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Digital gene expres...
Digital gene expression profiling of primary acute lymphoblastic leukemia cells
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- Nordlund, Jessica (author)
- Uppsala universitet,Molekylär medicin,Uppsala University, Sweden
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- Kiialainen, A. (author)
- Uppsala universitet,Molekylär medicin,Uppsala University, Sweden
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- Karlberg, Olof (author)
- Uppsala universitet,Molekylär medicin,Uppsala University, Sweden
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- Berglund, Eva C (author)
- Uppsala universitet,Molekylär medicin,Uppsala University, Sweden
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- Göransson-Kultima, Hanna (author)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin,Onkologisk farmakologi och informatik,Uppsala University, Sweden
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- Sonderkaer, M. (author)
- Aalborg University, Denmark
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- Nielsen, K. L. (author)
- Aalborg University, Denmark
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- Gustafsson, Mats G (author)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin,Onkologisk farmakologi och informatik,Uppsala University, Sweden
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- Behrendtz, M. (author)
- Östergötlands Läns Landsting,Barn- och ungdomskliniken i Linköping
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- Forestier, Erik (author)
- Umeå universitet,Institutionen för medicinsk biovetenskap,Umeå University, Sweden
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- Perkkio, M. (author)
- Kuopio University Hospital, Finland
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- Söderhäll, S. (author)
- Karolinska Institutet,Karolinska University Hospital, Sweden
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- Lönnerholm, Gudmar (author)
- Uppsala universitet,Pediatrik,Uppsala University, Sweden
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- Syvänen, Ann-Christine (author)
- Uppsala universitet,Molekylär medicin,Uppsala University, Sweden
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(creator_code:org_t)
- 2011-12-16
- 2012
- English.
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In: Leukemia. - : Nature Publishing Group. - 0887-6924 .- 1476-5551. ; 26:6, s. 1218-1227
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Abstract
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- 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
Keyword
- pediatric acute lymphoblastic leukemia; ALL; digital gene expression; second-generation sequencing; antisense transcript; alternative polyadenylation
- SOCIAL SCIENCES
- SAMHÄLLSVETENSKAP
Publication and Content Type
- ref (subject category)
- art (subject category)
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Leukemia
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- By the author/editor
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Nordlund, Jessic ...
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Kiialainen, A.
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Karlberg, Olof
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Berglund, Eva C
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Göransson-Kultim ...
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Sonderkaer, M.
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Nielsen, K. L.
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Gustafsson, Mats ...
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Behrendtz, M.
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Forestier, Erik
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Perkkio, M.
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Söderhäll, S.
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Lönnerholm, Gudm ...
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Syvänen, Ann-Chr ...
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
- Articles in the publication
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Leukemia
- By the university
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Linköping University
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Uppsala University
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Karolinska Institutet
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Umeå University