Identification of expressed sequence tags preferentially expressed in human placentas by in silico subtraction

Objectives To identify expressed sequence tag (EST) clusters preferentially expressed in placentas. Methods The National Center for Biotechnology's online UniGene database contains 14 placenta libraries. In silico (compute r-based) subtraction compared placenta libraries against the remaining libraries to identify transcripts preferentially expressed in placentas. For known genes, placental expression or their use in prenatal diagnosis was then explored online using LocusLink and PubMed. Results Placentas preferentially expressed 475 EST clusters. Of these. 18 EST clusters with no known function were expressed exclusively in placentas. Of the remaining 457 EST clusters, 90 showed preferential placental expression by >25 times. Of these 90, literature searches on the 45 EST clusters with known functions showed 44 linked to placental physiology or proposed as markers for prenatal diagnosis [i.e. beta-hCG, pregnancy-specific glycoproteins, human placental lacto.-ens, pregnancy-associated plasma protein A (PAPP-A)]. Selected genes with known function in pregnancy but whose preferential placental expression fell below the factor of 25 threshold were also identified. Conclusion In silico subtraction identified 44 previously studied genes involved in placental physiology as well as 63 EST clusters preferentially expressed in placental tissue, which may serve as targets for future studies seeking novel markers for prenatal diagnosis or to better understand placental genetics. Copyright (C) 2003 John Wiley Sons, Ltd.