title: Building a comprehensive genomic program for hepatocellular carcinoma.
abstract: BACKGROUND
  Hepatocellular carcinoma (HCC) is the most common primary liver cancer, causing approximately 660,000 deaths worldwide annually. The preferred treatment of HCC is surgical resection or orthotopic liver transplantation (OLT) for patients meeting specific criteria. For patients outside these criteria, options are limited and include medical therapy, radiofrequency ablation, chemoembolization, or palliative measures, and these result in poor outcomes. Various centers at Baylor are elucidating the genomics of HCC to improve treatment options, with a focus on three etiologies: hepatitis C virus, hepatitis B virus, and non-viral.
  
  
  METHODS
  Through collaborative efforts, we have established an effective specimen biobanking protocol, and we are using several techniques to analyze HCC, including whole genome sequencing, whole exome sequencing, gene-specific analysis, gene expression, and epigenetic analysis.
  
  
  RESULTS
  We have completed whole genome sequencing on two patient samples, whole exome sequencing on 47 patient samples, gene-specific analysis on 94 patient samples, gene expression on 4 patient samples, and epigenetic analysis on 1 patient sample.
  
  
  CONCLUSIONS
  We hope to use these results to define novel genetic therapeutic strategies that may work in conjunction with surgical approaches to improve long-term patient and graft survival rates in patients with HCC. We also aim to provide a functional framework of a comprehensive program for genomic analysis that may be imitated by other institutions and for other tumors in the global quest toward personalized genomic medicine.
authors.affiliation: Michael E. DeBakey Department of Surgery, Baylor College of Medicine, One Baylor Plaza, Jewish Bldg #404D, Houston, TX 77030, USA.
authors.forename: Theresa R
authors.initials: TR
authors.lastname: Harring
authors.forename: Jacfranz J
authors.initials: JJ
authors.lastname: Guiteau
authors.forename: N Thao T
authors.initials: NT
authors.lastname: Nguyen
authors.forename: Ron T
authors.initials: RT
authors.lastname: Cotton
authors.forename: Marie-Claude
authors.initials: MC
authors.lastname: Gingras
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
authors.forename: Christine A
authors.initials: CA
authors.lastname: O'Mahony
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: F Charles
authors.initials: FC
authors.lastname: Brunicardi
authors.forename: John A
authors.initials: JA
authors.lastname: Goss
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D002471:Cell Transformation, Neoplastic / Q000235:genetics; D030561:Databases, Nucleic Acid; D018450:Disease Progression; D057890:Epigenomics / Q000379:methods; D059472:Exome / Q000235:genetics; D005544:Forecasting; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D057285:Precision Medicine / Q000639:trends*; D014015:Tissue Banks