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Comparison of Precision Oncology Annotation Services in the National Precision Oncology Program
BACKGROUND
The National Precision Oncology Program (NPOP) provides comprehensive genomic profiling (CGP) through external vendors to patients within the Veterans Affairs Healthcare System who meet testing guidelines. We sought to assess the concordance of cancer therapy recommendations between Foundation Medicine (FM), one of the NPOP vendors, and OncoKB, an FDA-recognized public precision oncology knowledge database, which annotates human genetic variants associated with therapies guidance at varying levels of evidence.
METHODS
We selected FM CGP test reports with at least one therapy recommendation regardless of FDA approval or level of evidence were selected to compare FM and OncoKB therapy annotations of different mutation types, including short variants (SVs), rearrangements, and copy number alterations (CNAs) between 02/01/2019-03/13/2023. Therapy recommendations of annotations for unique combinations of gene, variant, and cancer type from FM and OncoKB were compared. Comparisons were scored as an Exact Match (EM) if FM and OncoKB therapy annotation was the same or a Partial Match (PM) if the FM therapy annotation was a subset of OncoKB’s or vice versa.
RESULTS
For annotations involving FDA-approved therapies, a total of 10,435 cases were compared for SVs, 546 for rearrangements, and 732 for CNAs. Among SVs annotations, 7,029 (67.4%) were EM and 787 (7.5%) were PM. Of rearrangement annotations, 328 (60.1%) were EM and 95 (17.4%) were PM. Of CNA annotations, 469 (64.1%) were EM and 28 (3.8%) were PM. For off-label therapies, agreement between annotation sources was much lower in all above scenarios. Examples included 3022 (29%) cases were identified as EM plus PM for SVs, 324 (59.3%) for rearrangements, and 42 (5.7%) for CNAs.
CONCLUSIONS
Therapy recommendations were inconsistent between FM and OncoKB annotation services, with a substantial disagreement among both FDA-approved and off-label therapy annotations. The limitation of time difference of annotations performed between FM and OncoKB therapy annotations accounted for some disagreement. Establishing accuracy and improving concordance between different annotation services is needed to better match treatments to patients and improve provider trust and reliability of annotation service.
BACKGROUND
The National Precision Oncology Program (NPOP) provides comprehensive genomic profiling (CGP) through external vendors to patients within the Veterans Affairs Healthcare System who meet testing guidelines. We sought to assess the concordance of cancer therapy recommendations between Foundation Medicine (FM), one of the NPOP vendors, and OncoKB, an FDA-recognized public precision oncology knowledge database, which annotates human genetic variants associated with therapies guidance at varying levels of evidence.
METHODS
We selected FM CGP test reports with at least one therapy recommendation regardless of FDA approval or level of evidence were selected to compare FM and OncoKB therapy annotations of different mutation types, including short variants (SVs), rearrangements, and copy number alterations (CNAs) between 02/01/2019-03/13/2023. Therapy recommendations of annotations for unique combinations of gene, variant, and cancer type from FM and OncoKB were compared. Comparisons were scored as an Exact Match (EM) if FM and OncoKB therapy annotation was the same or a Partial Match (PM) if the FM therapy annotation was a subset of OncoKB’s or vice versa.
RESULTS
For annotations involving FDA-approved therapies, a total of 10,435 cases were compared for SVs, 546 for rearrangements, and 732 for CNAs. Among SVs annotations, 7,029 (67.4%) were EM and 787 (7.5%) were PM. Of rearrangement annotations, 328 (60.1%) were EM and 95 (17.4%) were PM. Of CNA annotations, 469 (64.1%) were EM and 28 (3.8%) were PM. For off-label therapies, agreement between annotation sources was much lower in all above scenarios. Examples included 3022 (29%) cases were identified as EM plus PM for SVs, 324 (59.3%) for rearrangements, and 42 (5.7%) for CNAs.
CONCLUSIONS
Therapy recommendations were inconsistent between FM and OncoKB annotation services, with a substantial disagreement among both FDA-approved and off-label therapy annotations. The limitation of time difference of annotations performed between FM and OncoKB therapy annotations accounted for some disagreement. Establishing accuracy and improving concordance between different annotation services is needed to better match treatments to patients and improve provider trust and reliability of annotation service.
