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Drzymalla E, Green RF, Knuth M, Khoury MJ, Dotson WD, Gundlapalli A. COVID-19-related health outcomes in people with primary immunodeficiency: A systematic review. Clin Immunol 2022; 243:109097. [PMID: 35973637 PMCID: PMC9375253 DOI: 10.1016/j.clim.2022.109097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 12/29/2022]
Abstract
A better understanding of COVID-19 in people with primary immunodeficiency (PI), rare inherited defects in the immune system, is important for protecting this population, especially as population-wide approaches to mitigation change. COVID-19 outcomes in the PI population could have broader public health implications because some people with PI might be more likely to have extended illnesses, which could lead to increased transmission and emergence of variants. We performed a systematic review on COVID-19-associated morbidity and mortality in people with PI. Of the 1114 articles identified through the literature search, we included 68 articles in the review after removing 1046 articles because they were duplicates, did not involve COVID-19, did not involve PI, were not in English, were commentaries, were gene association or gene discovery studies, or could not be accessed. The 68 articles included outcomes for 459 people with PI and COVID-19. Using data from these 459 people, we calculated a case fatality rate of 9%, hospitalization rate of 49%, and oxygen supplementation rate of 29%. Studies have indicated that a number of people with PI showed at least some immune response to COVID-19 vaccination, with responses varying by type of PI and other factors, although vaccine effectiveness against hospitalization was lower in the PI population than in the general population. In addition to being up-to-date on vaccinations, current strategies for optimizing protection for people with PI can include pre-exposure prophylaxis for those eligible and use of therapeutics. Overall, people with PI, when infected, tested positive and showed symptoms for similar lengths of time as the general population. However, a number of people with X-linked agammaglobulinemia (XLA) or other B-cell pathway defects were reported to have prolonged infections, measured by time from first positive SARS-CoV-2 test to first negative test. As prolonged infections might increase the likelihood of genetic variants emerging, SARS-CoV2 isolates from people with PI and extended illness would be good candidates to prioritize for whole genome sequencing.
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Affiliation(s)
- Emily Drzymalla
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ridgely Fisk Green
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, GA, United States of America; Tanaq Support Services, LLC, Atlanta, GA, United States of America.
| | - Martha Knuth
- Stephen B Thacker Library, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Muin J Khoury
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - W David Dotson
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Adi Gundlapalli
- The Center for Surveillance, Epidemiology, and Laboratory Services, Office of the Director, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Khoury MJ, Dotson WD. From genes to public health: are we ready for DNA-based population screening? Genet Med 2021; 23:996-998. [PMID: 33790422 DOI: 10.1038/s41436-021-01141-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Affiliation(s)
- Muin J Khoury
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - W David Dotson
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, GA, USA
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3
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Allen CG, Green RF, Bowen S, Dotson WD, Yu W, Khoury MJ. Challenges and Opportunities for Communication about the Role of Genomics in Public Health. Public Health Genomics 2021; 24:67-74. [PMID: 33445172 DOI: 10.1159/000512485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/22/2020] [Indexed: 11/19/2022] Open
Abstract
Despite growing awareness about the potential for genomic information to improve population health, lingering communication challenges remain in describing the role of genomics in public health programs. Identifying and addressing these challenges provide an important opportunity for appropriate communication to ensure the translation of genomic discoveries for public health benefits. In this commentary, we describe 5 common communication challenges encountered by the Centers for Disease Control and Prevention's Office of Genomics and Precision Public Health based on over 20 years of experience in the field. These include (1) communicating that using genomics to assess rare diseases can have an impact on public health; (2) providing evidence that genetic factors can add important information to environmental, behavioral, and social determinants of health; (3) communicating that although genetic factors are nonmodifiable, they can increase the impact of public health programs and communication strategies; (4) addressing the concern that genomics is not ready for clinical practice; and (5) communicating that genomics is valuable beyond the domain of health care and can be integrated as part of public health programs. We discuss opportunities for addressing these communication challenges and provide examples of ongoing approaches to communication about the role of genomics in public health to the public, researchers, and practitioners.
