title: Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues.
abstract: The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.
authors.affiliation: Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, United States of America.|Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America.
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America.|Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, United States of America.
authors.forename: Natasha G
authors.initials: NG
authors.lastname: Deane
authors.affiliation: Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America.
authors.forename: Keeli B
authors.initials: KB
authors.lastname: Lewis
authors.affiliation: Affymetrix Inc., Santa Clara, California, United States of America.
authors.forename: Jiang
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Department of Pathology, Vanderbilt University, Nashville, Tennessee, United States of America.|Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, United States of America.
authors.forename: M Kay
authors.initials: MK
authors.lastname: Washington
authors.affiliation: Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America.|Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America.|Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, United States of America.|Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, United States of America.
authors.forename: R Daniel
authors.initials: RD
authors.lastname: Beauchamp
mesh_terms: D003110:Colonic Neoplasms / Q000235:genetics*; D005557:Formaldehyde; D005629:Frozen Sections; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016612:Paraffin Embedding / Q000379:methods*; D012334:RNA, Neoplasm / Q000302:isolation & purification; D016019:Survival Analysis; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D012334:RNA, Neoplasm; D005557:Formaldehyde