Volume 11 Supplement 1

Beyond the Genome: The true gene count, human evolution and disease genomics

Open Access

Identifying gene copy number variants associated with colorectal adenoma recurrence

  • Christina M Laukaitis1,
  • Patricia Thompson2,
  • Maria Elena Martinez3 and
  • Eugene W Gerner4
Genome Biology201011(Suppl 1):P24

https://doi.org/10.1186/gb-2010-11-s1-p24

Published: 11 October 2010

Background

Colorectal cancer is the third leading cancer cause and represents the final stage of a progressive, multi-step, carcinogenic process of evolution through an adenoma stage [1]. Removing colorectal adenomas at colonoscopy significantly decreases cancer risk [2, 3]. One-third of colorectal cancer occurs in familial clusters and increases risk to family members [4]; however, most causative genetic factors are unknown. Here we seek genetic factors associated with metachronous adenoma occurrence, hypothesizing that genetic risk factors have been missed because association studies have sought risk-associated single nucleotide polymorphisms, while ignoring structural variation causing gene copy number changes. We used the Database of Genomic Variants [5] to identify gene copy number variation (CNV) in candidate genes from the vitamin D, polyamine, and selenium pathways (Table 1). We re-analyzed Illlumina genotyping data (Figure 1), and experimentally determined candidate gene copy number status for individuals from two interventional trials using MLPA and TaqMan assays. CNV genotypes are compared between individuals who did and did not develop metachronous adenoma to identify associated variants.
Table 1

Population frequency of CNV in Vitamin D pathway genes [5].

Gene

#CNV / #samples studied

Estimate of average

RXRA

28/95; 3/485; 7/2026

10%

GC

2/112

1.2%

CASR

22/2026; 1/90

8%

No reported CNV: VDR

Figure 1

Illumina genotyping data suggesting of CNV in Vitamin D pathway genes.

Authors’ Affiliations

(1)
Department of Medicine, Arizona Cancer Center, University of Arizona
(2)
Department of Pathology, Arizona Cancer Center, University of Arizona
(3)
Department of Epidemiology and Nutrition, Arizona Cancer Center, University of Arizona
(4)
Arizona Cancer Center, University of Arizona

References

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Copyright

© Laukaitis et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd.

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