras Patients Pik3ca Signaling pathway Tissue Tumors

Corresponding Organization : Memorial Sloan Kettering Cancer Center

Other organizations : Mount Sinai Hospital

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Variable analysis

independent variables

Tumor specimen source (primary site, liver biopsy, lymph node biopsy, or lung metastasis biopsy)

dependent variables

Presence of mutations in KRAS, BRAF, NRAS, MEK1, PIK3CA, and AKT1 genes

control variables

Adequate DNA quality of tumor samples prior to testing

controls

Samples were tested in duplicate using multiplexed assays to interrogate mutations in hotspots of the target genes

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