Next Generation Sequencing Technologies to Investigate Autosomal  Recessive Polycystic Kidney Disease (ARPKD).
Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a rare paediatric disease primarily caused by mutations in the gene PKHD1. ARPKD presents with considerably clinical variability which is linked to the type of PKHD1 mutation but not position. Animal models of Polycystic Kidney Disease (PKD) suggest there is a complex genetic landscape with genetic modifiers as a potential cause of disease variability.  Transcriptomic analysis identified a considerable number of genes linked to cellular metabolism and development. Amongst these genes were those linked to WNT signalling. Two individuals in this cohort had the same mutations in PKHD1 but different rates of kidney disease progression. Amongst the transcriptomic differences of these two individuals were differences in the expression changes of WNT genes. Overall design: To identify transcriptomic changes in ARPKD, four human ARPKD kidney samples between the ages of 9 days and 10 years and were compared to four age-matched normal “healthy” kidney samples collected from the PKD funded biobank hosted by University College London.   RNA was extracted from kidney tissue samples using the Qiagen RNeasy mini kit with library preparation and sequencing performed by the Oxford Genomics Centre using NEBNext Ultra II Directional RNA Library Prep Kit on an Illumina NovaSeq6000.  Sequencing data underwent alignment using the HISAT2 aligner using the GRCH38 genome files provided by Ensembl. Raw count data was determined using StringTie and differential expression analysis was performed using Deseq2.