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Lee CE, Lanman RB, Banks KC, Nagy RJ, Mortimer S, Simon DA, Chudova D, Eltoukhy H, Talasaz A, Lastra E, Kopetz S, Strickler JH. Identification of novel EGFR ectodomain mutations based on a large database of clinical circulating cell-free DNA sequencing tests. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tran HT, Elamin Y, Simon GR, Blumenschein GR, Tsao AS, Papadimitrakopoulou V, Gibbons DL, Fossella FV, Lanman RB, Banks KC, Byers LA, Zhang J, Heymach J. Clinical utilization of a CLIA-certified cell-free DNA (cfDNA) blood test for identification of targetable molecular alterations in patients with non-small cell lung cancer (NSCLC). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Williams CB, Goldberg R, Williams KA, De P, Klein J, Dey N, Young BM, Banks KC, Lee CE, Lanman RB, Ali SM, Ross JS, Miller VA, Solomon BM, Krie AK, Leyland-Jones B. Investigating the Utility of comprehensive genomic Profiling for patients with newly diagnosed breast cancer. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.tps11617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Lin SH, Rao X, Banks KC, Xu T, He J, Lanman RB, Talasaz A, Wang J, Liao ZX. Circulating tumor DNA as a non-invasive tool to identify patients at risk for recurrence after chemoradiotherapy in stage III non-small cell lung cancer. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.8553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Baumgartner JM, Banks KC, Lanman RB, Tran L, Kelly KJ, Lowy AM, Kurzrock R. Circulating tumor DNA before and after surgical resection in patients with peritoneal carcinomatosis. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e13000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Abdueva D, Chudova D, Lanman RB, Banks KC, Nagy RJ, Mortimer S, Talasaz A, Eltoukhy H, Kurzrock R. Detection, frequency and actionability of recurrent copy number gains detected by non-invasive liquid biopsy of 3,942 lung and breast cancer samples. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.11541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Zill OA, Mortimer S, Banks KC, Nagy RJ, Chudova D, Jackson C, Baca A, Ye JZ, Lanman RB, Talasaz A, Eltoukhy H, Kurzrock R. Somatic genomic landscape of over 15,000 patients with advanced-stage cancer from clinical next-generation sequencing analysis of circulating tumor DNA. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.lba11501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Morgensztern D, Devarakonda SH, Masood A, Waqar SN, Carmack AC, Banks KC, Lanman RB, Govindan R. Circulating cell-free tumor DNA (cfDNA) testing in small cell lung cancer. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Fairclough SR, Zill OA, Chudova D, Lee CE, Lanman RB, Banks KC, Nagy RJ, Mortimer S, Eltoukhy H, Talasaz A, Ramalingam SS. Case series of EGFR C797S mutations in non-small cell lung cancer identified with cell-free circulating tumor DNA next generation sequencing. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Schwaederle MC, Patel SP, Husain H, Ikeda M, Lanman RB, Banks KC, Talasaz A, Bazhenova L, Kurzrock R. Utility of liquid biopsies to assess circulating tumor DNA in patients with lung adenocarcinoma. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kapoor NS, Banks KC. Should multi-gene panel testing replace limited BRCA1/2 testing? A review of genetic testing for hereditary breast and ovarian cancers. World J Surg Proced 2016; 6:13-18. [DOI: 10.5412/wjsp.v6.i1.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 12/12/2015] [Accepted: 01/07/2016] [Indexed: 02/06/2023] Open
Abstract
Clinical testing of patients for hereditary breast and ovarian cancer syndromes began in the mid-1990s with the identification of the BRCA1 and BRCA2 genes. Since then, mutations in dozens of other genes have been correlated to increased breast, ovarian, and other cancer risk. The following decades of data collection and patient advocacy allowed for improvements in medical, legal, social, and ethical advances in genetic testing. Technological advances have made it possible to sequence multiple genes at once in a panel to give patients a more thorough evaluation of their personal cancer risk. Panel testing increases the detection of mutations that lead to increased risk of breast, ovarian, and other cancers and can better guide individualized screening measures compared to limited BRCA testing alone. At the same time, multi-gene panel testing is more time-and cost-efficient. While the clinical application of panel testing is in its infancy, many problems arise such as lack of guidelines for management of newly identified gene mutations, high rates of variants of uncertain significance, and limited ability to screen for some cancers. Through on-going concerted efforts of pooled data collection and analysis, it is likely that the benefits of multi-gene panel testing will outweigh the risks in the near future.