BACKGROUND
The National Precision Oncology Program (NPOP) provides comprehensive genomic profiling (CGP) through external vendors to patients within the Veterans Affairs Healthcare System who meet testing guidelines. We sought to assess the concordance of cancer therapy recommendations between Foundation Medicine (FM), one of the NPOP vendors, and OncoKB, an FDA-recognized public precision oncology knowledge database, which annotates human genetic variants associated with therapies guidance at varying levels of evidence.
METHODS
We selected FM CGP test reports with at least one therapy recommendation regardless of FDA approval or level of evidence were selected to compare FM and OncoKB therapy annotations of different mutation types, including short variants (SVs), rearrangements, and copy number alterations (CNAs) between 02/01/2019-03/13/2023. Therapy recommendations of annotations for unique combinations of gene, variant, and cancer type from FM and OncoKB were compared. Comparisons were scored as an Exact Match (EM) if FM and OncoKB therapy annotation was the same or a Partial Match (PM) if the FM therapy annotation was a subset of OncoKB’s or vice versa.
RESULTS
For annotations involving FDA-approved therapies, a total of 10,435 cases were compared for SVs, 546 for rearrangements, and 732 for CNAs. Among SVs annotations, 7,029 (67.4%) were EM and 787 (7.5%) were PM. Of rearrangement annotations, 328 (60.1%) were EM and 95 (17.4%) were PM. Of CNA annotations, 469 (64.1%) were EM and 28 (3.8%) were PM. For off-label therapies, agreement between annotation sources was much lower in all above scenarios. Examples included 3022 (29%) cases were identified as EM plus PM for SVs, 324 (59.3%) for rearrangements, and 42 (5.7%) for CNAs.
CONCLUSIONS
Therapy recommendations were inconsistent between FM and OncoKB annotation services, with a substantial disagreement among both FDA-approved and off-label therapy annotations. The limitation of time difference of annotations performed between FM and OncoKB therapy annotations accounted for some disagreement. Establishing accuracy and improving concordance between different annotation services is needed to better match treatments to patients and improve provider trust and reliability of annotation service.
Evaluating the Incidence of Febrile Neutropenia and the Appropriate Use of Prophylactic Granulocyte Colony Stimulating Factors in Veterans Who Received Treatment for Non- Hodgkin’s Lymphoma
Introduction
Febrile neutropenia (FN) is one of the most concerning complications associated with chemotherapy treatment, often leading to hospitalizations and delays in chemotherapy. The NCCN Guideline recommends primary prophylaxis with G-CSFs for patients receiving chemotherapy regimens that have an intermediate risk for FN if the patients have risk factors. A common intermediate risk for FN regimen is CHOP plus an anti-CD20 monoclonal antibody (mAb) for the treatment of non-Hodgkin’s lymphoma (NHL). At VASDHCS, an evaluation of the appropriate use of prophylactic GCSFs in this risk group would allow better optimization of patient care.
Objective
To evaluate the incidence of FN in correlation with the appropriate use of G-CSFs in patients who received CHOP plus an anti-CD20 mAb for the treatment of NHL
Methods
This is a retrospective study at VA San Diego of adult veterans with a confirmed diagnosis of NHL who received the first cycle of CHOP plus an anti- CD20 mAb between January 1, 2006, to October 1, 2021. Patients were categorized based on whether they received prophylactic G-CSF during the first cycle. The primary outcome measured was the incidence of FN in veterans with risk factor(s) who received CHOP plus an anti-CD20 mAb. The secondary outcome was the percentage of patients with risk factors who received G-CSF regardless of FN incidence. Primary outcome was analyzed using 2-tailed Fisher exact test.
Results
57 patients were included in the final analysis. In patients with at least one risk factor for FN, 26 (60%) received prophylactic G-CSF and 17 (40%) did not. There is 1 case of FN in the group that received G-CSF and 2 cases of FN in the group without G-CSF (RR, 0.33; P = .55; 95% CI, 0.03-3.33).
Conculsions
In patients receiving treatment for NHL with CHOP plus an anti-CD20 mAb, most of the patients with at least 1 risk factor for FN were initiated on G-CSF. Based on the results of the study, our veteran population does not appear to have an increased risk for FN without G-CSF. A larger study is warranted to further evaluate the significance of FN in correlation with prophylactic G-CSF.
