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Analysis of the Frequency of level 1 OncoKB Genomic Alterations in Veterans With Various Solid Organ Malignancies
Purpose
The aim of this study is to quantify the frequency of Memorial Sloan Kettering (MSK) Precision Oncology Knowledge Base (OncoKB) Level 1 genetic alterations in Veterans with various solid organ malignancies and evaluate the clinical benefit and impact of testing on treatment of these patients.
Background
The VA National Precision Oncology Program (NPOP) facilitates comprehensive genomic profiling (CGP) testing of Veterans with advanced cancer. While CGP is increasingly utilized and routinely ordered in patients with advanced solid organ malignancies, the clinical utility and value has not been proven in certain cancers. We present data from 5,979 patients with head and neck (H&N), pancreatic, hepatocellular (HCC), esophageal and kidney cancers who underwent CGP.
Methods
Our cohort consists of Veterans that received CGP testing to identify somatic variants between 1/1/2019 and 4/2/2025. Identified variants and biomarkers were formatted for use with oncoKB-annotator, a publicly available tool to annotate genomic variants with FDA approved drug recommendations stored as Level 1 annotations in OncoKB, and prescribed drugs were extracted from the Veteran Health Administration’s (VHA) Corporate Data Warehouse (CDW). Cancers were grouped by MSK’s OncoTree codes, and summary counts of Veterans tested, Veterans recommended, Veterans prescribed recommended FDA approved drugs were determined. Percentages were calculated using the total number of Veterans tested as the denominator.
Results
Level 1 OncoKB alterations were infrequent in H&N (0.94%), kidney (0.45%), HCC(0.28%), and pancreatic adenocarcinomas (1%). The frequency of Level 1 alterations in esophageal adenocarcinomas (EAC) was 20%. Approximately 98% of the Level 1 alterations in EAC patients were HER2 positivity or MSI-High status, which can be determined by other diagnostic methodologies such as IHC. The remaining 2% of EAC patients with level 1 alterations had BRAF V600E or NTRK rearrangements.
Conclusions
The incidence of level 1 genetic variants in H&N, kidney, HCC and pancreatic adenocarcinoma is very low and would very uncommonly result in clinical benefit. Although there is an expanding number of precision oncology-based therapies available, the proportion of patients with the aforementioned solid organ malignancies who benefitted from CGP was low, suggesting CGP has minimal impact on the treatment of Veterans with these malignancies.
Purpose
The aim of this study is to quantify the frequency of Memorial Sloan Kettering (MSK) Precision Oncology Knowledge Base (OncoKB) Level 1 genetic alterations in Veterans with various solid organ malignancies and evaluate the clinical benefit and impact of testing on treatment of these patients.
Background
The VA National Precision Oncology Program (NPOP) facilitates comprehensive genomic profiling (CGP) testing of Veterans with advanced cancer. While CGP is increasingly utilized and routinely ordered in patients with advanced solid organ malignancies, the clinical utility and value has not been proven in certain cancers. We present data from 5,979 patients with head and neck (H&N), pancreatic, hepatocellular (HCC), esophageal and kidney cancers who underwent CGP.
Methods
Our cohort consists of Veterans that received CGP testing to identify somatic variants between 1/1/2019 and 4/2/2025. Identified variants and biomarkers were formatted for use with oncoKB-annotator, a publicly available tool to annotate genomic variants with FDA approved drug recommendations stored as Level 1 annotations in OncoKB, and prescribed drugs were extracted from the Veteran Health Administration’s (VHA) Corporate Data Warehouse (CDW). Cancers were grouped by MSK’s OncoTree codes, and summary counts of Veterans tested, Veterans recommended, Veterans prescribed recommended FDA approved drugs were determined. Percentages were calculated using the total number of Veterans tested as the denominator.
Results
Level 1 OncoKB alterations were infrequent in H&N (0.94%), kidney (0.45%), HCC(0.28%), and pancreatic adenocarcinomas (1%). The frequency of Level 1 alterations in esophageal adenocarcinomas (EAC) was 20%. Approximately 98% of the Level 1 alterations in EAC patients were HER2 positivity or MSI-High status, which can be determined by other diagnostic methodologies such as IHC. The remaining 2% of EAC patients with level 1 alterations had BRAF V600E or NTRK rearrangements.
Conclusions
The incidence of level 1 genetic variants in H&N, kidney, HCC and pancreatic adenocarcinoma is very low and would very uncommonly result in clinical benefit. Although there is an expanding number of precision oncology-based therapies available, the proportion of patients with the aforementioned solid organ malignancies who benefitted from CGP was low, suggesting CGP has minimal impact on the treatment of Veterans with these malignancies.
Purpose
The aim of this study is to quantify the frequency of Memorial Sloan Kettering (MSK) Precision Oncology Knowledge Base (OncoKB) Level 1 genetic alterations in Veterans with various solid organ malignancies and evaluate the clinical benefit and impact of testing on treatment of these patients.
Background
The VA National Precision Oncology Program (NPOP) facilitates comprehensive genomic profiling (CGP) testing of Veterans with advanced cancer. While CGP is increasingly utilized and routinely ordered in patients with advanced solid organ malignancies, the clinical utility and value has not been proven in certain cancers. We present data from 5,979 patients with head and neck (H&N), pancreatic, hepatocellular (HCC), esophageal and kidney cancers who underwent CGP.
Methods
Our cohort consists of Veterans that received CGP testing to identify somatic variants between 1/1/2019 and 4/2/2025. Identified variants and biomarkers were formatted for use with oncoKB-annotator, a publicly available tool to annotate genomic variants with FDA approved drug recommendations stored as Level 1 annotations in OncoKB, and prescribed drugs were extracted from the Veteran Health Administration’s (VHA) Corporate Data Warehouse (CDW). Cancers were grouped by MSK’s OncoTree codes, and summary counts of Veterans tested, Veterans recommended, Veterans prescribed recommended FDA approved drugs were determined. Percentages were calculated using the total number of Veterans tested as the denominator.
Results
Level 1 OncoKB alterations were infrequent in H&N (0.94%), kidney (0.45%), HCC(0.28%), and pancreatic adenocarcinomas (1%). The frequency of Level 1 alterations in esophageal adenocarcinomas (EAC) was 20%. Approximately 98% of the Level 1 alterations in EAC patients were HER2 positivity or MSI-High status, which can be determined by other diagnostic methodologies such as IHC. The remaining 2% of EAC patients with level 1 alterations had BRAF V600E or NTRK rearrangements.
Conclusions
The incidence of level 1 genetic variants in H&N, kidney, HCC and pancreatic adenocarcinoma is very low and would very uncommonly result in clinical benefit. Although there is an expanding number of precision oncology-based therapies available, the proportion of patients with the aforementioned solid organ malignancies who benefitted from CGP was low, suggesting CGP has minimal impact on the treatment of Veterans with these malignancies.