Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

Jon C. Strefford, Frederik W. Van Delft, Hazel M. Robinson, Helen Worley, Olga Yiannikouris, Rebecca Selzer, Todd Richmond, Ian Hann, Tony Bellotti, Manoj Raghavan, Bryan D. Young, Vaskar Saha, Christine J. Harrison

Research output: Journal PublicationArticlepeer-review

127 Citations (Scopus)

Abstract

We have previously identified a unique subtype of acute lymphoblastic leukemia (ALL) associated with a poor outcome and characterized by intrachromosomal amplification of chromosome 21 including the RUNX1 gene (iAMP21). In this study, array-based comparative genomic hybridization (aCGH) (n = 10) detected a common region of amplification (CRA) between 33.192 and 39.796 Mb and a common region of deletion (CRD) between 43.7 and 47 Mb in 100% and 70% of iAMP21 patients, respectively. High-resolution genotypic analysis (n = 3) identified allelic imbalances in the CRA. Supervised gene expression analysis showed a distinct signature for eight patients with iAMP21, with 10% of overexpressed genes located within the CRA. The mean expression of these genes was significantly higher in iAMP21 when compared to other ALL samples (n = 45). Although genomic copy number correlated with overall gene expression levels within areas of loss or gain, there was considerable individual variation. A unique subset of differentially expressed genes, outside the CRA and CRD, were identified when gene expression signatures of iAMP21 were compared to ALL samples with ETV6-RUNX1 fusion (n = 21) or high hyperdiploidy with additional chromosomes 21 (n = 23). From this analysis, LGMN was shown to be overexpressed in patients with iAMP21 (P = 0.0012). Genomic and expression data has further characterized this ALL subtype, demonstrating high levels of 21q instability in these patients leading to proposals for mechanisms underlying this clinical phenotype and plausible alternative treatments.

Original languageEnglish
Pages (from-to)8167-8172
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume103
Issue number21
DOIs
Publication statusPublished - 23 May 2006
Externally publishedYes

Keywords

  • Array CGH
  • Expression profiling
  • Genomic instability
  • RUNX1
  • iAMP21

ASJC Scopus subject areas

  • General

Fingerprint

Dive into the research topics of 'Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21'. Together they form a unique fingerprint.

Cite this