PMID- 33537766
OWN - NLM
STAT- MEDLINE
DCOM- 20211015
LR  - 20211015
IS  - 2576-9456 (Print)
IS  - 2475-7241 (Linking)
VI  - 6
IP  - 4
DP  - 2021 Jul 7
TI  - Gene Fusion Identification Using Anchor-Based Multiplex PCR and Next-Generation 
      Sequencing.
PG  - 917-930
LID - 10.1093/jalm/jfaa230 [doi]
AB  - BACKGROUND: Methods for identifying gene fusion events, such as fluorescence in 
      situ hybridization (FISH), immunohistochemistry (IHC), and transcriptome 
      analysis, are either single gene approaches or require bioinformatics expertise 
      not generally available in clinical laboratories. We analytically validated a 
      customized next-generation sequencing (NGS) panel targeting fusion events in 34 
      genes involving soft-tissue sarcomas. METHODS: Specimens included 87 
      formalin-fixed paraffin-embedded (FFPE) tissues with known gene fusion status. 
      Isolated total nucleic acid was used to identify fusion events at the RNA level. 
      The potential fusions were targeted by gene-specific primers, followed by primer 
      extension and nested PCR to enrich for fusion candidates with subsequent 
      bioinformatics analysis. RESULTS: The study generated results using the following 
      quality metrics for fusion detection: (a) >/=100 ng total nucleic acid, (b) RNA 
      average unique start sites per gene-specific primer control >/=10, (c) quantitative 
      PCR assessing input RNA quality had a crossing point <30, (d) total RNA 
      percentage >/=30%, and (e) total sequencing fragments >/=500 000. CONCLUSIONS: The 
      test validation study demonstrated analytical sensitivity of 98.7% and analytical 
      specificity of 90.0%. The NGS-based panel generated highly concordant results 
      compared to alternative testing methods.
CI  - (c) American Association for Clinical Chemistry 2021. All rights reserved. For 
      permissions, please email: journals.permissions@oup.com.
FAU - Cheng, Yu-Wei
AU  - Cheng YW
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
FAU - Meyer, Anders
AU  - Meyer A
AD  - Department of Pathology and Laboratory Medicine, The University of Kansas, Kansas 
      City, KS.
AD  - Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine 
      Institute, Cleveland Clinic, Cleveland, OH.
FAU - Jakubowski, Maureen A
AU  - Jakubowski MA
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
FAU - Keenan, Sean O
AU  - Keenan SO
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
AD  - CellNetix Pathology & Laboratories, Seattle, WA.
FAU - Brock, Jay E
AU  - Brock JE
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
FAU - Azzato, Elizabeth M
AU  - Azzato EM
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
FAU - Weindel, Michael
AU  - Weindel M
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
FAU - Farkas, Daniel H
AU  - Farkas DH
AD  - Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory 
      Medicine Institute, Cleveland Clinic, Cleveland, OH.
FAU - Rubin, Brian P
AU  - Rubin BP
AD  - Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine 
      Institute, Cleveland Clinic, Cleveland, OH.
LA  - eng
PT  - Journal Article
PL  - England
TA  - J Appl Lab Med
JT  - The journal of applied laboratory medicine
JID - 101693884
SB  - IM
MH  - Gene Fusion
MH  - *High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - Immunohistochemistry
MH  - In Situ Hybridization, Fluorescence
MH  - *Multiplex Polymerase Chain Reaction
OTO - NOTNLM
OT  - bone and soft-tissue neoplasms
OT  - formalin-fixed paraffin-embedded (FFPE) tissue
OT  - gene fusion
OT  - neurotrophin receptor tyrosine kinase (NTRK)
OT  - next-generation sequencing
EDAT- 2021/02/05 06:00
MHDA- 2021/10/16 06:00
CRDT- 2021/02/04 05:54
PHST- 2020/08/30 00:00 [received]
PHST- 2020/10/30 00:00 [accepted]
PHST- 2021/02/05 06:00 [pubmed]
PHST- 2021/10/16 06:00 [medline]
PHST- 2021/02/04 05:54 [entrez]
AID - 6127554 [pii]
AID - 10.1093/jalm/jfaa230 [doi]
PST - ppublish
SO  - J Appl Lab Med. 2021 Jul 7;6(4):917-930. doi: 10.1093/jalm/jfaa230.