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  • 1
    In: The Journal of Rural Health, Wiley, Vol. 38, No. 1 ( 2022-01), p. 5-13
    Abstract: Large‐scale genomic sequencing studies are driving oncology drug development. However, rural populations, like those residing in Appalachian Kentucky, are underrepresented in these efforts. In this study, we determined the frequency of participation, reasons for nonparticipation, and factors predicting the decision to participate in the Total Cancer Care (TCC) prospective genomic cohort study. Methods A total of 1,188 patients were invited to enroll in the TCC prospective cohort from December 2018 to May 2019. Declining patients were queried for their rationale for nonparticipation and their patient data were obtained from the Kentucky Cancer Registry (KCR). Logistic regression was used to assess the association between characteristics and study participation. The association of study participation with survival was modeled with Cox proportional‐hazards regression. Results 90.9% (1,081) patients consented to participate. In multivariate analysis, factors significantly associated with participation were age, gender, treatment status, and race. Though overall more women participated in the study, men were more likely to participate than women when invited (OR 1.57). Younger, Caucasian individuals who had received chemotherapy, but not surgery, were also more likely to participate. Patients in the Kentucky Appalachian cohort were primarily rural, had less educational attainment, and lower socioeconomic status. Kentucky Appalachian patients were no less likely to enroll in TCC than non‐Appalachian patients. Consented individuals had higher overall survival compared to those who declined. Conclusion Though minorities, those with low socioeconomic status, and rural populations are underrepresented in genomic studies, they were no less likely to participate when given the opportunity, and participation was associated with better clinical outcomes.
    Type of Medium: Online Resource
    ISSN: 0890-765X , 1748-0361
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2159889-7
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  • 2
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2018
    In:  Cancer Chemotherapy and Pharmacology Vol. 81, No. 5 ( 2018-5), p. 965-968
    In: Cancer Chemotherapy and Pharmacology, Springer Science and Business Media LLC, Vol. 81, No. 5 ( 2018-5), p. 965-968
    Type of Medium: Online Resource
    ISSN: 0344-5704 , 1432-0843
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 1458488-8
    SSG: 15,3
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  • 3
    In: Cancers, MDPI AG, Vol. 13, No. 18 ( 2021-09-08), p. 4524-
    Abstract: The purpose of this study was to determine the frequency of clinically actionable treatment-relevant germline pharmacogenomic variants in patients with cancer and assess the real-world clinical utility of universal screening using whole-exome sequencing in this population. Cancer patients underwent research-grade germline whole-exome sequencing as a component of sequencing for somatic variants. Analysis in a clinical bioinformatics pipeline identified clinically actionable pharmacogenomic variants. Clinical Pharmacogenetics Implementation Consortium guidelines defined clinical actionability. We assessed clinical utility by reviewing electronic health records to determine the frequency of patients receiving pharmacogenomically actionable anti-cancer agents and associated outcomes. This observational study evaluated 291 patients with cancer. More than 90% carried any clinically relevant pharmacogenetic variant. At least one disease-relevant variant impacting anti-cancer agents was identified in 26.5% (77/291). Nine patients with toxicity-associated pharmacogenomic variants were treated with a relevant medication: seven UGT1A1 intermediate metabolizers were treated with irinotecan, one intermediate DPYD metabolizer was treated with 5-fluorouracil, and one TPMT poor metabolizer was treated with mercaptopurine. These individuals were more likely to experience treatment-associated toxicities than their wild-type counterparts (p = 0.0567). One UGT1A1 heterozygote died after a single dose of irinotecan due to irinotecan-related adverse effects. Identifying germline pharmacogenomic variants was feasible using whole-exome sequencing. Actionable pharmacogenetic variants are common and relevant to patients undergoing cancer treatment. Universal pharmacogenomic screening can be performed using whole-exome sequencing data originally obtained for quality control purposes and could be considered for patients who are candidates for irinotecan, 5-fluorouracil, capecitabine, and mercaptopurine.
