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Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia
Lund Univ, Sweden.
Uppsala Univ, Sweden; Uppsala Univ, Sweden.
Lund Univ, Sweden.
Lund Univ, Sweden; Dept Clin Genet and Pathol, Sweden.
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2018 (English)In: Leukemia, ISSN 0887-6924, E-ISSN 1476-5551, Vol. 32, no 10, p. 2117-2125Article in journal (Refereed) Published
Abstract [en]

High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs. 35%; P = 0.42). Only 0.6% of the 36,259 CpGs on 1q were differentially methylated between cases w (n = 14)/wo (n = 13) dup(1q). RNA sequencing of high hyperdiploid (HeH) and t(1;19)(q23;p13)-positive cases w (n = 14)/wo (n = 52) dup(1q) identified 252 and 424 differentially expressed genes, respectively; only seven overlapped. Of the overexpressed genes in the HeH and t(1;19) groups, 23 and 31%, respectively, mapped to 1q; 60-80% of these encode nucleic acid/protein binding factors or proteins with catalytic activity. We conclude that the pathogenetically important consequence of dup(1q) in BCP ALL is a gene-dosage effect, with the deregulated genes differing between genetic subtypes, but involving similar molecular functions, biological processes, and protein classes.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP , 2018. Vol. 32, no 10, p. 2117-2125
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Medical Genetics
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URN: urn:nbn:se:liu:diva-152063DOI: 10.1038/s41375-018-0092-2ISI: 000446171800003PubMedID: 29626196OAI: oai:DiVA.org:liu-152063DiVA, id: diva2:1259440
Note

Funding Agencies|Swedish Cancer Society [CAN 2017/291]; Swedish Childhood Cancer Foundation [PR2015-0006]; Swedish Research Council [2016-01084]; Governmental Funding of Clinical Research within the National Health Service [2014/354]; Royal Physiographic Society of Lund

Available from: 2018-10-29 Created: 2018-10-29 Last updated: 2019-05-02

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Behrendtz, Mikael

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H.K.H. Kronprinsessan Victorias barn- och ungdomssjukhusDivision of Children's and Women's healthFaculty of Medicine and Health Sciences
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Leukemia
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