Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer
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Esa Pitkänen1,2, Tatiana Cajuso1,2, Riku Katainen1,2, Eevi Kaasinen1,2, Niko Välimäki1,2, Kimmo Palin1,2, Jussi Taipale1,3, Lauri A. Aaltonen1,2, and Outi Kilpivaara1,2
1 Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
2 Department of Medical Genetics, University of Helsinki, Helsinki, Finland
3 Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
Lauri A. Aaltonen, email:
Keywords: colorectal cancer, genome, sequencing, retrotransposon, L1
Received: February 10, 2014 Accepted: February 14, 2014 Published: February 14, 2014
L1 element retrotranspositions have been found to alter expression of genes neighboring the insertion sites, potentially involving them in tumorigenesis and tumor progression. In colorectal cancer (CRC), L1 insertions have been found to target genes with a role in tumorigenesis. Structural changes such as L1 insertions are identifiable by whole genome sequencing (WGS). In this study, we observed frequent somatic L1 retrotranspositions originating from TTC28 using deep coverage WGS data from 92 CRC tumor-normal sample pairs. In two cases the event had targeted NOVA1 gene (p=0.025). In addition, a germline retrotransposition event from TTC28 to GABRA4 was found to be a common polymorphism in the Finnish population. Thus while some events may be tumorigenic, others are likely to be neutral. Our data contradict a recent study where a similar signal in TTC28 was interpreted as a common inactivating translocation. While much work remains to be performed to understand the biological significance of retrotranspositions in cancer, accurate identification of these events is a prerequisite for success.
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