    Type of Medium: Online Resource
    ISSN: 2072-6694
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2527080-1
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  • 4
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. 10602-10602
    Abstract: 10602 Background: The American College of Medical Genomics and Genetics (ACMG) has identified genes with highly penetrant phenotypes with treatment, prevention, or early disease identification strategies called secondary findings (SF) genes. ACMG recommends clinical laboratories report pathogenic/likely pathogenic (P/LP) SF variants identified during genomic testing. Cancer patients may undergo germline sequencing as part of research studies that can identify valuable SF variants. The objective of this institutional sub-study is to evaluate the feasibility of using ACMG SF genes to assess hereditary disease risk in a cancer population undergoing research sequencing. Methods: Between June 2017 and January 2021, patients unselected for family history, disease site, or stage enrolled in the prospective, observational Total Cancer Care study. Patients underwent research-grade germline whole exome sequencing, with bioinformatic analysis in a CLIA certified laboratory to identify P/LP variants in any ACMG SF v2.0 genes. P/LP variants were reported to treating oncologists with recommendations for genetic counseling referral. We assessed if patients with P/LP variants met NCCN guideline-directed germline testing criteria to quantify benefit from reporting research results. Results: We enrolled 786 patients, which included those with gynecologic (182, 23%), colorectal (124, 16%), lung/bronchus (83, 11%), and head/neck (82, 10%) cancers. The median age was 61 (IQR 52-68) years, 57% were female, 96% were non-Hispanic White, 51% had stage III/IV disease, and 64% resided in an Appalachian community. We identified 57 patients (7%) with cancer predisposition and 14 (2%) with other hereditary disease variants. 2021 NCCN guideline-directed testing would have missed 59% (42/71) of these patients. Incremental high penetrance cancer gene variants included: BRCA1 – endometrial cancer (n = 1); BRCA2– cholangiocarcinoma (n = 1), colon neuroendocrine tumor (n = 1), and lung (n = 2), endometrial (n = 1), and non-epithelial ovarian (n = 1) cancers; MSH6 – duodenal cancer (n = 1); SDHAF2 – non-melanoma skin cancer (n = 1); SDHB – head/neck cancer (n = 1); and TP53 – CNS tumor (n = 1) and head/neck cancer (n = 1). We identified patients at risk for other hereditary diseases including hypertrophic/dilated cardiomyopathy (n = 1), malignant hyperthermia (n = 3), arrhythmogenic right ventricular cardiomyopathy (n = 1), Romano-Ward long QT / Brugada syndromes (n = 4), familial hypercholesterolemia (n = 4), and ornithine transcarbamylase deficiency (n = 1). Conclusions: Reporting germline variants identified during research sequencing is feasible and can benefit cancer patients and their relatives. Though not traditionally assessed, non-cancer predisposition genetic variants may have important intervention opportunities and unexpected patterns may have oncologic implications that require further study.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
    detail.hit.zdb_id: 2005181-5
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  • 5
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. 2026-2026
    Abstract: 2026 Background: Bevacizumab remains the standard second line therapy in glioblastoma (GBM) with reported improved progression free survival, but not overall survival. We investigated a large clinico-genomic database of GBM patients treated with bevacizumab for molecular alterations associated with treatment outcome. Methods: Molecular profiles of GBM were tested by next-generation sequencing (NGS) of DNA (592 genes, NextSeq or whole-exome sequencing, Novaseq) and RNA (whole transcriptome sequencing, NovaSeq) at Caris Life Sciences (Phoenix, AZ). Gene amplification was determined by NGS with a threshold of 〉 = 6 copies. Real-world survival information was obtained from insurance claims data. Time-on-treatment (TOT) of bevacizumab was calculated from start to finish of treatment while post-bevacizumab overall survival (bevOS) from start of bevacizumab to last day of contact. Short-term (ST) and long-term (LT) responders were defined as those with TOT ≤6 months and ≥1 year, respectively. Kaplan-Meier estimates were calculated and significance was determined as p values of 〈 0.05. For molecular comparisons, Fisher’s exact tests and Mann-Whiney U were used when appropriate. Results: Among the total of 383 ST and 107 LT patients identified, no significant difference in gender or age were seen. The LT cohort had significantly longer bevOS compared to the ST cohort (HR 0.27, [95% CI: 0.28-0.35], p 〈 0.0001). Interestingly, CDK4 amplification was seen in 23% (18/78) of LT patients but only 7% (21/300, p = 0.0002) of ST. When investigating the total cohort of 498 GBM treated with bevacizumab, CDK4 amplified patients demonstrated significantly improved TOT compared to non-amplified (HR: 0.639, [0.48-0.85, p = 0.002]). Conversely, the ST cohort had significantly more EGFR amplifications than the LT cohort (43%, 130/300 vs. 19%, 15/79, p 〈 0.0001). In the total bevacizumab-treated cohort, EGFR-amplified GBM had significantly worse TOT on bevacizumab than non-EGFR amplified GBM (HR 1.387, [1.15-1.67], p 〈 0.001). No associations were seen in other alterations explored including PIK3CA mutation (HR = 0.81 [0.587-1.113], p = 0.2), EGFR mutation (HR: 1.209, [0.977-1.495] , p = 0.1) or RAF1 (HR: 0.647, [0.318-1.317], p = 0.2). Conclusions: Using a large clinical genomic database with GBM subjected to comprehensive molecular profiling, we demonstrated that amplification of CDK4 and EGFR were associated with long-term and short-term responses to bevacizumab, respectively. This warrants further investigation in independent cohorts controlled for age and other prognostic factors. If confirmed, a genetic basis for treatment optimization may provide meaningful clinical outcomes.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
    detail.hit.zdb_id: 2005181-5
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