title: Identification of two gene variants associated with risk of advanced fibrosis in patients with chronic hepatitis C.
abstract: OBJECTIVE
  Previously identified clinical risk factors such as sex, alcohol consumption, and age at infection do not accurately predict which patients with chronic hepatitis C (CHC) will develop advanced fibrosis (bridging fibrosis and cirrhosis). The aim of this study was to identify genetic polymorphisms that can predict the risk of advanced fibrosis in patients with CHC.
  
  
  METHODS
  A total of 916 subjects with CHC was enrolled from 2 centers. A gene-centric disease association study of 24,832 putative functional, single nucleotide polymorphisms (SNPs) was performed. Of the 1609 SNPs that were significantly associated (P </= .05) with advanced fibrosis in the discovery cohort (University of California San Francisco [UCSF], N = 433), the first batch of 100 SNPs were selected for validation in the replication cohort (Virginia Commonwealth University [VCU], N = 483).
  
  
  RESULTS
  A missense SNP in the DEAD box polypeptide 5 (DDX5) gene was significantly associated with an increased risk of advanced fibrosis in both the UCSF and the VCU cohorts (OR, 1.8 and 2.2, respectively). Two diplotype groups, carrying the haplotypes composed of the DDX5 SNP and 2 neighboring POLG2 SNPs were also significantly associated with an increased risk of advanced fibrosis and had comparable or better risk estimates. In addition, a missense SNP in the carnitine palmitoyltransferase 1A (CPT1A) gene was associated with a decreased risk of advanced fibrosis in both the UCSF and the VCU cohorts (OR, 0.3 and 0.6, respectively).
  
  
  CONCLUSIONS
  Subjects with CHC carrying DDX5 minor allele or DDX5-POLG2 haplotypes are at an increased risk of developing advanced fibrosis, whereas those carrying the CPT1A minor allele are at a decreased risk.
authors.affiliation: Celera Diagnostics, Alameda, California, USA. hongjin.huang@celera.diagnostics.com
authors.forename: Hongjin
authors.initials: H
authors.lastname: Huang
authors.forename: Mitchell L
authors.initials: ML
authors.lastname: Shiffman
authors.forename: Ramsey C
authors.initials: RC
authors.lastname: Cheung
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Layden
authors.forename: Scott
authors.initials: S
authors.lastname: Friedman
authors.forename: Olivia T
authors.initials: OT
authors.lastname: Abar
authors.forename: Linda
authors.initials: L
authors.lastname: Yee
authors.forename: Anand P
authors.initials: AP
authors.lastname: Chokkalingam
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Schrodi
authors.forename: Jason
authors.initials: J
authors.lastname: Chan
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Catanese
authors.forename: Diane U
authors.initials: DU
authors.lastname: Leong
authors.forename: David
authors.initials: D
authors.lastname: Ross
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Hu
authors.forename: Alexander
authors.initials: A
authors.lastname: Monto
authors.forename: Linda B
authors.initials: LB
authors.lastname: McAllister
authors.forename: Samuel
authors.initials: S
authors.lastname: Broder
authors.forename: Thomas
authors.initials: T
authors.lastname: White
authors.forename: John J
authors.initials: JJ
authors.lastname: Sninsky
authors.forename: Teresa L
authors.initials: TL
authors.lastname: Wright
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000483:Alleles; D053487:DEAD-box RNA Helicases; D018450:Disease Progression; D005260:Female; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease; D006239:Haplotypes; D019698:Hepatitis C, Chronic / Q000235:genetics* / Q000473:pathology*; D006579:Heterozygote; D006801:Humans; D008103:Liver Cirrhosis / Q000235:genetics* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011336:Probability; D011379:Prognosis; D011446:Prospective Studies; D011494:Protein Kinases / Q000235:genetics*; D020365:RNA Helicases / Q000235:genetics*; D018570:Risk Assessment; D012680:Sensitivity and Specificity; D012720:Severity of Illness Index
chemical_list: D011494:Protein Kinases; C506749:Ddx5 protein, human; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases