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Romagnoli KM, Salvati ZM, Johnson DK, Ramey HM, Chang AR, Williams MS. Genomics in nephrology: identifying informatics opportunities to improve diagnosis of genetic kidney disorders using a human-centered design approach. J Am Med Inform Assoc 2024; 31:1247-1257. [PMID: 38497946 PMCID: PMC11105128 DOI: 10.1093/jamia/ocae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Genomic kidney conditions often have a long lag between onset of symptoms and diagnosis. To design a real time genetic diagnosis process that meets the needs of nephrologists, we need to understand the current state, barriers, and facilitators nephrologists and other clinicians who treat kidney conditions experience, and identify areas of opportunity for improvement and innovation. METHODS Qualitative in-depth interviews were conducted with nephrologists and internists from 7 health systems. Rapid analysis identified themes in the interviews. These were used to develop service blueprints and process maps depicting the current state of genetic diagnosis of kidney disease. RESULTS Themes from the interviews included the importance of trustworthy resources, guidance on how to order tests, and clarity on what to do with results. Barriers included lack of knowledge, lack of access, and complexity surrounding the case and disease. Facilitators included good user experience, straightforward diagnoses, and support from colleagues. DISCUSSION The current state of diagnosis of kidney diseases with genetic etiology is suboptimal, with information gaps, complexity of genetic testing processes, and heterogeneity of disease impeding efficiency and leading to poor outcomes. This study highlights opportunities for improvement and innovation to address these barriers and empower nephrologists and other clinicians who treat kidney conditions to access and use real time genetic information.
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Affiliation(s)
- Katrina M Romagnoli
- Department of Population Health Sciences, Geisinger Clinic, Danville, PA 17822, United States
| | - Zachary M Salvati
- Department of Genomic Health, Geisinger, Danville, PA 17822, United States
| | - Darren K Johnson
- Department of Genomic Health, Geisinger, Danville, PA 17822, United States
| | - Heather M Ramey
- Department of Genomic Health, Geisinger, Danville, PA 17822, United States
| | - Alexander R Chang
- Department of Population Health Sciences, Geisinger Clinic, Danville, PA 17822, United States
- Department of Nephrology, Geisinger, Danville, PA 17822, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger, Danville, PA 17822, United States
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Lennon AM, Buchanan AH, Rego SP, Choudhry OA, Elias PZ, Sadler JR, Roberta J, Zhang Y, Flake DD, Honushefsky A, Salvati ZM, Sheridan K, Wagner ES, Fishman EK, Papadopoulos N, Beer TM. Outcomes following a false positive multi-cancer early detection (MCED) test: Results from DETECT-A, the first large, prospective, interventional MCED study. Cancer Prev Res (Phila) 2024:745184. [PMID: 38705577 DOI: 10.1158/1940-6207.capr-23-0451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/23/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
Guideline recommended standard of care (SoC) screening is available for four cancer types; most cancer-related deaths are caused by cancers without SoC screening. DETECT-A is the first prospective interventional trial evaluating an MCED blood test (CancerSEEK) in women without a history of cancer, providing the first opportunity to assess the long-term outcomes of individuals with false positive (FP) MCED results. This prospective analysis of DETECT-A participants with FP results evaluates the performance of an imaging-based diagnostic workflow and examines cancer risk following a FP result. This analysis included all DETECT-A participants with a positive CancerSEEK test and subsequent flourine-18 fluorodeoxyglucose positron emission tomography-IV contrast enhanced computed tomography (18-F-FDG PET-CT) imaging and clinical workup indicating no evidence of cancer within one year