RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome
Lillian M Zwemer, Lisa Hui, Heather C Wick, Diana W Bianchi
Prenatal Diagnosis | WILEY-BLACKWELL | Published : 2014
OBJECTIVE: The aim of this study was to compare the complexity of the amniotic fluid supernatant cell-free fetal transcriptome as described by RNA Sequencing (RNA-Seq) and gene expression microarrays. METHODS: Cell-free fetal RNA from the amniotic fluid supernatant of five euploid mid-trimester samples was divided and prepared in tandem for analysis by either the Affymetrix HG-U133 Plus 2.0 Gene Chip microarray or Illumina HiSeq. Transcriptomes were assembled and compared on the basis of the presence of signal, rank-order gene expression, and pathway enrichment using Ingenuity Pathway Analysis (IPA). RNA-Seq data were also examined for evidence of alternative splicing. RESULTS: Within indivi..View full abstract
Awarded by Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awarded by EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT
This work was supported by Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01 HD 042053-10 to Dr. Bianchi). DWB reported grants from the National Institute of Child Health and Human Development during the course of the study. Grants and personal fees are received by DWB from Illumina (formerly Verinata Health), outside the submitted work. In addition, DWB has a patent pending on the use of cell-free RNA in amniotic fluid to develop novel fetal therapies.