PMID- 31211614
OWN - NLM
STAT- MEDLINE
DCOM- 20200508
LR  - 20200508
IS  - 1543-2165 (Electronic)
IS  - 0003-9985 (Linking)
VI  - 144
IP  - 1
DP  - 2020 Jan
TI  - Validation of a Next-Generation Sequencing Assay Targeting RNA for the 
      Multiplexed Detection of Fusion Transcripts and Oncogenic Isoforms.
PG  - 90-98
LID - 10.5858/arpa.2018-0441-OA [doi]
AB  - CONTEXT.-: Next-generation sequencing is a high-throughput method for detecting 
      genetic abnormalities and providing prognostic and therapeutic information for 
      patients with cancer. Oncogenic fusion transcripts are among the various 
      classifications of genetic abnormalities present in tumors and are typically 
      detected clinically with fluorescence in situ hybridization (FISH). However, FISH 
      probes only exist for a limited number of targets, do not provide any information 
      about fusion partners, cannot be multiplex, and have been shown to be limited in 
      specificity for common targets such as ALK. OBJECTIVE.-: To validate an anchored 
      multiplex polymerase chain reaction-based panel for the detection of fusion 
      transcripts in a university hospital-based clinical molecular diagnostics 
      laboratory. DESIGN.-: We used 109 unique clinical specimens to validate a custom 
      panel targeting 104 exon boundaries from 17 genes involved in fusions in solid 
      tumors. The panel can accept as little as 100 ng of total nucleic acid from 
      PreservCyt-fixed tissue, and formalin-fixed, paraffin-embedded specimens with as 
      little as 10% tumor nuclei. RESULTS.-: Using FISH as the gold standard, this 
      assay has a sensitivity of 88.46% and a specificity of 95.83% for the detection 
      of fusion transcripts involving ALK, RET, and ROS1 in lung adenocarcinomas. Using 
      a validated next-generation sequencing assay as the orthogonal gold standard for 
      the detection of EGFR variant III (EGFRvIII) in glioblastomas, the assay is 
      92.31% sensitive and 100% specific. CONCLUSIONS.-: This multiplexed assay is 
      tumor and fusion partner agnostic and will provide clinical utility in therapy 
      selection for patients with solid tumors.
FAU - Sussman, Robyn T
AU  - Sussman RT
AD  - From the Center for Personalized Diagnostics, Department of Pathology and 
      Laboratory Medicine, University of Pennsylvania, Philadelphia.
FAU - Oran, Amanda R
AU  - Oran AR
AD  - From the Center for Personalized Diagnostics, Department of Pathology and 
      Laboratory Medicine, University of Pennsylvania, Philadelphia.
FAU - Paolillo, Carmela
AU  - Paolillo C
AD  - From the Center for Personalized Diagnostics, Department of Pathology and 
      Laboratory Medicine, University of Pennsylvania, Philadelphia.
FAU - Lieberman, David
AU  - Lieberman D
AD  - From the Center for Personalized Diagnostics, Department of Pathology and 
      Laboratory Medicine, University of Pennsylvania, Philadelphia.
FAU - Morrissette, Jennifer J D
AU  - Morrissette JJD
AD  - From the Center for Personalized Diagnostics, Department of Pathology and 
      Laboratory Medicine, University of Pennsylvania, Philadelphia.
FAU - Rosenbaum, Jason N
AU  - Rosenbaum JN
AD  - From the Center for Personalized Diagnostics, Department of Pathology and 
      Laboratory Medicine, University of Pennsylvania, Philadelphia.
LA  - eng
PT  - Journal Article
PT  - Validation Study
DEP - 20190618
PL  - United States
TA  - Arch Pathol Lab Med
JT  - Archives of pathology & laboratory medicine
JID - 7607091
RN  - 0 (Oncogene Proteins, Fusion)
RN  - 0 (Protein Isoforms)
SB  - IM
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Humans
MH  - Multiplex Polymerase Chain Reaction/methods
MH  - Oncogene Proteins, Fusion/*analysis
MH  - Protein Isoforms/analysis
MH  - Sequence Analysis, RNA/*methods
EDAT- 2019/06/19 06:00
MHDA- 2020/05/10 06:00
CRDT- 2019/06/19 06:00
PHST- 2019/06/19 06:00 [pubmed]
PHST- 2020/05/10 06:00 [medline]
PHST- 2019/06/19 06:00 [entrez]
AID - 10.5858/arpa.2018-0441-OA [doi]
PST - ppublish
SO  - Arch Pathol Lab Med. 2020 Jan;144(1):90-98. doi: 10.5858/arpa.2018-0441-OA. Epub 
      2019 Jun 18.