of enrollment (n=98). Medical records, study interactions, and study surveys were used to assess cancer incidence, treatments, and clinical outcomes through August 2023. Ninety-five of 98 participants with a FP result remained cancer-free with a median follow-up of 3.6 years (IQR: 2.5-4.1) from determination of FP status. Three incident cancers were observed over the follow-up period. One bilateral stage IIIC ovarian cancer was diagnosed 1.9 years after determination of FP status; two stage I breast cancers were diagnosed 0.1 and 1.6 years from determination of FP status. The annual incidence rate of cancer during follow-up from FP determination was 1.0% (95% CI: 0.2%-2.8%). Participants with a positive CancerSEEK test who underwent 18-F-FDG PET-CT and clinical workup without cancer findings had low risk for cancer over the following several years.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tomasz M Beer
- Exact Sciences (United States), Madison, WI, United States
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Schneider JL, Firemark AJ, Gille S, Davis J, Pawloski PA, Liang SY, Epstein MM, Lowery J, Lu CY, Sharaf RN, Burnett-Hartman AN, Schlieder V, Salvati ZM, Cragun D, Rahm AK, Hunter JE. "Go ahead and screen" - advice to healthcare systems for routine lynch syndrome screening from interviews with newly diagnosed colorectal cancer patients. Hered Cancer Clin Pract 2023; 21:24. [PMID: 37978552 PMCID: PMC10657118 DOI: 10.1186/s13053-023-00270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Lynch syndrome (LS) is the most common cause of inherited colorectal cancer (CRC). Universal tumor screening (UTS) of newly diagnosed CRC cases is recommended to aid in diagnosis of LS and reduce cancer-related morbidity and mortality. However, not all health systems have adopted UTS processes and implementation may be inconsistent due to system and patient-level complexities. METHODS To identify barriers, facilitators, and suggestions for improvements of the UTS process from the patient perspective, we conducted in-depth, semi-structured interviews with patients recently diagnosed with CRC, but not screened for or aware of LS. Patients were recruited from eight regionally diverse US health systems. Interviews were conducted by telephone, 60-minutes, audio-recorded, and transcribed. An inductive, constant comparative analysis approach was employed. RESULTS: We completed 75 interviews across the eight systems. Most participants were white (79%), about half (52%) were men, and the mean age was 60 years. Most self-reported either no (60%) or minimal (40%) prior awareness of LS. Overall, 96% of patients stated UTS should be a routine standard of care for CRC tumors, consistently citing four primary motivations for wanting to know their LS status and engage in the process for LS identification: "knowledge is power"; "family knowledge"; "prevention and detection"; and "treatment and surveillance." Common concerns pertaining to the process of screening for and identifying LS included: creating anticipatory worry for patients, the potential cost and the accuracy of the genetic test, and possibly having one's health insurance coverage impacted by the LS diagnosis. Patients suggested health systems communicate LS results in-person or by phone from a trained expert in LS; offer proactive verbal and written education about LS, the screening steps, and any follow-up surveillance recommendations; and support patients in communicating their LS screening to any of their blood relatives. CONCLUSION Our qualitative findings demonstrate patients with CRC have a strong desire for healthcare systems to regularly implement and offer UTS. Patients offer key insights for health systems to guide future implementation and optimization of UTS and other LS screening programs and maximize diagnosis of individuals with LS and improve cancer-related surveillance and outcomes. TRIAL REGISTRATION Not available: not a clinical trial.
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Affiliation(s)
- Jennifer L Schneider
- Kaiser Permanente Center for Health Research, 3800 N Interstate Ave, 97227, Portland, OR, USA.