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Schwaederle M, Husain H, Fanta PT, Piccioni DE, Kesari S, Schwab RB, Banks KC, Lanman RB, Talasaz A, Parker BA, Kurzrock R. Detection rate of actionable mutations in diverse cancers using a biopsy-free (blood) circulating tumor cell DNA assay. Oncotarget 2016; 7:9707-17. [PMID: 26848768 PMCID: PMC4891078 DOI: 10.18632/oncotarget.7110] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/23/2016] [Indexed: 12/31/2022] Open
Abstract
Analysis of cell-free DNA using next-generation sequencing (NGS) is a powerful tool for the detection/monitoring of alterations present in circulating tumor DNA (ctDNA). Plasma extracted from 171 patients with a variety of cancers was analyzed for ctDNA (54 genes and copy number variants (CNVs) in three genes (EGFR, ERBB2 and MET)). The most represented cancers were lung (23%), breast (23%), and glioblastoma (19%). Ninety-nine patients (58%) had at least one detectable alteration. The most frequent alterations were TP53 (29.8%), followed by EGFR (17.5%), MET (10.5%), PIK3CA (7%), and NOTCH1 (5.8%). In contrast, of 222 healthy volunteers, only one had an aberration (TP53). Ninety patients with non-brain tumors had a discernible aberration (65% of 138 patients; in 70% of non-brain tumor patients with an alteration, the anomaly was potentially actionable). Interestingly, nine of 33 patients (27%) with glioblastoma had an alteration (6/33 (18%) potentially actionable). Overall, sixty-nine patients had potentially actionable alterations (40% of total; 69.7% of patients (69/99) with alterations); 68 patients (40% of total; 69% of patients with alterations), by a Food and Drug Administration (FDA) approved drug. In summary, 65% of diverse cancers (as well as 27% of glioblastomas) had detectable ctDNA aberration(s), with the majority theoretically actionable by an approved agent.
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Banks KC, Mortimer SAW, Zill OA, Lanman RB, Eltoukhy H, Talasaz A. Abstract B140: Genomic profiling of over 5,000 consecutive cancer patients with a CLIA-certified cell-free DNA NGS test: Analytic and clinical validity and utility. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-b140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Analysis of cell-free circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) enables non-invasive real-time testing. The Guardant360® (G360) ctDNA panel includes all NCCN-recommended solid tumor genomic targets and sequences complete exons of 68 genes for single nucleotide variants (SNVs), and fusions, amplifications and indels for a subset. We conducted updated validity studies for this larger panel.
Methods: Analytical sensitivity was assessed via serial dilution studies of cell-free DNA (cfDNA) with known alterations spiked into healthy cfDNA background. SNVs detected with G360 were compared to whole-exome sequencing at an outside lab for analytic specificity. Tissue NGS for fusions, SNVs, indels, and/or amplifications was compared to G360 results. Consecutive G360 tests over 12 months were analyzed for assay success rate, yield, mutant allele fractions (MAF), and actionability.
