title: Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR.
abstract: Formed from a reciprocal translocation t(9:22)(q34;q11) of genetic material between the long arms of human chromosomes 9 and 22, the constitutively active breakpoint cluster region (BCR) Abelson 1 (ABL) tyrosine kinase BCR-ABL is known to be causative of chronic myelogenous leukemia (CML). In 98% of CML patients harboring the t(9:22)(q34;q11) translocation, known as the Philadelphia chromosome, the chimeric BCR-ABL oncogene is created through cleavage of the BCR gene within its major breakpoint region (M-BCR) and breakage of the ABL gene within a 100-kbp region downstream of exon 2a. Clinical detection of the fused BCR-ABL oncogene currently relies on direct visualization by fluorescence in situ hybridization (FISH), a relatively tedious assay that typically offers a detection limit of ca. 2%. Here, we describe a novel assay that uses droplet digital PCR (ddPCR) technology to reliably measure M-BCR status and the presence of BCR-ABL. When applied to cell-line models of CML, the assay accurately quantifies BCR-ABL frequency to a detection limit of 0.25%. It therefore offers improved specificity relative to FISH, and may allow identification of variant translocation patterns, including derivative chromosome 9 deletions.
authors.affiliation: Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.|Genome Science and Technology Program, University of British Columbia, 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Helen Louise
authors.initials: HL
authors.lastname: Lund
authors.affiliation: Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Curtis B
authors.initials: CB
authors.lastname: Hughesman
authors.affiliation: Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, V6T 2B5, Canada.
authors.forename: Kelly
authors.initials: K
authors.lastname: McNeil
authors.affiliation: Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, V6T 2B5, Canada.
authors.forename: Shahira
authors.initials: S
authors.lastname: Clemens
authors.affiliation: Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, V6T 2B5, Canada.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Hocken
authors.affiliation: Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, V6T 2B5, Canada.
authors.forename: Ryan
authors.initials: R
authors.lastname: Pettersson
authors.affiliation: Cancer Genetics Laboratory, Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, V6T 2B5, Canada.
authors.forename: Aly
authors.initials: A
authors.lastname: Karsan
authors.affiliation: Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.|Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
authors.affiliation: Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada. israels@mail.ubc.ca.|RES'EAU NSERC Research Network, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada. israels@mail.ubc.ca.
authors.forename: Charles
authors.initials: C
authors.lastname: Haynes
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D056905:Chromosome Breakpoints; D002899:Chromosomes, Human, Pair 9; D016044:Fusion Proteins, bcr-abl / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D020014:K562 Cells; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000175:diagnosis* / Q000235:genetics*; D057230:Limit of Detection; D015233:Models, Statistical; D016133:Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*; D051562:Proto-Oncogene Proteins c-bcr / Q000235:genetics*; D014178:Translocation, Genetic
chemical_list: D016044:Fusion Proteins, bcr-abl; C496613:BCR protein, human; D051562:Proto-Oncogene Proteins c-bcr
keywords: BCR-ABL; Cancer diagnostics; Chronic myeloid leukemia; Digital PCR; Molecular diagnostics; Philadelphia chromosome