TY - JOUR
T1 - Ultra-Rapid Reporting of GENomic Targets (URGENTseq)
T2 - Clinical Next-Generation Sequencing Results within 48 Hours of Sample Collection
AU - Patel, Keyur Pravinchandra
AU - Ruiz-Cordero, Roberto
AU - Chen, Wei
AU - Routbort, Mark J
AU - Floyd, Kristen
AU - Rodriguez, Sergio
AU - Galbincea, John
AU - Barkoh, Bedia A.
AU - Hatfield, David
AU - Khogeer, Haitham A
AU - Kanagal Shamanna, Rashmi
AU - Yin, Cheng Cameron
AU - Zuo, Zhuang
AU - Loghavi, Sanam
AU - Ok, Chi Young
AU - DiNardo, Courtney
AU - Luthra, Rajyalakshmi
AU - Medeiros, L Jeffrey
N1 - Publisher Copyright:
© 2019 American Society for Investigative Pathology and the Association for Molecular Pathology
PY - 2019/1
Y1 - 2019/1
N2 - Next-generation sequencing (NGS)-based mutation panels profile multiple genes simultaneously, allowing the reporting of numerous genes while saving labor and resources. However, one drawback of using NGS is that the turnaround time is often longer than conventional single gene tests. This delay can be problematic if molecular results are required to guide therapy in patients with clinically aggressive diseases, such as acute myeloid leukemia. To overcome this limitation, we developed a novel custom platform designated as Ultra-rapid Reporting of GENomic Targets (URGENTseq), an integrated solution that includes workflow optimization and an innovative custom bioinformatics pipeline to provide targeted NGS results on fresh peripheral blood and bone marrow samples within an actionable time period. URGENTseq was validated for clinical use by determining mutant allelic frequency and minimum coverage in silico to achieve 100% concordance for all positive and negative calls between the URGENTseq and conventional sequencing approach. URGENTseq enables the reporting of selected genes useful for immediate diagnosis (CALR, CSF3R, JAK2, KRAS, MPL, NPM1, NRAS, SF3B1) and treatment decisions (IDH1, IDH2) in hematologic malignancies within 48 hours of specimen collection. In addition, we summarize the molecular findings of the first 272 clinical test results performed using the URGENTseq platform.
AB - Next-generation sequencing (NGS)-based mutation panels profile multiple genes simultaneously, allowing the reporting of numerous genes while saving labor and resources. However, one drawback of using NGS is that the turnaround time is often longer than conventional single gene tests. This delay can be problematic if molecular results are required to guide therapy in patients with clinically aggressive diseases, such as acute myeloid leukemia. To overcome this limitation, we developed a novel custom platform designated as Ultra-rapid Reporting of GENomic Targets (URGENTseq), an integrated solution that includes workflow optimization and an innovative custom bioinformatics pipeline to provide targeted NGS results on fresh peripheral blood and bone marrow samples within an actionable time period. URGENTseq was validated for clinical use by determining mutant allelic frequency and minimum coverage in silico to achieve 100% concordance for all positive and negative calls between the URGENTseq and conventional sequencing approach. URGENTseq enables the reporting of selected genes useful for immediate diagnosis (CALR, CSF3R, JAK2, KRAS, MPL, NPM1, NRAS, SF3B1) and treatment decisions (IDH1, IDH2) in hematologic malignancies within 48 hours of specimen collection. In addition, we summarize the molecular findings of the first 272 clinical test results performed using the URGENTseq platform.
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U2 - 10.1016/j.jmoldx.2018.08.002
DO - 10.1016/j.jmoldx.2018.08.002
M3 - Article
C2 - 30577887
AN - SCOPUS:85058221491
SN - 1525-1578
VL - 21
SP - 89
EP - 98
JO - Journal of Molecular Diagnostics
JF - Journal of Molecular Diagnostics
IS - 1
ER -