Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms.

Molecular Diagnosis & Therapy
Joonhong ParkMyungshin Kim

Abstract

Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies. Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms. Certified reference materials and clinical research samples were used, including 60 genomic DNA and 56 RNA samples. NGS was performed using OMA, which enables the interrogation of 40 target genes, 29 gene fusions, and five expression target genes with five expression control genes by the Ion S5 XL Sequencer. The analyzed data were compared with clinical data using karyotyping, reverse transcription polymerase chain reaction (PCR), fluorescence in situ hybridization, Sanger sequencing, customized NGS panel, and fragment analysis. All targets of reference materials were detected except three (two ASXL1 and one CEBPA) mutations, which we had not expected OMA to detect. In clinical search samples, OMA satisfactorily identified DNA variants, including 90 single nucleotide variants (SNVs), 48 small insertions and deletions (indels), and eight FLT3 internal tandem duplications (ITDs) (Kappa agreement 0.938). The variant allele frequencies of SNVs and indels measured by OMA co...Continue Reading

References

Jan 6, 2016·British Journal of Haematology·Adil A Hinai, Peter J M Valk
May 21, 2016·European Journal of Haematology·Erik B R MalmbergLinda Fogelstrand
Jun 28, 2016·Molecular Diagnosis & Therapy·Karl HaslamKen I Mills
Jul 23, 2016·Experimental & Molecular Medicine·Yonggoo KimMyungshin Kim
Jan 5, 2017·Pathology, Research and Practice·Reza ShahsiahZahra Mehdizadeh Kashi
Jun 4, 2017·Molecular Cancer Therapeutics·Maria Larrosa-Garcia, Maria R Baer
May 8, 2018·Blood Reviews·Evgenii ShumilovUlrike Bacher
Aug 15, 2018·Virchows Archiv : an International Journal of Pathology·Hannah L WilliamsZandra C Deans
Oct 18, 2018·American Journal of Hematology·Elihu H Estey
Dec 20, 2018·Leukemia Research·Hoon Seok KimBin Cho
Dec 24, 2018·The Journal of Molecular Diagnostics : JMD·Carmen M AlonsoEva Barragán
Jan 10, 2019·Annals of Laboratory Medicine·Jin JungYonggoo Kim
Jan 13, 2019·Experimental & Molecular Medicine·Woori JangYonggoo Kim

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Methods Mentioned

BETA
PCR
chip
Assay

Software Mentioned

TMAP
SIFT
Ion Torrent
Ion Torrent Server
OMA
Ion Reporter
NextGENe
Oncomine Myeloid Torrent Suite
Polyphen
MedCalc

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