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VHA-Wide Automated Assessment of EGFR Mutation Testing in Advanced Stage, Non-Squamous, Non-Small Cell Lung Cancer (nsNSCLC)
Purpose: To assess feasibility of implementing an automated method to identify patients who should have EGFR testing, and whether they have been tested, as a tool for quality improvement.
Background: Approximately 7% of veterans with metastatic, nsNSCLC have sensitizing mutation of EGFR, which predicts sensitivity to oral EGFR inhibitors. Prior studies have shown under testing for EGFR mutations in this population in VHA.
Methods: An endorsed quality measure (NQF and ASCO) for EGFR testing was utilized. Data to implement the measure were extracted from the cancer registry (ONC RAW), problem and encounter ICD codes, national oncology note template-generated health factors, laboratory test results, National Precision Oncology Program NGS testing, vital status, and pharmacy drug file to populate a SQL database. A dashboard in SharePoint allowed users to retrieve data based on national data access permissions. Descriptive statistics were used.
Results: The initial algorithm implementation was evaluated by comparison to manual review of patient records from one medical center. The second generation algorithm was then evaluated in the same manner at a second medical center (MC2). Among 117 cases identified during 2018, 68 (58%) were identified as having been tested and 49 (42%) not tested (31 living and 18 deceased patients). 48 of the non-tested samples were reviewed: 28 had not been tested, 14 had data documentation or coding problems (11 correctable by using the national note template), 1 correctable limitation of the national note template, and 5 limitations of the algorithm (all but 1 of which has been corrected). For stage 3 and stage VA-wide, there were 871 and 2832 cases, respectively, with documented testing rates of 26% and 36%, and a facility testing rate range of 0% to 100%.
Implications: The EGFR testing dashboard, in conjunction with appropriate structured documentation, has high accuracy of EGFR testing in patients with metastatic nsNSCLC. Current documented testing rates vary widely with a low system-wide rate, that can be improved through utilization of the dashboard.
Purpose: To assess feasibility of implementing an automated method to identify patients who should have EGFR testing, and whether they have been tested, as a tool for quality improvement.
Background: Approximately 7% of veterans with metastatic, nsNSCLC have sensitizing mutation of EGFR, which predicts sensitivity to oral EGFR inhibitors. Prior studies have shown under testing for EGFR mutations in this population in VHA.
Methods: An endorsed quality measure (NQF and ASCO) for EGFR testing was utilized. Data to implement the measure were extracted from the cancer registry (ONC RAW), problem and encounter ICD codes, national oncology note template-generated health factors, laboratory test results, National Precision Oncology Program NGS testing, vital status, and pharmacy drug file to populate a SQL database. A dashboard in SharePoint allowed users to retrieve data based on national data access permissions. Descriptive statistics were used.
Results: The initial algorithm implementation was evaluated by comparison to manual review of patient records from one medical center. The second generation algorithm was then evaluated in the same manner at a second medical center (MC2). Among 117 cases identified during 2018, 68 (58%) were identified as having been tested and 49 (42%) not tested (31 living and 18 deceased patients). 48 of the non-tested samples were reviewed: 28 had not been tested, 14 had data documentation or coding problems (11 correctable by using the national note template), 1 correctable limitation of the national note template, and 5 limitations of the algorithm (all but 1 of which has been corrected). For stage 3 and stage VA-wide, there were 871 and 2832 cases, respectively, with documented testing rates of 26% and 36%, and a facility testing rate range of 0% to 100%.
Implications: The EGFR testing dashboard, in conjunction with appropriate structured documentation, has high accuracy of EGFR testing in patients with metastatic nsNSCLC. Current documented testing rates vary widely with a low system-wide rate, that can be improved through utilization of the dashboard.
Purpose: To assess feasibility of implementing an automated method to identify patients who should have EGFR testing, and whether they have been tested, as a tool for quality improvement.
Background: Approximately 7% of veterans with metastatic, nsNSCLC have sensitizing mutation of EGFR, which predicts sensitivity to oral EGFR inhibitors. Prior studies have shown under testing for EGFR mutations in this population in VHA.
Methods: An endorsed quality measure (NQF and ASCO) for EGFR testing was utilized. Data to implement the measure were extracted from the cancer registry (ONC RAW), problem and encounter ICD codes, national oncology note template-generated health factors, laboratory test results, National Precision Oncology Program NGS testing, vital status, and pharmacy drug file to populate a SQL database. A dashboard in SharePoint allowed users to retrieve data based on national data access permissions. Descriptive statistics were used.
