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Discovery of a 29-Gene Panel in Peripheral Blood Mononuclear Cells for the Detection of Colorectal Cancer and Adenomas Using High Throughput Real-Time PCR

Author

Listed:
  • Laura Ciarloni
  • Sahar Hosseinian
  • Sylvain Monnier-Benoit
  • Natsuko Imaizumi
  • Gian Dorta
  • Curzio Ruegg
  • On behalf of the DGNP-COL-0310 Study Group

Abstract

Colorectal cancer (CRC) is the second leading cause of cancer-related death in developed countries. Early detection of CRC leads to decreased CRC mortality. A blood-based CRC screening test is highly desirable due to limited invasiveness and high acceptance rate among patients compared to currently used fecal occult blood testing and colonoscopy. Here we describe the discovery and validation of a 29-gene panel in peripheral blood mononuclear cells (PBMC) for the detection of CRC and adenomatous polyps (AP). Blood samples were prospectively collected from a multicenter, case-control clinical study. First, we profiled 93 samples with 667 candidate and 3 reference genes by high throughput real-time PCR (OpenArray system). After analysis, 160 genes were retained and tested again on 51 additional samples. Low expressed and unstable genes were discarded resulting in a final dataset of 144 samples profiled with 140 genes. To define which genes, alone or in combinations had the highest potential to discriminate AP and/or CRC from controls, data were analyzed by a combination of univariate and multivariate methods. A list of 29 potentially discriminant genes was compiled and evaluated for its predictive accuracy by penalized logistic regression and bootstrap. This method discriminated AP >1cm and CRC from controls with a sensitivity of 59% and 75%, respectively, with 91% specificity. The behavior of the 29-gene panel was validated with a LightCycler 480 real-time PCR platform, commonly adopted by clinical laboratories. In this work we identified a 29-gene panel expressed in PBMC that can be used for developing a novel minimally-invasive test for accurate detection of AP and CRC using a standard real-time PCR platform.

Suggested Citation

  • Laura Ciarloni & Sahar Hosseinian & Sylvain Monnier-Benoit & Natsuko Imaizumi & Gian Dorta & Curzio Ruegg & On behalf of the DGNP-COL-0310 Study Group, 2015. "Discovery of a 29-Gene Panel in Peripheral Blood Mononuclear Cells for the Detection of Colorectal Cancer and Adenomas Using High Throughput Real-Time PCR," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-17, April.
    • Handle: RePEc:plo:pone00:0123904
    DOI: 10.1371/journal.pone.0123904
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    References listed on IDEAS

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    1. Friedman, Jerome H. & Hastie, Trevor & Tibshirani, Rob, 2010. "Regularization Paths for Generalized Linear Models via Coordinate Descent," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i01).
    2. Mee Young Park & Trevor Hastie, 2007. "L1‐regularization path algorithm for generalized linear models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 69(4), pages 659-677, September.
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