title: COBL is a novel hotspot for IKZF1 deletions in childhood acute lymphoblastic leukemia.
abstract: IKZF1 deletion (ΔIKZF1) is an important predictor of relapse in childhood B-cell precursor acute lymphoblastic leukemia. Because of its clinical importance, we previously mapped breakpoints of intragenic deletions and developed a multiplex PCR assay to detect recurrent intragenic ΔIKZF1. Since the multiplex PCR was not able to detect complete deletions (IKZF1 Δ1-8), which account for ~30% of all ΔIKZF1, we aimed at investigating the genomic scenery of IKZF1 Δ1-8. Six samples of cases with IKZF1 Δ1-8 were analyzed by microarray assay, which identified monosomy 7, isochromosome 7q, and large interstitial deletions presenting breakpoints within COBL gene. Then, we established a multiplex ligation-probe amplification (MLPA) assay and screened copy number alterations within chromosome 7 in 43 diagnostic samples with IKZF1 Δ1-8. Our results revealed that monosomy and large interstitial deletions within chromosome 7 are the main causes of IKZF1 Δ1-8. Detailed analysis using long distance inverse PCR showed that six patients (16%) had large interstitial deletions starting within intronic regions of COBL at diagnosis, which is ~611 Kb downstream of IKZF1, suggesting that COBL is a hotspot for ΔIKZF1. We also investigated a series of 25 intragenic deletions (Δ2-8, Δ3-8 or Δ4-8) and 24 relapsed samples, and found one IKZF1-COBL tail-to-tail fusion, thus supporting that COBL is a novel hotspot for ΔIKZF1. Finally, using RIC score methodology, we show that breakpoint sequences of IKZF1 Δ1-8 are not analog to RAG-recognition sites, suggesting a different mechanism of error promotion than that suggested for intragenic ΔIKZF1.
authors.affiliation: Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.
authors.forename: Bruno Almeida
authors.initials: BA
authors.lastname: Lopes
authors.affiliation: Diagnostic Center of Acute Leukemia/Institute of Pharmaceutical Biology/ZAFES, Goethe-University of Frankfurt, Biocenter, Germany.
authors.forename: Claus
authors.initials: C
authors.lastname: Meyer
authors.affiliation: Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.
authors.forename: Thayana Conceição
authors.initials: TC
authors.lastname: Barbosa
authors.affiliation: Center for Diagnostics, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Zur Stadt
authors.affiliation: Center for Diagnostics, University Medical Center Hamburg Eppendorf, Hamburg, Germany.|Research Institute Children's Cancer Center, Hamburg, Germany.|Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Horstmann
authors.affiliation: Children's Cancer Institute, Lowy Cancer Research Centre UNSW, Sydney, New South Wales, Australia.
authors.forename: Nicola C
authors.initials: NC
authors.lastname: Venn
authors.affiliation: South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.|Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Susan
authors.initials: S
authors.lastname: Heatley
authors.affiliation: South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.|Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Deborah L
authors.initials: DL
authors.lastname: White
authors.affiliation: Children's Cancer Institute, Lowy Cancer Research Centre UNSW, Sydney, New South Wales, Australia.
authors.forename: Rosemary
authors.initials: R
authors.lastname: Sutton
authors.affiliation: Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.
authors.forename: Maria S
authors.initials: MS
authors.lastname: Pombo-de-Oliveira
authors.affiliation: Diagnostic Center of Acute Leukemia/Institute of Pharmaceutical Biology/ZAFES, Goethe-University of Frankfurt, Biocenter, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Marschalek
authors.affiliation: Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.
authors.forename: Mariana
authors.initials: M
authors.lastname: Emerenciano
mesh_terms: D000293:Adolescent; D000595:Amino Acid Sequence; D001483:Base Sequence; D002675:Child, Preschool; D056905:Chromosome Breakpoints; D002872:Chromosome Deletion; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics; D056915:DNA Copy Number Variations; D005260:Female; D017353:Gene Deletion; D006801:Humans; D051740:Ikaros Transcription Factor / Q000235:genetics*; D007223:Infant; D018404:Isochromosomes / Q000235:genetics; D008297:Male; D008840:Microfilament Proteins / Q000235:genetics*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: C561633:Cobl protein, human; C497239:IKZF1 protein, human; D008840:Microfilament Proteins; D051740:Ikaros Transcription Factor
keywords: COBL; IKZF1; RAG; acute lymphoblastic leukemia; relapse