Results: The initial algorithm implementation was evaluated by comparison to manual review of patient records from one medical center. The second generation algorithm was then evaluated in the same manner at a second medical center (MC2). Among 117 cases identified during 2018, 68 (58%) were identified as having been tested and 49 (42%) not tested (31 living and 18 deceased patients). 48 of the non-tested samples were reviewed: 28 had not been tested, 14 had data documentation or coding problems (11 correctable by using the national note template), 1 correctable limitation of the national note template, and 5 limitations of the algorithm (all but 1 of which has been corrected). For stage 3 and stage VA-wide, there were 871 and 2832 cases, respectively, with documented testing rates of 26% and 36%, and a facility testing rate range of 0% to 100%.
Implications: The EGFR testing dashboard, in conjunction with appropriate structured documentation, has high accuracy of EGFR testing in patients with metastatic nsNSCLC. Current documented testing rates vary widely with a low system-wide rate, that can be improved through utilization of the dashboard.
The Current State of VHA’s National Precision Oncology Program
Purpose: To inform VA stakeholders of the availability of Precision Oncology (PO) services for Veterans with advanced cancer.
Background: PO offers the promise of effective, lowtoxicity targeted therapies tailored to individual tumor genomics but is unequally available within VHA. A system-wide National PO Program (NPOP) including patients in rural areas launched in July 2016.
Methods: Patients tested with multigene next generation sequencing (NGS) tumor testing through 2 contracted vendors were identified from NPOP records and cancer characteristics were extracted from NPOP and medical records. Drug use data was obtained from the VA Corporate Data Warehouse. NGS testing results and annotations were extracted from NPOP records.
Results: In all, 3,981 samples have been sent for NGS sequencing via NPOP. 3,036 samples were sequenced successfully and 597 failed (83.57% successful). Of the successful samples, 99 are liquid biopsies and 2,880 have Watson for Genomics treatment recommendations. Utilization of NPOP services has increased across VHA since the national rollout, from 4 participating facilities in NPOP’s first quarter (Q4 2016) to 51 facilities last quarter (Q3 2018). Average samples sent per month in 2018 is 182, up from 105 in 2017. Despite these increases, NGS testing is not yet systematically utilized at all participating facilities and 79 facilities did not participate last quarter. NPOP is servicing a large rural population (34% rural), which is similar to that of all VHA patients (33%) and more than twice the national rate (14%). The top diagnoses were lung (1,333: 917 adeno, 283 squamous, 133 non-small cell), colorectal (307), prostate (297), skin (154) and head and neck (75). 158 patients have been prescribed 225 of the recommended treatments before (130) and after (95) the NGS results date.
Conclusions: Utilization of NGS testing in the VHA population has grown significantly over the past year throughout most of the country. The higher volume has been facilitated through improvements in NPOP’s data infrastructure. Additional VHA patients can benefit from NGS gene panel testing to guide therapeutic decisionmaking.
Purpose: To inform VA stakeholders of the availability of Precision Oncology (PO) services for Veterans with advanced cancer.
Background: PO offers the promise of effective, lowtoxicity targeted therapies tailored to individual tumor genomics but is unequally available within VHA. A system-wide National PO Program (NPOP) including patients in rural areas launched in July 2016.
Methods: Patients tested with multigene next generation sequencing (NGS) tumor testing through 2 contracted vendors were identified from NPOP records and cancer characteristics were extracted from NPOP and medical records. Drug use data was obtained from the VA Corporate Data Warehouse. NGS testing results and annotations were extracted from NPOP records.
Results: In all, 3,981 samples have been sent for NGS sequencing via NPOP. 3,036 samples were sequenced successfully and 597 failed (83.57% successful). Of the successful samples, 99 are liquid biopsies and 2,880 have Watson for Genomics treatment recommendations. Utilization of NPOP services has increased across VHA since the national rollout, from 4 participating facilities in NPOP’s first quarter (Q4 2016) to 51 facilities last quarter (Q3 2018). Average samples sent per month in 2018 is 182, up from 105 in 2017. Despite these increases, NGS testing is not yet systematically utilized at all participating facilities and 79 facilities did not participate last quarter. NPOP is servicing a large rural population (34% rural), which is similar to that of all VHA patients (33%) and more than twice the national rate (14%). The top diagnoses were lung (1,333: 917 adeno, 283 squamous, 133 non-small cell), colorectal (307), prostate (297), skin (154) and head and neck (75). 158 patients have been prescribed 225 of the recommended treatments before (130) and after (95) the NGS results date.