| | - Alison J Firemark
- Kaiser Permanente Center for Health Research, 3800 N Interstate Ave, 97227, Portland, OR, USA
| | - Sara Gille
- Kaiser Permanente Center for Health Research, 3800 N Interstate Ave, 97227, Portland, OR, USA
| | - James Davis
- Kaiser Permanente Center for Health Research, 3800 N Interstate Ave, 97227, Portland, OR, USA
| | | | - Su-Ying Liang
- Palo Alto Medical Foundation Research Institute, Palo Alto, CA, USA
| | - Mara M Epstein
- Division of Health Systems Science, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jan Lowery
- University of Colorado Cancer Center, Aurora, CO, USA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Ravi N Sharaf
- Division of Gastroenterology, Department of Medicine, Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Deborah Cragun
- University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, Fl, USA
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4
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Savatt JM, Johns A, Schwartz MLB, McDonald WS, Salvati ZM, Oritz NM, Masnick M, Hatchell K, Hao J, Buchanan AH, Williams MS. Testing and Management of Iron Overload After Genetic Screening-Identified Hemochromatosis. JAMA Netw Open 2023; 6:e2338995. [PMID: 37870835 PMCID: PMC10594145 DOI: 10.1001/jamanetworkopen.2023.38995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023] Open
Abstract
Importance HFE gene-associated hereditary hemochromatosis type 1 (HH1) is underdiagnosed, resulting in missed opportunities for preventing morbidity and mortality. Objective To assess whether screening for p.Cys282Tyr homozygosity is associated with recognition and management of asymptomatic iron overload. Design, Setting, and Participants This cross-sectional study obtained data from the Geisinger MyCode Community Health Initiative, a biobank of biological samples and linked electronic health record data from a rural, integrated health care system. Participants included those who received a p.Cys282Tyr homozygous result via genomic screening (MyCode identified), had previously diagnosed HH1 (clinically identified), and those negative for p.Cys282Tyr homozygosity between 2017 and 2018. Data were analyzed from April 2020 to August 2023. Exposure Disclosure of a p.Cys282Tyr homozygous result. Main Outcomes and Measures Postdisclosure management and HFE-associated phenotypes in MyCode-identified participants were analyzed. Rates of HFE-associated phenotypes in MyCode-identified participants were compared with those of clinically identified participants. Relevant laboratory values and rates of laboratory iron overload among participants negative for p.Cys282Tyr homozygosity were compared with those of MyCode-identified participants. Results A total of 86 601 participants had available exome sequences at the time of analysis, of whom 52 994 (61.4%) were assigned female at birth, and the median (IQR) age was 62.0 (47.0-73.0) years. HFE p.Cys282Tyr homozygosity was disclosed to 201 participants, of whom 57 (28.4%) had a prior clinical HH1 diagnosis, leaving 144 participants who learned of their status through screening. There were 86 300 individuals negative for p.Cys282Tyr homozygosity. After result disclosure, among MyCode-identified participants, 99 (68.8%) had a recommended laboratory test and 36 (69.2%) with laboratory or liver biopsy evidence of iron overload began phlebotomy or chelation. Fifty-three (36.8%) had iron overload; rates of laboratory iron overload were higher in MyCode-identified participants than participants negative for p.Cys282Tyr homozygosity (females: 34.1% vs 2.1%, P < .001; males: 39.0% vs 2.9%, P < .001). Iron overload (females: 34.1% vs 79.3%, P < .001; males: 40.7% vs 67.9%, P = .02) and some liver-associated phenotypes were observed at lower frequencies in MyCode-identified participants compared with clinically identified individuals. Conclusions and Relevance Results of this cross-sectional study showed the ability of genomic screening to identify undiagnosed iron overload and encourage relevant management, suggesting the potential benefit of population screening for HFE p.Cys282Tyr homozygosity. Further studies are needed to examine the implications of genomic screening for health outcomes and cost-effectiveness.
