1
|
Hernandez KM, Venkat A, Elbers DC, Bihn JR, Brophy MT, Do NV, La J, Liu Q, Prokhorenkov A, Metoki-Shlubsky N, Sung FC, Paller CJ, Fillmore NR, Grossman RL. Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons. Cold Spring Harb Mol Case Stud 2023; 9:a006298. [PMID: 38050021 PMCID: PMC10815278 DOI: 10.1101/mcs.a006298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/31/2023] [Indexed: 12/06/2023] Open
Abstract
Veterans are at an increased risk for prostate cancer, a disease with extraordinary clinical and molecular heterogeneity, compared with the general population. However, little is known about the underlying molecular heterogeneity within the veteran population and its impact on patient management and treatment. Using clinical and targeted tumor sequencing data from the National Veterans Affairs health system, we conducted a retrospective cohort study on 45 patients with advanced prostate cancer in the Veterans Precision Oncology Data Commons (VPODC), most of whom were metastatic castration-resistant. We characterized the mutational burden in this cohort and conducted unsupervised clustering analysis to stratify patients by molecular alterations. Veterans with prostate cancer exhibited a mutational landscape broadly similar to prior studies, including KMT2A and NOTCH1 mutations associated with neuroendocrine prostate cancer phenotype, previously reported to be enriched in veterans. We also identified several potential novel mutations in PTEN, MSH6, VHL, SMO, and ABL1 Hierarchical clustering analysis revealed two subgroups containing therapeutically targetable molecular features with novel mutational signatures distinct from those reported in the Catalogue of Somatic Mutations in Cancer database. The clustering approach presented in this study can potentially be used to clinically stratify patients based on their distinct mutational profiles and identify actionable somatic mutations for precision oncology.
Collapse
Affiliation(s)
| | - Aarti Venkat
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Danne C Elbers
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - John R Bihn
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
| | - Mary T Brophy
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Nhan V Do
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Jennifer La
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Qiong Liu
- Frederick National laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Andrew Prokhorenkov
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Noah Metoki-Shlubsky
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Feng-Chi Sung
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
| | - Channing J Paller
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA;
| | - Nathanael R Fillmore
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA;
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Robert L Grossman
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
- Open Commons Consortium, Chicago, Illinois 60611, USA
| |
Collapse
|
2
|
Mutational profiles of head and neck squamous cell carcinomas based upon human papillomavirus status in the Veterans Affairs National Precision Oncology Program. J Cancer Res Clin Oncol 2023; 149:69-77. [PMID: 36117189 DOI: 10.1007/s00432-022-04358-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/12/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Patients with advanced head and neck squamous cell carcinoma (HNSCC) associated with human papillomavirus (HPV) demonstrate favorable clinical outcomes compared to patients bearing HPV-negative HNSCC. We sought to characterize the association between HPV status and mutational profiles among patients served by the Veterans Health Administration (VHA). METHODS We performed a retrospective analysis of all Veterans with primary HNSCC tumors who underwent next-generation sequencing (NGS) through the VHA's National Precision Oncology Program between July 2016 and February 2019. HPV status was determined by clinical pathology reports of p16 immunohistochemical staining; gene variant pathogenicity was classified using OncoKB, an online precision oncology knowledge database, and mutation frequencies were compared using Fisher's exact test. RESULTS A total of 79 patients met inclusion criteria, of which 48 (60.8%) had p16-positive tumors. Patients with p16-negative HNSCC were more likely to have mutations in TP53 (p < 0.0001), and a trend towards increased mutation frequency was observed within NOTCH1 (p = 0.032) and within the composite CDK/Rb pathway (p = 0.065). Mutations in KRAS, NRAS, HRAS, and FBXW7 were exclusively identified within p16-positive tumors, and a trend towards increased frequency was observed within the PI3K pathway (p = 0.051). No difference in overall mutational burden was observed between the two groups. CONCLUSIONS In accordance with the previous studies, no clear molecular basis for improved prognosis among patients harboring HPV-positive disease has been elucidated. Though no targeted therapies are approved based upon HPV-status, current efforts to trial PI3K inhibitors and mTOR inhibitors across patients with HPV-positive disease bear genomic rationale based upon the current findings.