Conclusions: Utilization of NGS testing in the VHA population has grown significantly over the past year throughout most of the country. The higher volume has been facilitated through improvements in NPOP’s data infrastructure. Additional VHA patients can benefit from NGS gene panel testing to guide therapeutic decisionmaking.
Purpose: To inform VA stakeholders of the availability of Precision Oncology (PO) services for Veterans with advanced cancer.
Background: PO offers the promise of effective, lowtoxicity targeted therapies tailored to individual tumor genomics but is unequally available within VHA. A system-wide National PO Program (NPOP) including patients in rural areas launched in July 2016.
Methods: Patients tested with multigene next generation sequencing (NGS) tumor testing through 2 contracted vendors were identified from NPOP records and cancer characteristics were extracted from NPOP and medical records. Drug use data was obtained from the VA Corporate Data Warehouse. NGS testing results and annotations were extracted from NPOP records.
Results: In all, 3,981 samples have been sent for NGS sequencing via NPOP. 3,036 samples were sequenced successfully and 597 failed (83.57% successful). Of the successful samples, 99 are liquid biopsies and 2,880 have Watson for Genomics treatment recommendations. Utilization of NPOP services has increased across VHA since the national rollout, from 4 participating facilities in NPOP’s first quarter (Q4 2016) to 51 facilities last quarter (Q3 2018). Average samples sent per month in 2018 is 182, up from 105 in 2017. Despite these increases, NGS testing is not yet systematically utilized at all participating facilities and 79 facilities did not participate last quarter. NPOP is servicing a large rural population (34% rural), which is similar to that of all VHA patients (33%) and more than twice the national rate (14%). The top diagnoses were lung (1,333: 917 adeno, 283 squamous, 133 non-small cell), colorectal (307), prostate (297), skin (154) and head and neck (75). 158 patients have been prescribed 225 of the recommended treatments before (130) and after (95) the NGS results date.
Conclusions: Utilization of NGS testing in the VHA population has grown significantly over the past year throughout most of the country. The higher volume has been facilitated through improvements in NPOP’s data infrastructure. Additional VHA patients can benefit from NGS gene panel testing to guide therapeutic decisionmaking.
Update on the VA Precision Oncology Program
Purpose: To inform VA stakeholders of the availability of precision oncology (PO) services for Veterans with advanced cancer.
Background: PO offers the promise of effective, low-toxicity targeted therapies tailored to individual tumor genomics but is unequally available within VHA. A systemwide PO program (POP), including patients in rural areas, launched in July 2016.
Methods: Patients tested with multigene next generation sequencing (NGS) tumor testing through 2 contracted vendors were identified from POP records and cancer characteristics were extracted from POP and medical records. Drug use data were obtained from the VA Corporate Data Warehouse. NGS testing results, and annotations were extracted from POP records.
Results: 1,442 tumor samples were sent for NGS testing as of 5/21/17 from 61 facilities. Rural patient testing (35%) was similar to VHA rurality (33%) and more than twice the US rate (14%). Most common diagnoses: lung (688: adeno 482, squamous 134), unknown (114), colorectal (103), skin (96), prostate (76), and H&N (66). Sample test requests increased rapidly after national implementation in July 2016 (23 samples/month prior to implementation to mean 126 samples/month 3 months later) as did the number of participating facilities (10/quarter to 39/month). Sequencing success rate increased from 68% to 71% over the same interval, while mean turn around time remained similar at 19.7 and 19.1 days, respectively. To date, 26 patients received a recommended drug outside a clinical trial, some more than 9 months after NGS. 5 additional patients had received an NGS-recommended drug prior to testing. NGS results are available for a cohort of 344 patients including: lung 200 (adeno 138, squamous 51), skin 28, LN 20, liver 19, GI 16. 979 variants were found most commonly in TP53, KRAS, STK11, APC, PIK3CA, and CDKN2A. 228 patients (66%) had actionable results (on-label drug 24, off-label drug 165, clinical trial 213). A PO consultation service (available by IFC) and a liquid biopsy are now available nationally.