Results: Serial dilution studies confirmed the previously reported 0.1% lower limit of detection. The accuracy and analytic specificity studies were 98.6% concordant, with 3 putative false positives. Sanger sequencing by a 3rd lab for these discordant calls confirmed the G360 calls as true positives, verifying the previously reported >99.9999% specificity. Retrospective review of outside tumor test reports of 56 patients with varied genomic alterations found 90% concordance with G360 (77/86 variants: 4/4 fusions, 9/9 indels, 13/17 amps, 51/56 SNVs). Of 5,491 tests, 99.5% were successfully reported with somatic alterations found in 76% [median MAF 0.42% (range 0.1-92.8%)]. Lung, breast and colon cancers were most common (see Table). Overall, 10% of patients had >1 on-label matched therapy identified, 54% off-label, and 77% had clinical trial options. On-label matched therapy rates rose for lung adenocarcinoma (15%), breast (16%) and colon (16%) cancers (Table 1).
Conclusion: The updated G360 test achieves single-molecule sensitivity to 0.1% MAF and analytical specificity of >99.9999%, as reported previously. Clinical concordance of plasma to tissue-based NGS across all four types of genomic alterations was high, and actionability rose modestly, especially in lung, breast and colon cancer. Clinical utility included biopsy avoidance, rescue of tissue samples with insufficient DNA and tissue-false negatives due to tumor evolution and heterogeneity.
Table 1Cancer Type% of 4,888 unique patients% with ctDNA alterations identified% with on-label therapy options identified% with off-label therapy options identified% with clinical trial options identifiedMost commonly involved gene2nd most commonly involved gene3rd most commonly involved geneLung - ALL33%82%10%52%78%TP53 (55%)KRAS (18%)EGFR (18%)Lung adenocarcinoma11%82%15%56%78%TP53 (51%)EGFR (23%)KRAS (19%)Breast15%74%16%58%79%TP53 (43%)PIK3CA (28%)ERBB2/ESR1 (10%) / (9%)CRC12%82%16%72%88%TP53 (61%)APC (38%)KRAS (38%)PDAC7%70%3%57%72%TP53 (47%)KRAS (42%)PIK3CA (6%)Ovarian3%81%1%42%81%TP53 (69%)PIK3CA (15%)KRAS (11%)CUP3%85%0%64%83%TP53 (40%)KRAS (24%)PIK3CA (14%)All100%76%10%54%77%TP53 (50%)KRAS (17%)PIK3CA (14%)
Citation Format: Kimberly C. Banks, Stefanie A. W. Mortimer, Oliver A. Zill, Richard B. Lanman, Helmy Eltoukhy, AmirAli Talasaz. Genomic profiling of over 5,000 consecutive cancer patients with a CLIA-certified cell-free DNA NGS test: Analytic and clinical validity and utility. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B140.
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Kapoor NS, Curcio LD, Blakemore CA, Bremner AK, McFarland RE, West JG, Banks KC. Benefits and safety of multigene panel testing in patients at risk for hereditary breast cancer. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.28_suppl.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
16 Background: Recently introduced multi-gene panel testing including BRCA1 and BRCA2 genes (BRCA1/2) for hereditary cancer risk has raised concerns with the ability to detect all deleterious BRCA1/2 mutations compared to older methods of sequentially testing BRCA1/2 separately. The purpose of this study is to evaluate rates of pathogenic BRCA1/2mutations and variants of uncertain significance (VUS) between previous restricted algorithms of genetic testing and newer approaches of multi-gene testing. Methods: Data was collected retrospectively from 966 patients who underwent genetic testing at one of three sites from a single institution. Test results were compared between patients who underwent BRCA1/2testing only (limited group, n = 629) to those who underwent multi-gene testing with 5-43 cancer-related genes (panel group, n = 337). Results: Deleterious BRCA1/2 mutations were identified in 37 patients, with equivalent rates between limited and panel groups (4.0% vs 3.6%, respectively, p = 0.86). Thirty-nine patients had a BRCA1/2 VUS, with similar rates between limited and panel groups (4.5% vs 3.3%, respectively, p = 0.49). On multivariate analysis, there was no difference in detection of either BRCA1/2 mutations or VUS between both groups. Of patients undergoing panel testing, an additional 3.9% (n = 13) had non-BRCA pathogenic mutations and 13.4% (n = 45) had non-BRCA VUSs. Mutations in PALB2, CHEK2, and ATM were the most common non-BRCA mutations identified. Conclusions: Multi-gene panel testing detects pathogenic BRCA1/2 mutations at equivalent rates as limited testing and increases the diagnostic yield. Panel testing increases the VUS rate, mainly due to non-BRCA genes. Patients at risk for hereditary breast cancer can safely benefit from upfront, more efficient, multi-gene panel testing.
