title: Panhandle PCR strategy to amplify MLL genomic breakpoints in treatment-related leukemias.
abstract: Panhandle PCR amplifies genomic DNA with known 5' and unknown 3' sequences from a template with an intrastrand loop schematically shaped like a pan with a handle. We used panhandle PCR to clone MLL genomic breakpoints in two pediatric treatment-related leukemias. The karyotype in a case of treatment-related acute lymphoblastic leukemia showed the t(4;11)(q21;q23). Panhandle PCR amplified the translocation breakpoint at position 2158 in intron 6 in the 5' MLL breakpoint cluster region (bcr). The karyotype in a case of treatment-related acute myeloid leukemia was normal, but Southern blot analysis showed a single MLL gene rearrangement. Panhandle PCR amplified the breakpoint at position 1493 in MLL intron 6. Screening of somatic cell hybrid and radiation hybrid DNAs by PCR and reverse transcriptase-PCR analysis of the leukemic cells indicated that panhandle PCR identified a fusion of MLL intron 6 with a previously uncharacterized sequence in MLL intron 1, consistent with a partial duplication. In both cases, the breakpoints in the MLL bcr were in Alu repeats, and there were Alu repeats in proximity to the breakpoints in the partner DNAs, suggesting that Alu sequences were relevant to these rearrangements. This study shows that panhandle PCR is an effective method for cloning MLL genomic breakpoints in treatment-related leukemias. Analysis of additional pediatric cases will determine whether breakpoint distribution deviates from the predilection for 3' distribution in the bcr that has been found in adult cases.
authors.affiliation: Division of Oncology, Jr. Research Institute, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4318, USA.
authors.forename: M D
authors.initials: MD
authors.lastname: Megonigal
authors.forename: E F
authors.initials: EF
authors.lastname: Rappaport
authors.forename: D H
authors.initials: DH
authors.lastname: Jones
authors.forename: C S
authors.initials: CS
authors.lastname: Kim
authors.forename: P C
authors.initials: PC
authors.lastname: Nowell
authors.forename: B J
authors.initials: BJ
authors.lastname: Lange
authors.forename: C A
authors.initials: CA
authors.lastname: Felix
mesh_terms: D000328:Adult; D019677:Artificial Gene Fusion; D001483:Base Sequence; D001853:Bone Marrow / Q000473:pathology; D002648:Child; D002874:Chromosome Mapping; D002880:Chromosomes, Human, Pair 11; D002894:Chromosomes, Human, Pair 4; D017931:DNA Primers; D004268:DNA-Binding Proteins / Q000235:genetics*; D005260:Female; D015321:Gene Rearrangement; D011495:Histone-Lysine N-Methyltransferase; D006801:Humans; D007438:Introns; D007938:Leukemia / Q000209:etiology / Q000235:genetics* / Q000473:pathology; D008297:Male; D008969:Molecular Sequence Data; D051788:Myeloid-Lymphoid Leukemia Protein; D009369:Neoplasms / Q000628:therapy*; D016609:Neoplasms, Second Primary / Q000209:etiology* / Q000235:genetics* / Q000473:pathology; D016133:Polymerase Chain Reaction / Q000379:methods*; D011519:Proto-Oncogenes; D012091:Repetitive Sequences, Nucleic Acid; D014157:Transcription Factors; D014178:Translocation, Genetic; D016335:Zinc Fingers
chemical_list: D017931:DNA Primers; D004268:DNA-Binding Proteins; C497422:KMT2A protein, human; D014157:Transcription Factors; D051788:Myeloid-Lymphoid Leukemia Protein; D011495:Histone-Lysine N-Methyltransferase