Conclusions: Implementation of tumor NGS testing in VHA has been successful. Further program expansion, addition of hematological malignancies, deployment of informatics tools and efforts to expand access to appropriate drugs are ongoing.
Purpose: To inform VA stakeholders of the availability of precision oncology (PO) services for Veterans with advanced cancer.
Background: PO offers the promise of effective, low-toxicity targeted therapies tailored to individual tumor genomics but is unequally available within VHA. A systemwide PO program (POP), including patients in rural areas, launched in July 2016.
Methods: Patients tested with multigene next generation sequencing (NGS) tumor testing through 2 contracted vendors were identified from POP records and cancer characteristics were extracted from POP and medical records. Drug use data were obtained from the VA Corporate Data Warehouse. NGS testing results, and annotations were extracted from POP records.
Results: 1,442 tumor samples were sent for NGS testing as of 5/21/17 from 61 facilities. Rural patient testing (35%) was similar to VHA rurality (33%) and more than twice the US rate (14%). Most common diagnoses: lung (688: adeno 482, squamous 134), unknown (114), colorectal (103), skin (96), prostate (76), and H&N (66). Sample test requests increased rapidly after national implementation in July 2016 (23 samples/month prior to implementation to mean 126 samples/month 3 months later) as did the number of participating facilities (10/quarter to 39/month). Sequencing success rate increased from 68% to 71% over the same interval, while mean turn around time remained similar at 19.7 and 19.1 days, respectively. To date, 26 patients received a recommended drug outside a clinical trial, some more than 9 months after NGS. 5 additional patients had received an NGS-recommended drug prior to testing. NGS results are available for a cohort of 344 patients including: lung 200 (adeno 138, squamous 51), skin 28, LN 20, liver 19, GI 16. 979 variants were found most commonly in TP53, KRAS, STK11, APC, PIK3CA, and CDKN2A. 228 patients (66%) had actionable results (on-label drug 24, off-label drug 165, clinical trial 213). A PO consultation service (available by IFC) and a liquid biopsy are now available nationally.
Conclusions: Implementation of tumor NGS testing in VHA has been successful. Further program expansion, addition of hematological malignancies, deployment of informatics tools and efforts to expand access to appropriate drugs are ongoing.
Purpose: To inform VA stakeholders of the availability of precision oncology (PO) services for Veterans with advanced cancer.
Background: PO offers the promise of effective, low-toxicity targeted therapies tailored to individual tumor genomics but is unequally available within VHA. A systemwide PO program (POP), including patients in rural areas, launched in July 2016.
Methods: Patients tested with multigene next generation sequencing (NGS) tumor testing through 2 contracted vendors were identified from POP records and cancer characteristics were extracted from POP and medical records. Drug use data were obtained from the VA Corporate Data Warehouse. NGS testing results, and annotations were extracted from POP records.
Results: 1,442 tumor samples were sent for NGS testing as of 5/21/17 from 61 facilities. Rural patient testing (35%) was similar to VHA rurality (33%) and more than twice the US rate (14%). Most common diagnoses: lung (688: adeno 482, squamous 134), unknown (114), colorectal (103), skin (96), prostate (76), and H&N (66). Sample test requests increased rapidly after national implementation in July 2016 (23 samples/month prior to implementation to mean 126 samples/month 3 months later) as did the number of participating facilities (10/quarter to 39/month). Sequencing success rate increased from 68% to 71% over the same interval, while mean turn around time remained similar at 19.7 and 19.1 days, respectively. To date, 26 patients received a recommended drug outside a clinical trial, some more than 9 months after NGS. 5 additional patients had received an NGS-recommended drug prior to testing. NGS results are available for a cohort of 344 patients including: lung 200 (adeno 138, squamous 51), skin 28, LN 20, liver 19, GI 16. 979 variants were found most commonly in TP53, KRAS, STK11, APC, PIK3CA, and CDKN2A. 228 patients (66%) had actionable results (on-label drug 24, off-label drug 165, clinical trial 213). A PO consultation service (available by IFC) and a liquid biopsy are now available nationally.
Conclusions: Implementation of tumor NGS testing in VHA has been successful. Further program expansion, addition of hematological malignancies, deployment of informatics tools and efforts to expand access to appropriate drugs are ongoing.