Article

The signatures of autozygosity among patients with colorectal cancer.

Department of Microbiology, Weill Medical College of Cornell University, New York, NY 10021, USA.
Cancer Research (impact factor: 7.86). 05/2008; 68(8):2610-21. DOI:10.1158/0008-5472.CAN-07-5250
Source: PubMed

ABSTRACT Previous studies have shown that among populations with a high rate of consanguinity, there is a significant increase in the prevalence of cancer. Single nucleotide polymorphism (SNP) array data (Affymetrix, 50K XbaI) analysis revealed long regions of homozygosity in genomic DNAs taken from tumor and matched normal tissues of colorectal cancer (CRC) patients. The presence of these regions in the genome may indicate levels of consanguinity in the individual's family lineage. We refer to these autozygous regions as identity-by-descent (IBD) segments. In this study, we compared IBD segments in 74 mostly Caucasian CRC patients (mean age of 66 years) to two control data sets: (a) 146 Caucasian individuals (mean age of 80 years) who participated in an age-related macular degeneration (AMD) study and (b) 118 cancer-free Caucasian individuals from the Framingham Heart Study (mean age of 67 years). Our results show that the percentage of CRC patients with IBD segments (>or=4 Mb length and 50 SNPs probed) in the genome is at least twice as high as the AMD or Framingham control groups. Also, the average length of these IBD regions in the CRC patients is more than twice the length of the two control data sets. Compared with control groups, IBD segments are found to be more common among individuals of Jewish background. We believe that these IBD segments within CRC patients are likely to harbor important CRC-related genes with low-penetrance SNPs and/or mutations, and, indeed, two recently identified CRC predisposition SNPs in the 8q24 region were confirmed to be homozygous in one particular patient carrying an IBD segment covering the region.

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Keywords

50 SNPs probed
 
age-related macular degeneration
 
autozygous regions
 
average length
 
colorectal cancer
 
control data sets
 
CRC patients
 
CRC predisposition SNPs
 
CRC-related genes
 
Framingham Heart Study
 
genomic DNAs
 
IBD regions
 
IBD segment
 
IBD segments
 
individual's family lineage
 
low-penetrance SNPs
 
normal tissues
 
Previous studies
 
Single nucleotide polymorphism
 
two control data sets