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Affiliation(s)
| | - Alicia Johns
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | - Marci L. B. Schwartz
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Nicole M. Oritz
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | - Max Masnick
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | | | - Jing Hao
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
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Salvati ZM, Rahm AK, Williams MS, Ladd I, Schlieder V, Atondo J, Schneider JL, Epstein MM, Lu CY, Pawloski PA, Sharaf RN, Liang SY, Burnett-Hartman AN, Hunter JE, Burton-Akright J, Cragun D. A picture is worth a thousand words: advancing the use of visualization tools in implementation science through process mapping and matrix heat mapping. Implement Sci Commun 2023; 4:43. [PMID: 37098602 PMCID: PMC10127322 DOI: 10.1186/s43058-023-00424-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/03/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Identifying key determinants is crucial for improving program implementation and achieving long-term sustainment within healthcare organizations. Organizational-level complexity and heterogeneity across multiple stakeholders can complicate our understanding of program implementation. We describe two data visualization methods used to operationalize implementation success and to consolidate and select implementation factors for further analysis. METHODS We used a combination of process mapping and matrix heat mapping to systematically synthesize and visualize qualitative data from 66 stakeholder interviews across nine healthcare organizations, to characterize universal tumor screening programs of all newly diagnosed colorectal and endometrial cancers and understand the influence of contextual factors on implementation. We constructed visual representations of protocols to compare processes and score process optimization components. We also used color-coded matrices to systematically code, summarize, and consolidate contextual data using factors from the Consolidated Framework for Implementation Research (CFIR). Combined scores were visualized in a final data matrix heat map. RESULTS Nineteen process maps were created to visually represent each protocol. Process maps identified the following gaps and inefficiencies: inconsistent execution of the protocol, no routine reflex testing, inconsistent referrals after a positive screen, no evidence of data tracking, and a lack of quality assurance measures. These barriers in patient care helped us define five process optimization components and used these to quantify program optimization on a scale from 0 (no program) to 5 (optimized), representing the degree to which a program is implemented and optimally maintained. Combined scores within the final data matrix heat map revealed patterns of contextual factors across optimized programs, non-optimized programs, and organizations with no program. CONCLUSIONS Process mapping provided an efficient method to visually compare processes including patient flow, provider interactions, and process gaps and inefficiencies across sites, thereby measuring implementation success via optimization scores. Matrix heat mapping proved useful for data visualization and consolidation, resulting in a summary matrix for cross-site comparisons and selection of relevant CFIR factors. Combining these tools enabled a systematic and transparent approach to understanding complex organizational heterogeneity prior to formal coincidence analysis, introducing a stepwise approach to data consolidation and factor selection.
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Affiliation(s)
- Zachary M Salvati
- Geisinger Department of Genomic Health, 100 N. Academy Ave, Danville, PA, 17822, USA.
| | - Alanna Kulchak Rahm
- Geisinger Department of Genomic Health, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Marc S Williams
- Geisinger Department of Genomic Health, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Ilene Ladd
- Geisinger Department of Genomic Health, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Victoria Schlieder
- Geisinger Department of Genomic Health, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Jamie Atondo
- Geisinger Department of Genomic Health, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Jennifer L Schneider
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97202, USA
| | - Mara M Epstein
- Department of Medicine and the Meyers Primary Care Institute, University of Massachusetts Medical School, 365 Plantation St. Biotech 1, Suite 100, Worcester, MA, 01605, USA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
| | | | - Ravi N Sharaf
- Division of Gastroenterology, Department of Medicine, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, USA
| | - Su-Ying Liang
- Palo Alto Medical Foundation Research Institute, 795 El Camino Real, Palo Alto, CA, 94301, USA
| | - Andrea N Burnett-Hartman
- Kaiser Permanente Colorado, Institute for Health Research, 2550 S. Parker Rd., Ste 200, Aurora, CO, 80014, USA
| | - Jessica Ezzell Hunter
- RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC, 27709-2194, USA
| | | | - Deborah Cragun
- University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, FL, 33612, USA