Collapse
|
3
|
Becker DJ, Lee KM, Lee SY, Lynch KE, Makarov DV, Sherman SE, Morrissey CD, Kelley MJ, Lynch JA. Uptake of KRAS Testing and Anti-EGFR Antibody Use for Colorectal Cancer in the VA. JCO Precis Oncol 2021; 5:PO.20.00359. [PMID: 34250412 DOI: 10.1200/po.20.00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 11/20/2022] Open
Abstract
Advances in precision oncology, including RAS testing to predict response to epidermal growth factor receptor monoclonal antibodies (EGFR mAbs) in colorectal cancer (CRC), can extend patients' lives. We evaluated uptake and clinical use of KRAS molecular testing, guideline recommended since 2010, in the Veterans Affairs Healthcare System (VA). MATERIALS AND METHODS We conducted a retrospective cohort study of patients with stage IV CRC diagnosed in the VA 2006-2015. We gathered clinical, demographic, molecular, and treatment data from the VA Corporate Data Warehouse and 29 commercial laboratories. We performed multivariable analyses of associations between patient characteristics, KRAS testing, and EGFR mAb treatment. RESULTS Among 5,943 patients diagnosed with stage IV CRC, only 1,053 (17.7%) had KRAS testing. Testing rates increased from 2.3% in 2006 to 28.4% in 2013. In multivariable regression, older patients (odds ratio, 0.17; 95% CI, 0.09 to 0.32 for ≥ age 85 v < 45 years) and those treated in the Northeast and South regions were less likely, and those treated at high-volume CRC centers were more likely to have KRAS testing (odds ratio, 2.32; 95% CI, 1.48 to 3.63). Rates of potentially guideline discordant care were high: 64.3% (321/499) of KRAS wild-type (WT) went untreated with EGFR mAb and 8.8% (401/4,570) with no KRAS testing received EGFR mAb. Among KRAS-WT patients, survival was better for patients who received EGFR mAb treatment (29.6 v 18.8 months; P < .001). CONCLUSION We found underuse of KRAS testing in advanced CRC, especially among older patients and those treated at lower-volume CRC centers. We found high rates of potentially guideline discordant underuse of EGFR mAb in patients with KRAS-WT tumors. Efforts to understand barriers to precision oncology are needed to maximize patient benefit.
Collapse
Affiliation(s)
- Daniel J Becker
- NYU Grossman School of Medicine, New York, NY.,VA-New York Harbor Health Care System, New York, NY
| | - Kyung M Lee
- VA Informatics and Computing Infrastructure, Washington, DC
| | | | - Kristine E Lynch
- VA Informatics and Computing Infrastructure, Washington, DC.,University of Utah, Salt Lake City, UT
| | - Danil V Makarov
- NYU Grossman School of Medicine, New York, NY.,VA-New York Harbor Health Care System, New York, NY
| | - Scott E Sherman
- NYU Grossman School of Medicine, New York, NY.,VA-New York Harbor Health Care System, New York, NY
| | | | - Michael J Kelley
- Durham Veteran Affairs Medical Center, Durham, NC.,Duke University, Durham, NC
| | - Julie A Lynch
- VA Salt Lake City Healthcare System, Salt Lake City, UT.,University of Massachusetts, Boston, MA
| |
Collapse
|
4
|
EGFR mutation testing and TKI treatment patterns among veterans with stage III and IV non-small cell lung cancer. Cancer Treat Res Commun 2021; 27:100327. [PMID: 33549984 DOI: 10.1016/j.ctarc.2021.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) mutation testing is recommended in metastatic non-small cell lung cancer (NSCLC). The objective of this study was to assess changes in EGFR mutation testing patterns and tyrosine kinase inhibitor (TKI) use in US veterans with stage III-IV NSCLC between 2013 and 2017. PATIENTS AND METHODS Retrospective study using linked data from Department of Veterans Affairs (VA) Cancer Registry System, Corporate Data Warehouse, commercial laboratories, and clinical notes. Generalized linear mixed models accounting for clustering by VA facility were used to determine factors associated with EGFR mutation testing. RESULTS From 2013 to 2017, EGFR mutation testing increased from 29.5% to 38.4% among veterans with stage III-IV NSCLC and from 47.0% to 57.4% among veterans with stage IV non-squamous disease. Factors associated with increased odds of testing included being married, Medicare enrollment, and adenocarcinoma histology. Factors associated with decreased odds of testing included Medicaid eligibility, stage III disease, increasing age, being a current or former smoker, increasing Charlson-Deyo comorbidity score, and receiving cancer care in the South. Appropriate use of a TKI rose from 2013 to 2017 (17.2% to 74.1%). CONCLUSION EGFR mutation testing rates increased to almost 60% in the stage IV non-squamous NSCLC population in 2017, with residual opportunity for further increase. Several sociodemographic characteristics, comorbidities, and geographic regions were associated with EGFR mutation testing suggestive of inequitable testing decisions. Appropriate use of TKI improved drastically from 2013 to 2017 demonstrating rapidly changing practice patterns through the adoption phase of new treatment options.
