Detection of chromosomal translocations in formalin-fixed paraffin-embedded (FFPE) leukemic specimens by digital expression profiling

Abstract

Introduction: Detection of chromosomal translocations in formalin-fixed paraffin-embedded (FFPE) leukemic samples is important for confirmation of histopathological findings, classification, prognostication, and therapeutic decisions. Herein, we aim to determine whether digital expression profiling could detect chromosomal translocations in FFPE leukemic samples identified by RT-PCR, FISH, and/or karyotyping.

Methods: RNA was extracted from 28 FFPE bone marrow specimens from 19 patients diagnosed with leukemia. Eight patients were translocation t(9;22) positive, three inv(16)/t(16/16) positive, five translocation t(15;17) positive, and one translocation t(8;21) positive. Two patients (four specimens) were normal. The extracted RNA was hybridized to DNA reporter probes overnight at 65 °C, followed by purification of the labeled translocations. Six hundred fields of view were counted to enumerate the number of translocations.

Results: Digital expression profiling had 100% concordance with RT-PCR, FISH, or karyotyping analysis in the two normal individuals, eight translocation t(9;22) samples, five translocation t(15;17) samples, and one translocation t(8;21) sample. None of the inv(16) positive samples were detected. Digital expression profiling detected translocations with 0.014 p190 allelic burden.

Conclusion: Digital expression profiling can be used to measure translocation t(9;22), t(15;17), and t(8;21) in FFPE samples and is useful when a confirmatory test from a FFPE sample is necessary.

Keywords: nCounter analysis system.