Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia

Abstract

Background: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue.

Findings: Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions.

Conclusions: Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL.

Figure 1

Outline of the experimental process. Genomic DNA samples were digested by restriction enzymes. Ditags (paired-end tags) were collected from both ends of restriction fragments and sequenced. The ditag sequences were compared to known human reference genome sequences. The unmapped ditags were used as sense and antisense PCR primers to amplify their original DNA fragments to generate full-length sequences. The sequences were mapped to reference genome sequences to determine the type of genomic aberrations.