Collapse
|
5
|
Katsoulakis E, Duffy JE, Hintze B, Spector NL, Kelley MJ. Comparison of Annotation Services for Next-Generation Sequencing in a Large-Scale Precision Oncology Program. JCO Precis Oncol 2020; 4:PO.19.00118. [PMID: 32923873 PMCID: PMC7446349 DOI: 10.1200/po.19.00118] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Next-generation sequencing (NGS) multigene panel testing has become widespread, including the Veterans Affairs (VA), through the VA National Precision Oncology Program (NPOP). The interpretation of genomic alterations remains a bottleneck for realizing precision medicine. We sought to examine the concordance for pathogenicity determination and clinical actionability of annotation services in NPOP. METHODS Unique gene variants were generated from NGS gene panel results using two sequencing services. For each unique gene variant, annotations were provided through N-of-One (NoO), IBM Watson for Genomics (WfG), and OncoKB. Annotations for pathogenicity (all three sources) and actionability (WfG and OncoKB) were examined for concordance. Cohen's kappa statistic was calculated to measure agreement between annotation services. RESULTS Among 1,227 NGS results obtained between 2015 and 2017, 1,388 unique variants were identified in 117 genes. The genes with the largest number of variants included TP53 (270), STK11 (92), and CDKN2A (81). The most common cancer type was lung adenocarcinoma (440), followed by colon adenocarcinoma (113). For pathogenic and likely pathogenic variants, there was 30% agreement between WfG and NoO (kappa, -0.26), 76% agreement between WfG and OncoKB (kappa, 0.22), and 42% agreement between NoO and OncoKB (kappa, -0.07). For level 1 drug actionability of gene variant-diagnosis combinations, there was moderate agreement between WfG and OncoKB (96.9%; kappa, 0.44), with 27 combinations identified as level 1 by both services, 58 by WfG alone, and 6 variants by OncoKB alone. CONCLUSION There is substantial variability in pathogenicity assessment of NGS variants in solid tumors by annotation services. In addition, there was only moderate agreement in level 1 therapeutic actionability recommendations between WfG and OncoKB. Improvement in the precision of NGS multigene panel annotation is needed.
Collapse
Affiliation(s)
- Evangelia Katsoulakis
- Department of Radiation Oncology, James A. Haley Veterans Affairs Healthcare System, Tampa, FL
| | | | - Bradley Hintze
- VA National Oncology Program Office, Durham, NC
- Medical Service, Durham VA Healthcare System, Durham, NC
| | - Neil L. Spector
- VA National Oncology Program Office, Durham, NC
- Medical Service, Durham VA Healthcare System, Durham, NC
- Department of Medicine and Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Michael J. Kelley
- VA National Oncology Program Office, Durham, NC
- Medical Service, Durham VA Healthcare System, Durham, NC
- Department of Medicine and Duke Cancer Institute, Duke University Medical Center, Durham, NC
| |
Collapse
|