A replication study of genome-wide CNV association for hepatic biomarkers identifies nine genes associated with liver function

BMB Rep. 2011 Sep;44(9):578-83. doi: 10.5483/bmbrep.2011.44.9.578.

Abstract

Aspartate aminotransferase (AST) and alanine aminotransferase (ALT) are biochemical markers used to test for liver diseases. Copy number variation (CNV) plays an important role in determining complex traits and is an emerging area in the study various diseases. We performed a genome-wide association study with liver function biomarkers AST and ALT in 407 unrelated Koreans. We assayed the genome-wide variations on an Affymetrix Genome-Wide 6.0 array, and CNVs were analyzed using HelixTree. Using single linear regression, 32 and 42 CNVs showed significance for AST and ALT, respectively (P value < 0.05). We compared CNV-based genes between the current study (KARE2; AST-140, ALT-172) and KARE1 (AST-1885, ALT-773) using NetBox. Results showed 9 genes (CIDEB, DFFA, PSMA3, PSMC5, PSMC6, PSMD12, PSMF1, SDC4, and SIAH1) were overlapped for AST, but no overlapped genes were found for ALT. Functional gene annotation analysis shown the proteasome pathway, Wnt signaling pathway, programmed cell death, and protein binding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Alanine Transaminase / genetics
  • Apoptosis / genetics
  • Asian Continental Ancestry Group / genetics
  • Aspartate Aminotransferases / genetics
  • Biomarkers / metabolism*
  • DNA Copy Number Variations
  • Female
  • Genome, Human*
  • Genome-Wide Association Study
  • Genotype
  • Humans
  • Liver Diseases / genetics*
  • Male
  • Middle Aged
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Binding
  • Republic of Korea
  • Signal Transduction
  • Wnt Signaling Pathway

Substances

  • Biomarkers
  • Aspartate Aminotransferases
  • Alanine Transaminase
  • Proteasome Endopeptidase Complex