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Dikilitas O, Sherafati A, Saadatagah S, Satterfield BA, Kochan DC, Anderson KC, Chung WK, Hebbring SJ, Salvati ZM, Sharp RR, Sturm AC, Gibbs RA, Rowley R, Venner E, Linder JE, Jones LK, Perez EF, Peterson JF, Jarvik GP, Rehm HL, Zouk H, Roden DM, Williams MS, Manolio TA, Kullo IJ. Familial Hypercholesterolemia in the Electronic Medical Records and Genomics Network: Prevalence, Penetrance, Cardiovascular Risk, and Outcomes After Return of Results. Circ Genom Precis Med 2023; 16:e003816. [PMID: 37071725 PMCID: PMC10113961 DOI: 10.1161/circgen.122.003816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/03/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND The implications of secondary findings detected in large-scale sequencing projects remain uncertain. We assessed prevalence and penetrance of pathogenic familial hypercholesterolemia (FH) variants, their association with coronary heart disease (CHD), and 1-year outcomes following return of results in phase III of the electronic medical records and genomics network. METHODS Adult participants (n=18 544) at 7 sites were enrolled in a prospective cohort study to assess the clinical impact of returning results from targeted sequencing of 68 actionable genes, including LDLR, APOB, and PCSK9. FH variant prevalence and penetrance (defined as low-density lipoprotein cholesterol >155 mg/dL) were estimated after excluding participants enrolled on the basis of hypercholesterolemia. Multivariable logistic regression was used to estimate the odds of CHD compared to age- and sex-matched controls without FH-associated variants. Process (eg, referral to a specialist or ordering new tests), intermediate (eg, new diagnosis of FH), and clinical (eg, treatment modification) outcomes within 1 year after return of results were ascertained by electronic health record review. RESULTS The prevalence of FH-associated pathogenic variants was 1 in 188 (69 of 13,019 unselected participants). Penetrance was 87.5%. The presence of an FH variant was associated with CHD (odds ratio, 3.02 [2.00-4.53]) and premature CHD (odds ratio, 3.68 [2.34-5.78]). At least 1 outcome occurred in 92% of participants; 44% received a new diagnosis of FH and 26% had treatment modified following return of results. CONCLUSIONS In a multisite cohort of electronic health record-linked biobanks, monogenic FH was prevalent, penetrant, and associated with presence of CHD. Nearly half of participants with an FH-associated variant received a new diagnosis of FH and a quarter had treatment modified after return of results. These results highlight the potential utility of sequencing electronic health record-linked biobanks to detect FH.
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Affiliation(s)
- Ozan Dikilitas
- Department of Internal Medicine (O.D.), Mayo Clinic, Rochester, MN
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Alborz Sherafati
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Seyedmohammad Saadatagah
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Benjamin A Satterfield
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - David C Kochan
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Katherine C Anderson
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York (W.K.C.)
| | | | - Zachary M Salvati
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Richard R Sharp
- Biomedical Ethics Research Program (R.R.S.), Mayo Clinic, Rochester, MN
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (R.A.G., E.V.)
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, MD (R.R., T.A.M.)
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (R.A.G., E.V.)
| | - Jodell E Linder
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Laney K Jones
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Emma F Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA (E.F.P.)
| | - Josh F Peterson
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle (G.P.J.)
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge (H.L.R., H.Z.)
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge (H.L.R., H.Z.)
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston (H.Z.)
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics (D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Teri A Manolio
- National Human Genome Research Institute, Bethesda, MD (R.R., T.A.M.)
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
- Gonda Vascular Ctr (I.J.K.), Mayo Clinic, Rochester, MN
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Sherafati A, Elsekaily O, Saadatagah S, Kochan DC, Lee C, Wiesner GL, Liu C, Dellefave-Castillo L, Namjou B, Perez EF, Salvati ZM, Connolly JJ, Hakonarson H, Williams MS, Jarvik GP, Chung WK, McNally EM, Manolio TA, Kullo IJ. Pathogenic variants in arteriopathy genes detected in a targeted sequencing study: Penetrance and 1-year outcomes after return of results. Genet Med 2022; 24:2123-2133. [PMID: 35943490 PMCID: PMC9837827 DOI: 10.1016/j.gim.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 01/18/2023] Open
Abstract
PURPOSE We estimated the penetrance of pathogenic/likely pathogenic (P/LP) variants in arteriopathy-related genes and assessed near-term outcomes following return of results. METHODS Participants (N = 24,520) in phase III of the Electronic Medical Records and Genomics network underwent targeted sequencing of 68 actionable genes, including 9 genes associated with arterial aneurysmal diseases. Penetrance was estimated on the basis of the presence of relevant clinical traits. Outcomes occurring within 1 year of return of results included new diagnoses, referral to a specialist, new tests ordered, surveillance initiated, and new medications started. RESULTS P/LP variants were present in 34 participants. The average penetrance across genes was 59%, ranging from 86% for FBN1 variants to 25% for SMAD3. Of 16 participants in whom results were returned, 1-year outcomes occurred in 63%. A new diagnosis was made in 44% of the participants, 56% were referred to a specialist, a new test was ordered in 44%, surveillance was initiated in 31%, and a new medication was started in 31%. CONCLUSION Penetrance of P/LP variants in arteriopathy-related genes, identified in a large, targeted sequencing study, was variable and overall lower than that reported in clinical cohorts. Meaningful outcomes within the first year were noted in 63% of participants who received results.
