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Decision Processes During Development of Molecular Biomarkers for Gonadal Phenotypic Sex
Citation:
HAASCH, M. L., K. M. FLYNN, AND R. D. JOHNSON. Decision Processes During Development of Molecular Biomarkers for Gonadal Phenotypic Sex. Presented at SETAC Annual Meeting, Tampa, FL, November 16 - 20, 2008.
Impact/Purpose:
Each case of biomarker development will be unique but will necessarily have to arrive at a reasonable approach by determining the best choice for each of the possible alternatives. Decision trees with pros and cons will be presented. The decision points and process should help to inform similar future efforts. This abstract does not necessarily reflect USEPA policy.
Description:
Molecular biomarkers for determination of gonadal phenotypic sex in the Japanese medaka (Oryzias latipes), will serve as a case study. The medaka has unique features that aid in the development of appropriate molecular biomarkers of gonad phenotype, a) genetic sex can be determined by fin-clip real time RT-PCR, and b) the genome sequence is available and is largely annotated (http://www. ensembl.org/Oryzias_latipes/ index.html or http://medaka.ut genome.org/). Development of molecular biomarkers for application in testing protocols requires multiple decisions all of which affect the efficiency and performance of the final biomarker protocol. Decision points arise throughout the process of molecular biomarker development such as 1) sources of information to be researched for candidate genes, 2) measures of published data reliability, 3) what species to be included in the search, 4) which genes to target for expression analysis, 5) sources and availability of gene sequence information, 6) PCR primer design and location, 7) method of quantification to be used, 8) number and type of biological controls, 9) number and type of internal controls, 10) degree of individual variability tolerated, 11) degree of inter-assay variability tolerated, 12) cost-effectiveness of the final protocol, and 13) types of assay validation. Each case of biomarker development will be unique but will necessarily have to arrive at a reasonable approach by determining the best choice for each of the possible alternatives. Decision trees with pros and cons will be presented. The decision points and process should help to inform similar future efforts. This abstract does not necessarily reflect USEPA policy.