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Study Description

In the US, CRC incidence has declined with uptake in colonoscopy for early detection and removal of polyps, the precursor lesion, can stop a cancer from developing but in spite of this, CRC remains the second leading cause of cancer death in the United States. One third of people who undergo screening colonoscopy will have adenomatous polyps, but less than 5% of the time are these polyps presumed to go on to develop into cancer. Why does one polyp develop into cancer while another one that looks very similar does not. In this proposal we will identify what molecular genetic changes in the genome, in the mRNA expression and genetic methylation patterns will distinguish a polyp that has already transformed into cancer from one that has not.

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Publicly Available Data
  Link to other NCBI resources related to this study
Study Inclusion/Exclusion Criteria

Inclusion Criteria:

  1. Patients scheduled for GI tract cancer; polyp or inflammatory bowel disease surgery or endoscopy for clinical reasons
  2. Patients with known, suspected or prior history of GI tract cancer or polyps, or family history of gastric cancer, small bowel cancer, GIST and/or colorectal cancer and/or inflammatory bowel disease and who are undergoing endoscopy as part of their medical evaluation.
  3. Patients with indications for endoscopy other than GI tract cancer, polyps and who are scheduled for endoscopy as part of their medical evaluation.
  4. Age ≥ 18
  5. Patients found to have a blood culture positive for Strep Bovis (infantarius, coli, gallolyticus or pasteurianus

Exclusion Criteria:

  1. Individuals who do not comprehend English (i.e., participants must be able to read and sign a consent form without the assistance of an interpreter.)
  2. Age < 18
  3. Individuals who are unable to sign consent (e.g., mentally challenged, those declared legally incompetent).
  4. Individuals regarded as belonging to a vulnerable population (e.g., prisoners).

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Sequencing Illumina HiSeq X N/A N/A Broad Institute developed one-well protocol; More information on the one-well library construction method can be found here: Genome Biology 2011, 12:R1, PMID: 21205303
RNA Sequencing Illumina TruSeq N/A N/A Illumina TruSeq Stranded mRNA Sample Preparation kit; Illumina's protocols using either the HiSeq 2000/2500, 2015
Reduced Representation and Bisulfite Sequencing Zymo Research EZ DNA Methylation Kit N/A N/A Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research, Catalog Number: D5001)
Reduced Representation and Bisulfite Sequencing Illumina cBot and HiSeq Paired end cluster kit version 3 N/A N/A
Selected Publications
Diseases/Traits Related to Study (MeSH terms)
Authorized Data Access Requests
See research articles citing use of the data from this study
Study Attribution
  • Principal Investigator
    • Lisa Boardman, MD. Mayo Clinic, Rochester, MN, USA.
  • Funding Sources
    • R01 CA170357. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.