title: Improved marker combination for detection of de novo genetic variation and aberrant DNA in colorectal neoplasia.
abstract: BACKGROUND
  The genetic heterogeneity of sporadic colorectal cancer (CRC) makes the choice of genetic markers and sequence variation-detection technologies critical to the performance of screening assays. We have previously described the effectiveness of a CRC assay composed of 22 known variants in KRAS, APC, TP53, and BAT-26 (V1). We introduce a new marker formulation (V2) that includes detection of de novo variation in APC, PIK3CA, and CTNNB1, hypermethylated sequences within SMARCA3 and VIM, and a single-base variation within BRAF. We compared the abilities of the V1 and V2 markers to detect aberrant DNA in colorectal neoplasias.
  
  
  METHODS
  V1 and V2 marker formulations were used to analyze 144 colorectal tissue samples comprising 50 precancerous adenomas, 94 carcinomas, and 11 nonpathologic tissues. V1 analysis consisted of single-base extension analysis of the 22 V1 variants. V2 analysis consisted of DNA scanning of the APC mutation cluster region, PIK3CA exons 9 and 20, CTNNB1 exon 3, analysis for the BRAF Val600Glu substitution, and methylation-specific PCR analysis of VIM and SMARCA3.
  
  
  RESULTS
  The V2 marker formulation had significantly higher sensitivity than the V1 markers for carcinomas (93.6% and 72.3%, respectively; P = 0.0002) and adenomas (92.0% and 62.0%, respectively; P = 0.0006). None of the nonpathologic samples were positive for any marker.
  
  
  CONCLUSIONS
  We demonstrate improved sensitivity of a new marker formulation (V2) to detect aberrant DNA in CRC and precancerous adenoma tumor tissues.
authors.affiliation: EXACT Sciences Corporation, Marlborough, Massachusetts, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Kann
authors.forename: James
authors.initials: J
authors.lastname: Han
authors.forename: David
authors.initials: D
authors.lastname: Ahlquist
authors.forename: Theodore
authors.initials: T
authors.lastname: Levin
authors.forename: Douglas
authors.initials: D
authors.lastname: Rex
authors.forename: Duncan
authors.initials: D
authors.lastname: Whitney
authors.forename: Sanford
authors.initials: S
authors.lastname: Markowitz
authors.forename: Anthony
authors.initials: A
authors.lastname: Shuber
mesh_terms: D018256:Adenomatous Polyps / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics*; D015179:Colorectal Neoplasms / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D011230:Precancerous Conditions / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm