title: Development of a NanoString assay to detect leukemogenic fusion transcripts in acute myeloid leukemia.
abstract: BACKGROUND
  Detection of leukemogenic fusion transcripts in acute myeloid leukemia (AML) is critical for AML diagnosis. NanoString nCounter system is a novel probe-based gene expression platform capable of measuring up to 800 targets with advantages of reproducibility, accuracy, and sample type flexibility. To study the potential application of NanoString in leukemia at clinic, we used this technology to detect AML leukemogenic fusion transcripts and compared the performances with clinical molecular assays.
  
  
  METHODS
  We developed a NanoString assay to detect seven leukemogenic fusion transcripts, namely RUNX1-RUNX1T1 (e5e12), PML-RARA (bcr1, bcr2, and bcr3), and CBFB-MYH11 (e5e12, e5e8, and e5e7). We set up the cut-off value for each fusion transcript and tested 42 de novo AML samples. We compared the results with reverse transcriptase-polymerase chain reaction (RT-PCR) and TaqMan reverse quantitative-polymerase chain reaction (RQ-PCR), the molecular methods standardly used at clinic.
  
  
  RESULTS
  We demonstrated that the NanoString and RT-PCR results correlate well (P < 0.0001) and are highly concordant (95.2%). Using TaqMan RQ-PCR as a validation method and gold standard, we demonstrated superior accuracy and sensitivity of NanoString compared to RT-PCR and comparable specificity. Furthermore, we showed that NanoString is not as sensitive as TaqMan RQ-PCR in detecting very low level of fusion transcripts.
  
  
  CONCLUSIONS
  NanoString can serve as a reliable and alternative molecular method to multiplexed RT-PCR for diagnosis of de novo AML with the perspective of screening/quantitation of a large number of leukemogenic fusion transcripts and prognostic genes. However, NanoString may not be an alternative method for monitoring minimal residual disease in AML.
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: D
authors.identifier: http://orcid.org/0000-0003-4281-9017
authors.initials: D
authors.lastname: Hu
authors.affiliation: Kindstar Diagnostics, Wuhan, China.
authors.forename: W
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Kindstar Diagnostics, Wuhan, China.
authors.forename: F
authors.initials: F
authors.lastname: Wang
authors.affiliation: Kindstar Diagnostics, Wuhan, China.
authors.forename: S M
authors.initials: SM
authors.lastname: Shu
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: L L
authors.initials: LL
authors.lastname: Fan
authors.affiliation: Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: J
authors.initials: J
authors.lastname: He
authors.affiliation: Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: P
authors.initials: P
authors.lastname: Wang
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Y L
authors.initials: YL
authors.lastname: He
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: W
authors.initials: W
authors.lastname: Du
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: J H
authors.initials: JH
authors.lastname: Zhang
authors.affiliation: Kindstar Diagnostics, Wuhan, China.
authors.forename: J X
authors.initials: JX
authors.lastname: Duan
authors.affiliation: Kindstar Diagnostics, Wuhan, China.
authors.forename: L
authors.initials: L
authors.lastname: Sun
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: J
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: X Q
authors.initials: XQ
authors.lastname: Li
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: H Y
authors.initials: HY
authors.lastname: Li
authors.affiliation: British Columbia Cancer Agency, Vancouver Island Cancer Center, Victoria, BC, Canada.
authors.forename: X L
authors.initials: XL
authors.lastname: Feng
authors.affiliation: Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.|Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: S A
authors.initials: SA
authors.lastname: Huang
mesh_terms: D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000175:diagnosis* / Q000235:genetics; D018365:Neoplasm, Residual / Q000175:diagnosis; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D015514:Oncogene Proteins, Fusion
keywords: Acute myeloid leukemia; Nanostring nCounter technology; leukemogenic fusion transcripts; minimal residual disease; molecular diagnosis