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Kapoor NS, Curcio LD, Blakemore CA, Bremner AK, McFarland RE, West JG, Banks KC. Multigene Panel Testing Detects Equal Rates of Pathogenic BRCA1/2 Mutations and has a Higher Diagnostic Yield Compared to Limited BRCA1/2 Analysis Alone in Patients at Risk for Hereditary Breast Cancer. Ann Surg Oncol 2015. [PMID: 26219241 DOI: 10.1245/s10434-015-4754-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Recently introduced multigene panel testing including BRCA1 and BRCA2 genes for hereditary cancer risk has raised concerns with the ability to detect all deleterious BRCA1/2 mutations compared to older methods of sequentially testing BRCA1/2 separately. The purpose of this study was to evaluate rates of pathogenic BRCA1/2 mutations and variants of uncertain significance (VUS) between previous restricted algorithms of genetic testing and newer approaches of multigene testing. METHODS Data was collected retrospectively from 966 patients who underwent genetic testing at one of three sites from a single institution. Test results were compared between patients who underwent BRCA1/2 testing only (limited group, n = 629) to those who underwent multigene testing with 5-43 cancer-related genes (panel group, n = 337). RESULTS Deleterious BRCA1/2 mutations were identified in 37 patients, with equivalent rates between limited and panel groups (4.0 vs. 3.6%, respectively, p = 0.86). Thirty-nine patients had a BRCA1/2 VUS, with similar rates between limited and panel groups (4.5 vs. 3.3%, respectively, p = 0.49). On multivariate analysis, there was no difference in detection of either BRCA1/2 mutations or VUS between both groups. Of patients undergoing panel testing, an additional 3.9 % (n = 13) had non-BRCA pathogenic mutations and 13.4% (n = 45) had non-BRCA VUSs. Mutations in PALB2, CHEK2, and ATM were the most common non-BRCA mutations identified. CONCLUSIONS Multigene panel testing detects pathogenic BRCA1/2 mutations at equivalent rates as limited testing and increases the diagnostic yield. Panel testing increases the VUS rate, mainly as a result of non-BRCA genes. Patients at risk for hereditary breast cancer can safely benefit from up-front, more efficient, multigene panel testing.
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Espenschied CR, MacDonald DJ, Culver JO, Sand S, Hurley K, Banks KC, Weitzel JN, Blazer KR. Closing the loop: action research in a multimodal hereditary cancer patient conference is an effective tool to assess and address patient needs. JOURNAL OF CANCER EDUCATION : THE OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER EDUCATION 2012; 27:467-477. [PMID: 22610836 PMCID: PMC3540105 DOI: 10.1007/s13187-012-0373-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This paper describes the use of action research in a patient conference to provide updated hereditary cancer information, explore patient and family member needs and experiences related to genetic cancer risk assessment (GCRA), elicit feedback on how to improve the GCRA process, and inform future research efforts. Invitees completed GCRA at City of Hope or collaborating facilities and had a BRCA mutation or a strong personal or family history of breast cancer. Action research activities were facilitated by surveys, round table discussions, and reflection time to engage participants, faculty, and researchers in multiple cycles of reciprocal feedback. The multimodal action research design effectively engaged conference participants to share their experiences, needs, and ideas for improvements to the GCRA process. Participants indicated that they highly valued the information and resources provided and desired similar future conferences. The use of action research in a patient conference is an innovative and effective approach to provide health education, elicit experiences, identify and help address needs of high-risk patients and their family members, and generate research hypotheses. Insights gained yielded valuable feedback to inform clinical care, future health services research, and continuing medical education activities. These methods may also be effective in other practice settings.
