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Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A
Lund University, Sweden; Regional Labs, Sweden; Lund University, Sweden.
Lund University, Sweden.
Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Region Östergötland, Center of Paediatrics and Gynaecology and Obstetrics, Department of Paediatrics in Linköping.
Umeå University, Sweden.
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2015 (English)In: Journal of Hematology & Oncology, ISSN 1756-8722, E-ISSN 1756-8722, Vol. 8, no 42Article in journal (Refereed) Published
Abstract [en]

Background: Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that arises in a multistep fashion through acquisition of several genetic aberrations, subsequently giving rise to a malignant, clonal expansion of T-lymphoblasts. The aim of the present study was to identify additional as well as cooperative genetic events in T-ALL. Methods: A population-based pediatric T-ALL series comprising 47 cases was investigated by SNP array and deep sequencing analyses of 75 genes, in order to ascertain pathogenetically pertinent aberrations and to identify cooperative events. Results: The majority (92%) of cases harbored copy number aberrations/uniparental isodisomies (UPIDs), with a median of three changes (range 0-11) per case. The genes recurrently deleted comprised CDKN2A, CDKN2B, LEF1, PTEN, RBI, and STIL. No case had a whole chromosome UPID; in fact, literature data show that this is a rare phenomenon in T-ALL. However, segmental UPIDs (sUPIDs) were seen in 42% of our cases, with most being sUPID9p that always were associated with homozygous CDKN2A deletions, with a heterozygous deletion occurring prior to the sUPID9p in all instances. Among the 75 genes sequenced, 14 (19%) were mutated in 28 (72%) of 39 analyzed cases. The genes targeted are involved in signaling transduction, epigenetic regulation, and transcription. In some cases, NOTCH1 mutations were seen in minor subclones and lost at relapse; thus, such mutations can be secondary events. Conclusions: Deep sequencing and SNP array analyses of T-ALL revealed lack of wUPIDs, a high proportion of sUPID9p targeting CDKN2A, NOTCH1 mutations in subclones, and recurrent mutations of genes involved in signaling transduction, epigenetic regulation, and transcription.

Place, publisher, year, edition, pages
BioMed Central , 2015. Vol. 8, no 42
Keyword [en]
T-ALL; Pediatric; Genetic characterization; SNP array; Large-scale sequencing
National Category
Clinical Medicine
URN: urn:nbn:se:liu:diva-118245DOI: 10.1186/s13045-015-0138-0ISI: 000353761500001PubMedID: 25903014OAI: diva2:813540

Funding Agencies|Swedish Cancer Society; Swedish Childhood Cancer Foundation; Swedish Research Council

Available from: 2015-05-22 Created: 2015-05-22 Last updated: 2016-04-24

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Faculty of Medicine and Health SciencesDivision of Clinical SciencesDepartment of Paediatrics in Linköping
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Journal of Hematology & Oncology
Clinical Medicine

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