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Improved cytogenetic characterization and risk stratification of pediatric acute lymphoblastic leukemia using single nucleotide polymorphism array analysis: A single center experience of 296 cases
Div Lab Med, Sweden.
Lund Univ, Sweden.
Skåne Univ Hosp, Sweden.
Region Östergötland, Center of Paediatrics and Gynaecology and Obstetrics, H.K.H. Kronprinsessan Victorias barn- och ungdomssjukhus. Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
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2018 (English)In: Genes, Chromosomes and Cancer, ISSN 1045-2257, E-ISSN 1098-2264, Vol. 57, no 11, p. 604-607Article in journal (Refereed) Published
Abstract [en]

Single nucleotide polymorphism array (SNP-A) analyses are increasingly being introduced in routine genetic diagnostics of acute lymphoblastic leukemia (ALL). Despite this, only few studies that have compared the diagnostic value of SNP-A with conventional chromosome banding have been published. We here report such a comparison of 296 ALL cases, the largest series to date. Only genomic imbalances amp;gt;5Mb and microdeletions targeting the BTG1, CDKN2A/B, EBF1, ERG, ETV6, IKZF1, PAX5, and RB1 genes and the pseudoautosomal region 1 (PAR1) were ascertained, in agreement with recent guidelines. Of 36 T-cell ALL cases, the karyotypes of 24 cases (67%) were revised by SNP-A analyses that either revealed additional imbalances amp;gt;5Mb or better characterized the changes found by G-banding. Of 260 B-cell precursor (BCP) ALL cases, SNP-A analyses identified additional copy number alterations, including the above-mentioned microdeletions, or better characterized the imbalances found by G-banding in 236 (91%) cases. Furthermore, the cytogenetic subtype classification of 41/260 (16%) BCP ALL cases was revised based on the SNP-A findings. Of the subtype revisions, 12/41 (29%) had clinical implications as regards risk stratifying cytogenetic groups or genotype-specific minimal residual disease stratification. We conclude that SNP-A analyses dramatically improve the cytogenetic characterization of both T-cell and BCP ALL and also provide important information pertinent to risk stratification of BCP ALL.

Place, publisher, year, edition, pages
WILEY , 2018. Vol. 57, no 11, p. 604-607
Keywords [en]
array analysis; clinical genetic diagnostics; pediatric acute lymphoblastic leukemia; single nucleotide polymorphism
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Medical Genetics
Identifiers
URN: urn:nbn:se:liu:diva-152602DOI: 10.1002/gcc.22664ISI: 000447757100009PubMedID: 30203896OAI: oai:DiVA.org:liu-152602DiVA, id: diva2:1262130
Note

Funding Agencies|Governmental Funding of Clinical Research within the National Health Service [2014/354]; the Swedish Research Council [2016-01084]; The Swedish Childhood Cancer Foundation [PR2015-0006]; The Swedish cancer society [CAN 2017/291]; the Crafoord foundation

Available from: 2018-11-09 Created: 2018-11-09 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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Genes, Chromosomes and Cancer
Medical Genetics

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