Open Access Short Report

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

Yeong C Kim1, Yong-Chul Jung26, Jun Chen27, Ali H Alhasan38, Parawee Kaewsaard39, Yanming Zhang4, Shuo Ma5, Steve Rosen5 and San Ming Wang13*

Author Affiliations

1 Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Nebraska, USA

2 Northshore University Healthsystem Research Institute, Evanston, IL 60201, USA

3 McCormick School of Engineering and Applied Science, Northwestern University, Illinois, USA

4 Department of Medicine, University of Chicago Pritzker School of Medicine, Illinois, USA

5 Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Illinois, USA

6 ACGT Inc., Illinois, USA

7 School of Oceanography & Environment, Xiamen University, Xiamen, PR China

8 Interdepartmental Biological Science Graduate Program, Northwestern University, Illinois, USA

9 Food and Drug Administration, Bangkok, Thailand

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BMC Research Notes 2010, 3:341  doi:10.1186/1756-0500-3-341

Published: 20 December 2010

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.