title: Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform.
abstract: BACKGROUND
  Circulating tumor DNA (ctDNA) holds promise as a non-invasive means for tumor monitoring in solid malignancies. Assays with high sensitivity and multiplexed analysis of mutations are needed to enable broad application.
  
  
  METHODS
  We developed a new assay based on sequence-specific synchronous coefficient of drag alteration (SCODA) technology, which enriches for mutant DNA to achieve high sensitivity and specificity. This assay was applied to plasma and tumor tissue from non-metastatic and metastatic colorectal cancer (CRC) patients, including patients undergoing surgical resection for CRC liver metastases.
  
  
  RESULTS
  Across multiple characterization experiments, the assay demonstrated a limit of detection of 0.001% (1 molecule in 100,000) for the majority of the 46 mutations in the panel. In CRC patient samples (n=38), detected mutations were concordant in tissue and plasma for 93% of metastatic patients versus 54% of non-metastatic patients. For three patients, ctDNA identified additional mutations not detected in tumor tissue. In patients undergoing liver metastatectomy, ctDNA anticipated tumor recurrence earlier than carcinoembryonic antigen (CEA) value or imaging.
  
  
  CONCLUSIONS
  The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.
authors.affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Evelyn
authors.initials: E
authors.lastname: Kidess
authors.affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Kyra
authors.initials: K
authors.lastname: Heirich
authors.affiliation: Boreal Genomics, Mountain View, CA, USA and Vancouver, BC, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Wiggin
authors.affiliation: Boreal Genomics, Mountain View, CA, USA and Vancouver, BC, Canada.
authors.forename: Valentina
authors.initials: V
authors.lastname: Vysotskaia
authors.affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Brendan C
authors.initials: BC
authors.lastname: Visser
authors.affiliation: Boreal Genomics, Mountain View, CA, USA and Vancouver, BC, Canada.
authors.forename: Andre
authors.initials: A
authors.lastname: Marziali
authors.affiliation: Deparment of Medicine, Division of Hepatology and Gastroenterology, Charité University Hospital, Berlin, Germany.
authors.forename: Bertram
authors.initials: B
authors.lastname: Wiedenmann
authors.affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Norton
authors.affiliation: Boreal Genomics, Mountain View, CA, USA and Vancouver, BC, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Lee
authors.affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Stefanie S
authors.initials: SS
authors.lastname: Jeffrey
authors.affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: George A
authors.initials: GA
authors.lastname: Poultsides
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D058534:Class I Phosphatidylinositol 3-Kinases; D015179:Colorectal Neoplasms / Q000097:blood / Q000235:genetics* / Q000601:surgery; D004252:DNA Mutational Analysis / Q000379:methods*; D004273:DNA, Neoplasm / Q000097:blood / Q000235:genetics*; D066246:ErbB Receptors / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009362:Neoplasm Metastasis; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D016133:Polymerase Chain Reaction; D011518:Proto-Oncogene Proteins / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D015203:Reproducibility of Results; D018631:ras Proteins / Q000235:genetics
chemical_list: D004273:DNA, Neoplasm; C117307:KRAS protein, human; D011518:Proto-Oncogene Proteins; D019869:Phosphatidylinositol 3-Kinases; D058534:Class I Phosphatidylinositol 3-Kinases; C484760:PIK3CA protein, human; C512478:EGFR protein, human; D066246:ErbB Receptors; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins