Retrotransposition in Colorectal Cancer

The purpose of this study is to ascertain the locations of somatic LINE-1 retrotransposition events in human colon tumor samples by pooling multiple tumor samples from different patients and performing a targeted resequencing assay (Ewing and Kazazian, Genome Research 2010) to sequence the 3' flanking regions of all insertions in the pooled sample. The result is compared to the result of applying the same method to pooled normal samples from the same patients as were used in the pooled tumor sample and selecting sites that show an insertion in the tumor but not in the normaltissue and do not correspond to any known non-reference LINE-1 insertion allele. The selected sites are then validated by site-specific PCR and capillary sequencing to confirm that they represent LINE-1 insertions and to obtain breakpoint sequences.]]>
Colorectal tumor samples and adjacent non-cancerous colon tissue were collected from patients undergoing surgical intervention for colorectal cancer at the University of Minnesota Masonic Cancer Center. Control tissue samples were selected from the NIHCD Blood and Tissue Bank at the University of Maryland, Baltimore where brain, liver, and cerebrum tissues were available from the same adult patient.]]>