title: High rates of submicroscopic aberrations in karyotypically normal acute lymphoblastic leukemia.
abstract: BACKGROUND
  Acute lymphoblastic leukemia (ALL) is not a single uniform disease. It consists of several subgroups with different cytogenetic and molecular genetic aberrations, clinical presentations and outcomes. Banding cytogenetics plays a pivotal role in the detection of recurrent chromosomal rearrangements and is the starting point of genetic analysis in ALL, still. Nowadays, molecular (cyto)genetic tools provide substantially to identify previously non-detectable, so-called cryptic chromosomal aberrations in ALL. However, ALL according to banding cytogenetics with normal karyotype - in short cytogenetically normal ALL (CN-ALL) - represent up to ~50 % of all new diagnosed ALL cases. The overall goal of this study was to identify and characterize the rate of cryptic alterations in CN-ALL and to rule out if one single routine approach may be sufficient to detect most of the cryptic alterations present.
  
  
  RESULTS
  Sixty-one ALL patients with CN-ALL were introduced in this study. All of them underwent high resolution fluorescence in situ hybridization (FISH) analysis. Also DNA could be extracted from 34 ALL samples. These DNA-samples were studied using a commercially available MLPA (multiplex ligation-dependent probe amplification) probe set directed against 37 loci in hematological malignancies and/or array-comparative genomic hybridization (aCGH). Chromosomal aberrations were detected in 21 of 61 samples (~34 %) applying FISH approaches: structural abnormalities were present in 15 cases and even numerical ones were identified in 6 cases. Applying molecular approaches copy number alterations (CNAs) were detected in 27/34 samples. Overall, 126 CNAs were identified and only 34 of them were detectable by MLPA (~27 %). Loss of CNs was identified in ~80 % while gain of CNs was present in ~20 % of the 126 CNAs. A maximum of 13 aberrations was detected per case; however, only one aberration per case was found in 8 of all in detail studied 34 cases. Of special interest among the detected CNAs are the following new findings: del(15)(q26.1q26.1) including CHD2 gene was found in 20 % of the studied ALL cases, dup(18)(q21.2q21.2) with the DCC gene was present in 9 % of the cases, and the CDK6 gene in 7q21.2 was deleted in 12 % of the here in detail studied ALL cases.
  
  
  CONCLUSIONS
  In conclusion, high resolution molecular cytogenetic tools and molecular approaches like MLPA and aCGH need to be combined in a cost-efficient way, to identify disease and progression causing alterations in ALL, as majority of them are cryptic in banding cytogenetic analyses.
authors.affiliation: Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
authors.forename: Moneeb A K
authors.initials: MA
authors.lastname: Othman
authors.affiliation: Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO, Centro de Investigação em Meio Ambiente, Genéticae Oncobiologia, Coimbra, Portugal.
authors.forename: Joana B
authors.initials: JB
authors.lastname: Melo
authors.affiliation: Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO, Centro de Investigação em Meio Ambiente, Genéticae Oncobiologia, Coimbra, Portugal.
authors.forename: Isabel M
authors.initials: IM
authors.lastname: Carreira
authors.affiliation: Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany ; Croatian Institute of Brain Research, Zagreb, Croatia.
authors.forename: Martina
authors.initials: M
authors.lastname: Rincic
authors.affiliation: Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
authors.forename: Anita
authors.initials: A
authors.lastname: Glaser
authors.affiliation: Cytogenetic Laboratory, Maria Sklodowska-Curie Memorial Cancer Centre and Institute, Warsaw, Poland.
authors.forename: Beata
authors.initials: B
authors.lastname: Grygalewicz
authors.affiliation: Department of Pediatrics (Oncology and Hematology), Jena University Hospital, Friedrich Schiller University, Jena, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Gruhn
authors.affiliation: Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany ; Department of Pediatrics (Oncology and Hematology), Jena University Hospital, Friedrich Schiller University, Jena, Germany.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Wilhelm
authors.affiliation: Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Rittscher
authors.affiliation: ZytoVision GmbH, Bremerhaven, Germany.
authors.forename: Britta
authors.initials: B
authors.lastname: Meyer
authors.affiliation: Cytogenetics Department, Bone Marrow Transplantation Unit, National Cancer Institute, Rio de Janeiro, RJ Brazil ; Post Graduation Program in Oncology, National Cancer Institute (INCA), Rio de Janeiro, RJ Brazil.
authors.forename: Maria Luiza Macedo
authors.initials: ML
authors.lastname: Silva
authors.affiliation: Pediatric Oncohematology Center, Hospital Oswaldo Cruz/ Pos Graduation Course of the Faculty of Medical Sciences, University of Pernambuco, Recife, PE Brazil.
authors.forename: Terezinha
authors.initials: T
authors.lastname: de Jesus Marques Salles
authors.affiliation: Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Liehr
keywords: Acute lymphoblastic leukemia (ALL); Array-comparative genomic hybridization (aCGH); Cryptic rearrangements; Fluorescence in situ hybridization (FISH); Multiplex ligation-dependent probe amplification (MLPA); Multitude multicolor banding (mMCB)