Introduction
Febrile neutropenia (FN) is one of the most concerning complications associated with chemotherapy treatment, often leading to hospitalizations and delays in chemotherapy. The NCCN Guideline recommends primary prophylaxis with G-CSFs for patients receiving chemotherapy regimens that have an intermediate risk for FN if the patients have risk factors. A common intermediate risk for FN regimen is CHOP plus an anti-CD20 monoclonal antibody (mAb) for the treatment of non-Hodgkin’s lymphoma (NHL). At VASDHCS, an evaluation of the appropriate use of prophylactic GCSFs in this risk group would allow better optimization of patient care.
Objective
To evaluate the incidence of FN in correlation with the appropriate use of G-CSFs in patients who received CHOP plus an anti-CD20 mAb for the treatment of NHL
Methods
This is a retrospective study at VA San Diego of adult veterans with a confirmed diagnosis of NHL who received the first cycle of CHOP plus an anti- CD20 mAb between January 1, 2006, to October 1, 2021. Patients were categorized based on whether they received prophylactic G-CSF during the first cycle. The primary outcome measured was the incidence of FN in veterans with risk factor(s) who received CHOP plus an anti-CD20 mAb. The secondary outcome was the percentage of patients with risk factors who received G-CSF regardless of FN incidence. Primary outcome was analyzed using 2-tailed Fisher exact test.
Results
57 patients were included in the final analysis. In patients with at least one risk factor for FN, 26 (60%) received prophylactic G-CSF and 17 (40%) did not. There is 1 case of FN in the group that received G-CSF and 2 cases of FN in the group without G-CSF (RR, 0.33; P = .55; 95% CI, 0.03-3.33).
Conculsions
In patients receiving treatment for NHL with CHOP plus an anti-CD20 mAb, most of the patients with at least 1 risk factor for FN were initiated on G-CSF. Based on the results of the study, our veteran population does not appear to have an increased risk for FN without G-CSF. A larger study is warranted to further evaluate the significance of FN in correlation with prophylactic G-CSF.
Introduction
Febrile neutropenia (FN) is one of the most concerning complications associated with chemotherapy treatment, often leading to hospitalizations and delays in chemotherapy. The NCCN Guideline recommends primary prophylaxis with G-CSFs for patients receiving chemotherapy regimens that have an intermediate risk for FN if the patients have risk factors. A common intermediate risk for FN regimen is CHOP plus an anti-CD20 monoclonal antibody (mAb) for the treatment of non-Hodgkin’s lymphoma (NHL). At VASDHCS, an evaluation of the appropriate use of prophylactic GCSFs in this risk group would allow better optimization of patient care.
Objective
To evaluate the incidence of FN in correlation with the appropriate use of G-CSFs in patients who received CHOP plus an anti-CD20 mAb for the treatment of NHL
Methods
This is a retrospective study at VA San Diego of adult veterans with a confirmed diagnosis of NHL who received the first cycle of CHOP plus an anti- CD20 mAb between January 1, 2006, to October 1, 2021. Patients were categorized based on whether they received prophylactic G-CSF during the first cycle. The primary outcome measured was the incidence of FN in veterans with risk factor(s) who received CHOP plus an anti-CD20 mAb. The secondary outcome was the percentage of patients with risk factors who received G-CSF regardless of FN incidence. Primary outcome was analyzed using 2-tailed Fisher exact test.
Results
57 patients were included in the final analysis. In patients with at least one risk factor for FN, 26 (60%) received prophylactic G-CSF and 17 (40%) did not. There is 1 case of FN in the group that received G-CSF and 2 cases of FN in the group without G-CSF (RR, 0.33; P = .55; 95% CI, 0.03-3.33).
Conculsions
In patients receiving treatment for NHL with CHOP plus an anti-CD20 mAb, most of the patients with at least 1 risk factor for FN were initiated on G-CSF. Based on the results of the study, our veteran population does not appear to have an increased risk for FN without G-CSF. A larger study is warranted to further evaluate the significance of FN in correlation with prophylactic G-CSF.