liu.seSearch for publications in DiVA
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Digital gene expression profiling of primary acute lymphoblastic leukemia cells
Uppsala University, Sweden .
Uppsala University, Sweden .
Uppsala University, Sweden .
Uppsala University, Sweden .
Show others and affiliations
2012 (English)In: Leukemia, ISSN 0887-6924, E-ISSN 1476-5551, Vol. 26, no 6, 1218-1227 p.Article in journal (Refereed) Published
Abstract [en]

We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 21 patients taking advantage of `second-generation sequencing technology. Patients included in this study represent four cytogenetically distinct subtypes of B-cell precursor (BCP) ALL and T-cell lineage ALL (T-ALL). The robustness of DGE combined with supervised classification by nearest shrunken centroids (NSC) was validated experimentally and by comparison with published expression data for large sets of ALL samples. Genes that were differentially expressed between BCP ALL subtypes were enriched to distinct signaling pathways with dic(9;20) enriched to TP53 signaling, t(9;22) to interferon signaling, as well as high hyperdiploidy and t(12;21) to apoptosis signaling. We also observed antisense tags expressed from the non-coding strand of similar to 50% of annotated genes, many of which were expressed in a subtype-specific pattern. Antisense tags from 17 gene regions unambiguously discriminated between the BCP ALL and T-ALL subtypes, and antisense tags from 76 gene regions discriminated between the 4 BCP subtypes. We observed a significant overlap of gene regions with alternative polyadenylation and antisense transcription (Pless than1 x 10(-15)). Our study using DGE profiling provided new insights into the RNA expression patterns in ALL cells.

Place, publisher, year, edition, pages
Nature Publishing Group , 2012. Vol. 26, no 6, 1218-1227 p.
Keyword [en]
pediatric acute lymphoblastic leukemia; ALL; digital gene expression; second-generation sequencing; antisense transcript; alternative polyadenylation
National Category
Social Sciences
Identifiers
URN: urn:nbn:se:liu:diva-79818DOI: 10.1038/leu.2011.358ISI: 000305081000009OAI: oai:DiVA.org:liu-79818DiVA: diva2:544962
Available from: 2012-08-17 Created: 2012-08-14 Last updated: 2017-12-07

Open Access in DiVA

fulltext(955 kB)64 downloads
File information
File name FULLTEXT01.pdfFile size 955 kBChecksum SHA-512
f9746e41b5f3cf3d778fe83955fb9cce47488b65af9b1cb46427349e74a7e98a08da248ba4c73a8cb94f00e4f4d707f25115b60739528de0161c745aa5d907fd
Type fulltextMimetype application/pdf

Other links

Publisher's full text
By organisation
Department of Paediatrics in Linköping
In the same journal
Leukemia
Social Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 64 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 51 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf