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Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles
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- Marincevic-Zuniga, Yanara (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Dahlberg, Johan (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Nilsson, Sara (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Raine, Amanda (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Nystedt, Sara (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Lindqvist, Carl Mårten, 1979- (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Berglund, Eva C. (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Abrahamsson, Jonas, 1954 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för pediatrik,Institute of Clinical Sciences, Department of Pediatrics,Univ Gothenburg, Sahlgrenska Acad, Dept Pediat, Inst Clin Sci, Gothenburg, Sweden.
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- Cavelier, Lucia (author)
- Uppsala universitet,Medicinsk genetik och genomik
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- Forestier, Erik (author)
- Umeå universitet,Medicinsk och klinisk genetik
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- Heyman, M. (author)
- Karolinska Institutet,Karolinska Univ Hosp, Astrid Lindgren Childrens Hosp, Childhood Canc Res Unit, Karolinska Inst, Stockholm, Sweden.
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- Lönnerholm, Gudmar, 1941- (author)
- Uppsala universitet,Barnneurologi/Barnonkologi
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- Nordlund, Jessica (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Syvänen, Ann-Christine, 1950- (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2017-08-14
- 2017
- English.
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In: Journal of Hematology & Oncology. - : Springer Science and Business Media LLC. - 1756-8722. ; 10
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Abstract
Subject headings
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- Background: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. Methods: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. Results: We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. Conclusion: Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Hematologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Hematology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Pediatrik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Pediatrics (hsv//eng)
Keyword
- Pediatric acute lymphoblastic leukemia
- RNA sequencing
- Fusion genes
- BCP-ALL
- T-ALL
- Translocation
- GENOMIC ABNORMALITIES
- TUMOR-SUPPRESSOR
- HIGH-RISK
- ADOLESCENTS
- CANCER
- IMATINIB
- SUBTYPES
- LRIG1
- DUX4
- Pediatric acute lymphoblastic leukemia
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Marincevic-Zunig ...
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Dahlberg, Johan
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Nilsson, Sara
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Raine, Amanda
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Nystedt, Sara
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Lindqvist, Carl ...
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show more...
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Berglund, Eva C.
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Abrahamsson, Jon ...
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Cavelier, Lucia
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Forestier, Erik
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Heyman, M.
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Lönnerholm, Gudm ...
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Nordlund, Jessic ...
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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 Hematology
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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 ...
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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 Pediatrics
- Articles in the publication
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Journal of Hemat ...
- By the university
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University of Gothenburg
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Karolinska Institutet
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Uppsala University
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Umeå University