Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray.
Pediatric acute lymphoblastic leukemia (ALL) is a malignant disease resulting from accumulation of genetic alterations. A robust technology, single nucleotide polymorphism oligonucleotide genomic microarray (SNP-chip) in concert with bioinformatics offers the opportunity to discover the genetic lesions associated with ALL. We examined 399 pediatric ALL samples and their matched remission marrows at 50,000/250,000 SNP sites using an SNP-chip platform. Correlations between genetic abnormalities and clinical features were examined. Three common genetic alterations were found: deletion of ETV6, deletion of p16INK4A, and hyperdiploidy, as well as a number of novel recurrent genetic alterations. Uniparental disomy (UPD) was a frequent event, especially affecting chromosome 9. A cohort of children with hyperdiploid ALL without gain of chromosomes 17 and 18 had a poor prognosis. Molecular allelokaryotyping is a robust tool to define small genetic abnormalities including UPD, which is usually overlooked by standard methods. This technique was able to detect subgroups with a poor prognosis based on their genetic status.
Kawamata
Norihiko
N
Department of Hematology, Oncology, Cedars-Sinai Medical Center/University of California at Los Angeles School of Medicine 90048, USA. kawamatan@cshs.org
Ogawa
Seishi
S
Zimmermann
Martin
M
Kato
Motohiro
M
Sanada
Masashi
M
Hemminki
Kari
K
Yamatomo
Go
G
Nannya
Yasuhito
Y
Koehler
Rolf
R
Flohr
Thomas
T
Miller
Carl W
CW
Harbott
Jochen
J
Ludwig
Wolf-Dieter
WD
Stanulla
Martin
M
Schrappe
Martin
M
Bartram
Claus R
CR
Koeffler
H Phillip
HP
D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D002986:Clinical Trials as Topic; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics*; D005260:Female; D017353:Gene Deletion; D006801:Humans; D007223:Infant; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000175:diagnosis / Q000235:genetics*; D011237:Predictive Value of Tests; D050783:Proto-Oncogene Proteins c-ets / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics*; D012189:Retrospective Studies; D000097764:ETS Translocation Variant 6 Protein
D019941:Cyclin-Dependent Kinase Inhibitor p16; D050783:Proto-Oncogene Proteins c-ets; D012097:Repressor Proteins; D000097764:ETS Translocation Variant 6 Protein