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Affiliation(s)
- Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Omar Elsekaily
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | | | - David C Kochan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Christopher Lee
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Georgia L Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Boston MA
| | | | - John J Connolly
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA; Department of Genome Sciences, University of Washington Medical Center, Seattle, WA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY; Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN; Gonda Vascular Center, Mayo Clinic, Rochester, MN.
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Lennon AM, Buchanan AH, Kinde I, Warren A, Honushefsky A, Cohain AT, Ledbetter DH, Sanfilippo F, Sheridan K, Rosica D, Adonizio CS, Hwang HJ, Lahouel K, Cohen JD, Douville C, Patel AA, Hagmann LN, Rolston DD, Malani N, Zhou S, Bettegowda C, Diehl DL, Urban B, Still CD, Kann L, Woods JI, Salvati ZM, Vadakara J, Leeming R, Bhattacharya P, Walter C, Parker A, Lengauer C, Klein A, Tomasetti C, Fishman EK, Hruban RH, Kinzler KW, Vogelstein B, Papadopoulos N. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention. Science 2020; 369:eabb9601. [PMID: 32345712 PMCID: PMC7509949 DOI: 10.1126/science.abb9601] [Citation(s) in RCA: 296] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
Cancer treatments are often more successful when the disease is detected early. We evaluated the feasibility and safety of multicancer blood testing coupled with positron emission tomography-computed tomography (PET-CT) imaging to detect cancer in a prospective, interventional study of 10,006 women not previously known to have cancer. Positive blood tests were independently confirmed by a diagnostic PET-CT, which also localized the cancer. Twenty-six cancers were detected by blood testing. Of these, 15 underwent PET-CT imaging and nine (60%) were surgically excised. Twenty-four additional cancers were detected by standard-of-care screening and 46 by neither approach. One percent of participants underwent PET-CT imaging based on false-positive blood tests, and 0.22% underwent a futile invasive diagnostic procedure. These data demonstrate that multicancer blood testing combined with PET-CT can be safely incorporated into routine clinical care, in some cases leading to surgery with intent to cure.
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Affiliation(s)
- Anne Marie Lennon
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Medicine Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | | | - Isaac Kinde
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Andrew Warren
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
- Third Rock Ventures, LLC, 29 Newbury Street Boston, MA 02116, USA
| | | | - Ariella T Cohain
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Fred Sanfilippo
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 100 Woodruff Circle Atlanta, GA 30322, USA
| | | | | | - Christian S Adonizio
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
- Geisinger Cancer Institute, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Hee Jung Hwang
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Kamel Lahouel
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Joshua D Cohen
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Aalpen A Patel
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Leonardo N Hagmann
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Nirav Malani
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Shibin Zhou
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - David L Diehl
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Bobbi Urban
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Lisa Kann
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Julie I Woods
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | | | | | | | | | - Carroll Walter
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Alex Parker
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Christoph Lengauer
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
- Third Rock Ventures, LLC, 29 Newbury Street Boston, MA 02116, USA
| | - Alison Klein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street Baltimore, MD 21205, USA
| | - Cristian Tomasetti
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Biostatistics, the Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street Baltimore, MD 21205, USA
| | - Elliot K Fishman
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Radiology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Ralph H Hruban
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Bert Vogelstein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
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