title: Using MS-MLPA as an efficient screening tool for detecting 9p21 abnormalities in pediatric acute lymphoblastic leukemia.
abstract: BACKGROUND
  Characterization of recurrent genetic lesions in childhood acute lymphoblastic leukemia (ALL) has enabled therapeutic stratification with improved outcomes. The tumor suppressor genes, CDKN2A and CDKN2B, encoding p16(INK4a) , p14(ARF) , and p15(INK4b) have been localized to 9p21. Abnormalities of 9p21 have been reported in 10-30% of childhood ALL using conventional cytogenetics and fluorescence in situ hybridization (FISH). The incidence of 9p21 using more sensitive techniques, such as methylation specific multiplex ligation-dependent probe amplification (MS-MLPA), remains uncertain, and thus also the prognostic significance.
  
  
  METHODS
  We investigated the incidence and prognostic importance of 9p21 abnormalities in pediatric ALL patients using MS-MLPA and compared these results to FISH.
  
  
  RESULTS
  In total, MS-MLPA or FISH detected aberrations (both dosage and methylation abnormalities) at 9p21 in a remarkable 32/48 (67%) patients in contrast to a much lower rate of only 8% of patients identified to have deletions by standard G banding cytogenetics. MS-MLPA identified five deletions not found by FISH. Aberrant methylation at CDKN2B was found in 19 (46%) patients. 9p21 abnormalities were associated with National Cancer Institute (NCI) high-risk criteria (P = 0.04) and were present in all five patients with T-cell disease. Four pre-B-cell ALL patients relapsed, three of whom had prior 9p21 abnormalities.
  
  
  CONCLUSIONS
  MS-MLPA had a higher detection rate for 9p21 abnormalities than previously reported for other techniques. Given the ease of processing, minimal equipment and low cost of MS-MLPA, our results suggest that previous reports may have underestimated the true frequency of 9p21 abnormalities and their potential impact upon ALL outcome.
authors.affiliation: Department of Microbiology and Immunology, IWK Health Centre/Dalhousie University, Halifax, NS, Canada.
authors.forename: R Brett
authors.initials: RB
authors.lastname: Gardiner
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Morash
authors.forename: Christie
authors.initials: C
authors.lastname: Riddell
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.forename: Conrad V
authors.initials: CV
authors.lastname: Fernandez
authors.forename: Margaret
authors.initials: M
authors.lastname: Yhap
authors.forename: Jason N
authors.initials: JN
authors.lastname: Berman
mesh_terms: D002648:Child; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D019075:Electrophoresis, Capillary; D005260:Female; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*