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

Yeong C. Kim, Yong Chul Jung, Jun Chen, Ali H. Alhasan, Parawee Kaewsaard, Yanming Zhang, Shuo Ma, Steve Rosen, San Ming Wang

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish (US)
Article number341
JournalBMC Research Notes
Volume3
DOIs
StatePublished - Dec 23 2010

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B-Cell Chronic Lymphocytic Leukemia
Aberrations
Genes
Genome
Scanning
Leukemia
Polymorphism
Decoding
Human Genome
Defects

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Kim, Y. C., Jung, Y. C., Chen, J., Alhasan, A. H., Kaewsaard, P., Zhang, Y., ... Wang, S. M. (2010). Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia. BMC Research Notes, 3, [341]. https://doi.org/10.1186/1756-0500-3-341

Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia. / Kim, Yeong C.; Jung, Yong Chul; Chen, Jun; Alhasan, Ali H.; Kaewsaard, Parawee; Zhang, Yanming; Ma, Shuo; Rosen, Steve; Wang, San Ming.

In: BMC Research Notes, Vol. 3, 341, 23.12.2010.

Research output: Contribution to journalArticle

Kim, YC, Jung, YC, Chen, J, Alhasan, AH, Kaewsaard, P, Zhang, Y, Ma, S, Rosen, S & Wang, SM 2010, 'Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia', BMC Research Notes, vol. 3, 341. https://doi.org/10.1186/1756-0500-3-341
Kim, Yeong C. ; Jung, Yong Chul ; Chen, Jun ; Alhasan, Ali H. ; Kaewsaard, Parawee ; Zhang, Yanming ; Ma, Shuo ; Rosen, Steve ; Wang, San Ming. / Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia. In: BMC Research Notes. 2010 ; Vol. 3.
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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.",
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N2 - 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.

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