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Leachman SA, Carucci J, Kohlmann W, Banks KC, Asgari MM, Bergman W, Bianchi-Scarrà G, Brentnall T, Bressac-de Paillerets B, Bruno W, Curiel-Lewandrowski C, de Snoo FA, Debniak T, Demierre MF, Elder D, Goldstein AM, Grant-Kels J, Halpern AC, Ingvar C, Kefford RF, Lang J, MacKie RM, Mann GJ, Mueller K, Newton-Bishop J, Olsson H, Petersen GM, Puig S, Rigel D, Swetter SM, Tucker MA, Yakobson E, Zitelli JA, Tsao H. Selection criteria for genetic assessment of patients with familial melanoma. J Am Acad Dermatol 2009; 61:677.e1-14. [PMID: 19751883 DOI: 10.1016/j.jaad.2009.03.016] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 03/09/2009] [Accepted: 03/16/2009] [Indexed: 12/15/2022]
Abstract
Approximately 5% to 10% of melanoma may be hereditary in nature, and about 2% of melanoma can be specifically attributed to pathogenic germline mutations in cyclin-dependent kinase inhibitor 2A (CDKN2A). To appropriately identify the small proportion of patients who benefit most from referral to a genetics specialist for consideration of genetic testing for CDKN2A, we have reviewed available published studies of CDKN2A mutation analysis in cohorts with invasive, cutaneous melanoma and found variability in the rate of CDKN2A mutations based on geography, ethnicity, and the type of study and eligibility criteria used. Except in regions of high melanoma incidence, such as Australia, we found higher rates of CDKN2A positivity in individuals with 3 or more primary invasive melanomas and/or families with at least one invasive melanoma and two or more other diagnoses of invasive melanoma and/or pancreatic cancer among first- or second-degree relatives on the same side of the family. The work summarized in this review should help identify individuals who are appropriate candidates for referral for genetic consultation and possible testing.
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McKinnon W, Banks KC, Skelly J, Kohlmann W, Bennett R, Shannon K, Larson-Haidle J, Ashakaga T, Weitzel JN, Wood M. Survey of unaffected BRCA and mismatch repair (MMR) mutation positive individuals. Fam Cancer 2009; 8:363-9. [PMID: 19466581 DOI: 10.1007/s10689-009-9248-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 05/08/2009] [Indexed: 01/20/2023]
Abstract
Many individuals do not proceed with cancer predisposition testing due to fears of genetic discrimination (GD). We report the results of a survey of 47 unaffected, mutation positive individuals regarding insurance outcomes. Participants recruited from six different Cancer Risk Programs across the country were queried about their experiences with health, life, and disability insurance, as well as employment issues. Eighty-seven percent of participants carried a BRCA mutation and 87% were part of a group insurance plan at the time of testing. Forty-seven percent of participants self-paid for testing. Less than 10% of participants reported that their results were placed in the general medical record, while 43% did not know where their results were placed. Due to concerns about GD, 13% of participants stated they avoided changing jobs. Thirteen percent stated that their at-risk relatives had not undergone testing for the familial mutation due to fears about GD. Adverse events following genetic testing included two denials from private health insurers, one denial for average life insurance coverage and one denial for additional disability insurance. There were no reports of job discrimination. Results suggest fear of GD is prevalent, yet data do not support evidence that GD exists.
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Stefanik-Campisi C, Banks KC. Associate degree nursing students' presentations at psychiatric symposium reflect innovative teaching. Nurse Educ 1995; 20:11. [PMID: 7761022 DOI: 10.1097/00006223-199501000-00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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