TY - JOUR
T1 - Operationalization of Next-Generation Sequencing and Decision Support for Precision Oncology
AU - Zeng, Jia
AU - Johnson, Amber
AU - Shufean, Md Abu
AU - Kahle, Michael
AU - Yang, Dong
AU - Woodman, Scott E.
AU - Vu, Thuy
AU - Moorthy, Shhyam
AU - Holla, Vijaykumar
AU - Meric-Bernstam, Funda
N1 - Funding Information:
Supported in part by The Cancer Prevention and Research Institute of Texas (Award No. RP150535), the Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, National Center for Advancing Translational Sciences Grant No. UL1 TR000371 (Center for Clinical and Translational Sciences), and the MD Anderson Cancer Center Support Grant No. P30 CA016672.
Funding Information:
Supported in part by The Cancer Prevention and Research Institute of Texas (Award No. RP150535), the Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, National Center for Advancing Translational Sciences Grant No. UL1 TR000371 (Center for Clinical
Funding Information:
and Translational Sciences), and the MD Anderson Cancer Center Support Grant No. P30 CA016672.
Publisher Copyright:
© 2019 by American Society of Clinical Oncology
PY - 2019
Y1 - 2019
N2 - Genomic testing has become a part of routine oncology care and plays critical roles in diagnosis, prognostic assessment, and treatment selection. Thus, in parallel, the variety of genomic testing providers and sequencing platforms has grown exponentially. Selection of the best-fit panel for each case can be daunting, with many factors to consider. Among them is whether alteration interpretation and therapy/clinical trial matching are included and/or sufficient. In this article, we review some common commercially available sequencing platforms for the genes and types of alterations tested, samples needed, and reporting content provided. We review publicly available resources for a do-it-yourself approach to alteration interpretation when it is not provided or when supplemental research is needed, along with resources to identify genomically matched treatment options that are approved and/or investigational. However, with both commercially provided interpretation and publicly available resources, there are still caveats and limitations that can stem from insufficient or ambiguous nomenclature as well as from the presentation of information. Use cases in which clinical decision making was affected are discussed. After treatment options are identified, it is important to assess the level of evidence for use within the patient’s tumor type and molecular profile. However, numerous level-of-evidence scales have been published in recent years, so we provide a publicly available tool to facilitate interoperability. The level of evidence, along with other factors, such as allelic frequency and copy number, can be used to prioritize treatment options when multiple are identified.
AB - Genomic testing has become a part of routine oncology care and plays critical roles in diagnosis, prognostic assessment, and treatment selection. Thus, in parallel, the variety of genomic testing providers and sequencing platforms has grown exponentially. Selection of the best-fit panel for each case can be daunting, with many factors to consider. Among them is whether alteration interpretation and therapy/clinical trial matching are included and/or sufficient. In this article, we review some common commercially available sequencing platforms for the genes and types of alterations tested, samples needed, and reporting content provided. We review publicly available resources for a do-it-yourself approach to alteration interpretation when it is not provided or when supplemental research is needed, along with resources to identify genomically matched treatment options that are approved and/or investigational. However, with both commercially provided interpretation and publicly available resources, there are still caveats and limitations that can stem from insufficient or ambiguous nomenclature as well as from the presentation of information. Use cases in which clinical decision making was affected are discussed. After treatment options are identified, it is important to assess the level of evidence for use within the patient’s tumor type and molecular profile. However, numerous level-of-evidence scales have been published in recent years, so we provide a publicly available tool to facilitate interoperability. The level of evidence, along with other factors, such as allelic frequency and copy number, can be used to prioritize treatment options when multiple are identified.
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U2 - 10.1200/CCI.19.00089
DO - 10.1200/CCI.19.00089
M3 - Review article
C2 - 31550176
AN - SCOPUS:85081079777
SN - 2473-4276
VL - 3
JO - JCO Clinical Cancer Informatics
JF - JCO Clinical Cancer Informatics
ER -