title: Standardization for transcriptomic molecular markers to screen human colon cancer.
abstract: Establishing test performance criteria for a transcriptomic colon cancer marker approach must be carried out in a standardized fashion in order tso ensure that the test will perform the same way in any laboratory, anywhere. Condition of sample preservation and shipping prior to total RNA extraction is critical, and we recommend preserving stool samples in an appropriate preservative and shipping them in cold packs so as to keep stools at 4 degrees C. It is not necessary to isolate colonocytes to obtain adequate RNA for testing. It is, however, important to obtain samples from both mucin-rich and non-mucin rich to have a good representation of both left- and right-side colon cancers. Employing a commercial total RNA extraction kit that contains an RLT buffer from Qiagen Corporation (Valencia, CA, USA) removes bacterial RNA from stool preparations and results in a high yield of undegraded RNA of human origin. Genes selected based on the enormous resources of NCI's Cancer Genome Anatomy project give good results. Primers for PCR should span more than one exon. Use of semiquantitative PCR, preferably with several reference housekeeping genes of various copy numbers, depending on tested genes, should enhance confidence in the quantitative results. Having standardized the testing conditions in our ongoing work, it is now imperative that a larger prospective randomized clinical study utilizing stool and tissue samples derived from several control and colon cancer patients, to allow for statistically valid analyses, be conducted in order to determine the true sensitivity and specificity of the transcriptomic screening approach for this cancer whose incidence is on the rise worldwide.
authors.affiliation: Department of Radiation Oncology, Leo W Jenkins Cancer Center, Greenville, NC, USA. GEMToxConsultants@yahoo.com
authors.forename: Farid E
authors.initials: FE
authors.lastname: Ahmed
authors.forename: Paul W
authors.initials: PW
authors.lastname: Vos
authors.forename: Stephanie
authors.initials: S
authors.lastname: Ijames
authors.forename: Donald T
authors.initials: DT
authors.lastname: Lysle
authors.forename: Gordon
authors.initials: G
authors.lastname: Flake
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Sinar
authors.forename: Wade
authors.initials: W
authors.lastname: Naziri
authors.forename: Stephan P
authors.initials: SP
authors.lastname: Marcuard
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D016022:Case-Control Studies; D002469:Cell Separation; D003106:Colon / Q000166:cytology / Q000378:metabolism; D003110:Colonic Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D005243:Feces / Q000166:cytology; D020869:Gene Expression Profiling / Q000592:standards*; D015972:Gene Expression Regulation, Neoplastic; D005820:Genetic Testing / Q000592:standards; D006801:Humans; D018189:Immunomagnetic Separation; D007834:Lasers; D042282:Microdissection; D020871:RNA Stability; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D012334:RNA, Neoplasm