title: Comparing microarray versus RT-PCR assessment of renal allograft biopsies: similar performance despite different dynamic ranges.
abstract: In renal allografts, assessing gene expression can add relevant diagnostic information to histopathology. Results can be expressed as single genes or gene sets, representing pathogenesis-based transcript sets (PBTs): cytotoxic T-cell-associated, interferon gamma- induced or decreased kidney parenchymal transcripts. Two technology platforms are available: RT-PCR and microarrays. We compared RT-PCR, U133plus2.0 microarrays and histopathology in 86 biopsies. We compared 13 potentially diagnostic genes as RT-PCR probes to microarray-derived PBTs, 'mini'-PBTs (small sets of 3-5 transcripts) and a histology classifier. Most RT-PCR probes (10/13) correlated well with the corresponding microarray probe sets (r > 0.8). Exceptions included FASLG and CD8B1 microarray probe sets, which were not performing on microarrays but were detectable by RT-PCR most likely due to differences in sensitivity. In general, RT-PCR showed greater dynamic range, detecting small changes in normal kidneys, but RT-PCR and microarrays gave similar results in abnormal kidneys. Individual transcripts or mini-PBTs assessed by either platform correlated well with one another, with microarray PBTs and the histology classifier. Thus, microarrays and RT-PCR assessments agree strongly with one another and histopathology in assessing transplant inflammation, particularly, when results are expressed as PBTs or mini-PBTs. The dynamic range of both platforms was sufficient to detect the relevant changes in rejection.
authors.affiliation: Department of Medicine, Division of Nephrology & Immunology, Alberta Transplant Applied Genomics Centre, University of Alberta, Edmonton, Canada.
authors.forename: K
authors.initials: K
authors.lastname: Allanach
authors.forename: M
authors.initials: M
authors.lastname: Mengel
authors.forename: G
authors.initials: G
authors.lastname: Einecke
authors.forename: B
authors.initials: B
authors.lastname: Sis
authors.forename: L G
authors.initials: LG
authors.lastname: Hidalgo
authors.forename: T
authors.initials: T
authors.lastname: Mueller
authors.forename: P F
authors.initials: PF
authors.lastname: Halloran
mesh_terms: D001706:Biopsy; D002170:Canada; D005006:Ethnicity / Q000235:genetics; D006801:Humans; D016030:Kidney Transplantation / Q000276:immunology / Q000473:pathology*; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics / Q000302:isolation & purification; D044469:Racial Groups / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology; D014158:Transcription, Genetic; D014184:Transplantation, Homologous / Q000276:immunology / Q000473:pathology
chemical_list: D012313:RNA