Transcriptome analysis by next-generation sequencing (RNA-seq) allows investigation of a transcriptome at unsurpassed resolution. One major benefit is that RNA-seq analysis is independent of a priori knowledge on the sequence under investigation, thereby also allowing analysis of poorly characterized Plasmodium species. Several RNA Seq pipelines are developed for interpreting transcriptome and differential gene Expression.
Liver biopsies and clinical data were obtained from infants with cholestasis and from children without liver disease. mRNA samples were extracted and sequenced on Illumina RNA HiSeq panel. Data Analysis was performed using statistical analysis R package Superpc followed by regression analysis.
Heatmap above shows assignment of infants with biliary atresia into inflammation or fibrosis groups at diagnosis.
Gene expression profiling increases number of available methods to quantify prominent biological processes in biliary atresia. Gene expression profiling of liver at the time of diagnosis of biliary atresia identifies prominent signatures of inflammation or fibrosis in most patients. These signatures cannot be identified by traditional histological methods or by serum markers of liver injury or function. The segregation of inflammation with younger age at diagnosis and of fibrosis with decreased survival in correlation with the ability of molecular profiling to stage the liver disease at diagnosis.