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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

Olsson, Linda LU ; Lundin-Ström, Kristina B. LU ; Castor, Anders LU ; Behrendtz, Mikael; Biloglav, Andrea LU ; Norén-Nyström, Ulrika; Paulsson, Kajsa LU and Johansson, Bertil LU (2018) In Genes Chromosomes and Cancer 57(11). p.604-607
Abstract

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 >5 Mb 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 >5 Mb or better... (More)

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 >5 Mb 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 >5 Mb 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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
array analysis, clinical genetic diagnostics, pediatric acute lymphoblastic leukemia, single nucleotide polymorphism
in
Genes Chromosomes and Cancer
volume
57
issue
11
pages
604 - 607
publisher
John Wiley & Sons
external identifiers
  • scopus:85053404815
ISSN
1045-2257
DOI
10.1002/gcc.22664
language
English
LU publication?
yes
id
6e1ba612-f637-40bc-9fd1-b74fd757b050
date added to LUP
2018-10-24 09:33:44
date last changed
2019-01-14 16:35:33
@article{6e1ba612-f637-40bc-9fd1-b74fd757b050,
  abstract     = {<p>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 &gt;5 Mb 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 &gt;5 Mb 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.</p>},
  author       = {Olsson, Linda and Lundin-Ström, Kristina B. and Castor, Anders and Behrendtz, Mikael and Biloglav, Andrea and Norén-Nyström, Ulrika and Paulsson, Kajsa and Johansson, Bertil},
  issn         = {1045-2257},
  keyword      = {array analysis,clinical genetic diagnostics,pediatric acute lymphoblastic leukemia,single nucleotide polymorphism},
  language     = {eng},
  month        = {09},
  number       = {11},
  pages        = {604--607},
  publisher    = {John Wiley & Sons},
  series       = {Genes Chromosomes and Cancer},
  title        = {Improved cytogenetic characterization and risk stratification of pediatric acute lymphoblastic leukemia using single nucleotide polymorphism array analysis : A single center experience of 296 cases},
  url          = {http://dx.doi.org/10.1002/gcc.22664},
  volume       = {57},
  year         = {2018},
}