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Affiliation(s)
- Caitlin G Allen
- Department of Behavioral, Social, and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Ridgely Fisk Green
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Bowen
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - W David Dotson
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wei Yu
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Muin J Khoury
- Office of Genomics and Precision Public Health, Office of Science, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,
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4
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Naber SK, Kundu S, Kuntz KM, Dotson WD, Williams MS, Zauber AG, Calonge N, Zallen DT, Ganiats TG, Webber EM, Goddard KAB, Henrikson NB, van Ballegooijen M, Janssens ACJW, Lansdorp-Vogelaar I. Cost-Effectiveness of Risk-Stratified Colorectal Cancer Screening Based on Polygenic Risk: Current Status and Future Potential. JNCI Cancer Spectr 2019; 4:pkz086. [PMID: 32025627 PMCID: PMC6988584 DOI: 10.1093/jncics/pkz086] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/03/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
Background Although uniform colonoscopy screening reduces colorectal cancer (CRC) mortality, risk-based screening may be more efficient. We investigated whether CRC screening based on polygenic risk is a cost-effective alternative to current uniform screening, and if not, under what conditions it would be. Methods The MISCAN-Colon model was used to simulate a hypothetical cohort of US 40-year-olds. Uniform screening was modeled as colonoscopy screening at ages 50, 60, and 70 years. For risk-stratified screening, individuals underwent polygenic testing with current and potential future discriminatory performance (area under the receiver-operating curve [AUC] of 0.60 and 0.65–0.80, respectively). Polygenic testing results were used to create risk groups, for which colonoscopy screening was optimized by varying the start age (40–60 years), end age (70–85 years), and interval (1–20 years). Results With current discriminatory performance, optimal screening ranged from once-only colonoscopy at age 60 years for the lowest-risk group to six colonoscopies at ages 40–80 years for the highest-risk group. While maintaining the same health benefits, risk-stratified screening increased costs by $59 per person. Risk-stratified screening could become cost-effective if the AUC value would increase beyond 0.65, the price per polygenic test would drop to less than $141, or risk-stratified screening would lead to a 5% increase in screening participation. Conclusions Currently, CRC screening based on polygenic risk is unlikely to be cost-effective compared with uniform screening. This is expected to change with a greater than 0.05 increase in AUC value, a greater than 30% reduction in polygenic testing costs, or a greater than 5% increase in adherence with screening.
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Affiliation(s)
- Steffie K Naber
- See the Notes section for the full list of authors' affiliations
| | - Suman Kundu
- See the Notes section for the full list of authors' affiliations
| | - Karen M Kuntz
- See the Notes section for the full list of authors' affiliations
| | - W David Dotson
- See the Notes section for the full list of authors' affiliations
| | - Marc S Williams
- See the Notes section for the full list of authors' affiliations
| | - Ann G Zauber
- See the Notes section for the full list of authors' affiliations
| | - Ned Calonge
- See the Notes section for the full list of authors' affiliations
| | - Doris T Zallen
- See the Notes section for the full list of authors' affiliations
| | | | | | | | - Nora B Henrikson
- See the Notes section for the full list of authors' affiliations
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5
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Murray MF, Evans JP, Angrist M, Uhlmann WR, Lochner Doyle D, Fullerton SM, Ganiats TG, Hagenkord J, Imhof S, Rim SH, Ortmann L, Aziz N, Dotson WD, Matloff E, Young K, Kaphingst K, Bradbury A, Scott J, Wang C, Zauber A, Levine M, Korf B, Leonard DG, Wicklund C, Isham G, Khoury MJ. A Proposed Approach for Implementing Genomics-Based Screening Programs for Healthy Adults. NAM Perspect 2018. [DOI: 10.31478/201812a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joan Scott
- Health Resources and Services Administration
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6
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Roberts MC, Dotson WD, DeVore CS, Bednar EM, Bowen DJ, Ganiats TG, Green RF, Hurst GM, Philp AR, Ricker CN, Sturm AC, Trepanier AM, Williams JL, Zierhut HA, Wilemon KA, Hampel H. Delivery Of Cascade Screening For Hereditary Conditions: A Scoping Review Of The Literature. Health Aff (Millwood) 2018; 37:801-808. [PMID: 29733730 PMCID: PMC11022644 DOI: 10.1377/hlthaff.2017.1630] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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] [Indexed: 11/05/2022]
Abstract
Cascade screening is the process of contacting relatives of people who have been diagnosed with certain hereditary conditions. Its purpose is to identify, inform, and manage those who are also at risk. We conducted a scoping review to obtain a broad overview of cascade screening interventions, facilitators and barriers to their use, relevant policy considerations, and future research needs. We searched for relevant peer-reviewed literature in the period 1990-2017 and reviewed 122 studies. Finally, we described 45 statutes and regulations related to the use and release of genetic information across the fifty states. We sought standardized best practices for optimizing cascade screening across various geographic and policy contexts, but we found none. Studies in which trained providers contacted relatives directly, rather than through probands (index patients), showed greater cascade screening uptake; however, policies in some states might limit this approach. Major barriers to cascade screening delivery include suboptimal communication between the proband and family and geographic barriers to obtaining genetic services. Few US studies examined interventions for cascade screening or used rigorous study designs such as randomized controlled trials. Moving forward, there remains an urgent need to conduct rigorous intervention studies on cascade screening in diverse US populations, while accounting for state policy considerations.
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Affiliation(s)
- Megan C Roberts
- Megan C. Roberts is a Cancer Prevention Fellow in the Division of Cancer Control and Population Sciences, National Cancer Institute, in Rockville, Maryland
| | - W David Dotson
- W. David Dotson is a senior coordinating scientist in the Office of Public Health Genomics, Centers for Disease Control and Prevention (CDC), in Atlanta, Georgia
| | - Christopher S DeVore
- Christopher S. DeVore is a Public Health Fellow in the Office of Public Health Preparedness and Response, CDC, and a master of public health candidate at the Rollins School of Public Health, Emory University, in Atlanta
| | - Erica M Bednar
- Erica M. Bednar is a genetic counselor in the Department of Clinical Cancer Genetics and the Cancer Prevention and Control Platform at the University of Texas MD Anderson Cancer Center, in Houston, Texas
| | - Deborah J Bowen
- Deborah J. Bowen is a professor of bioethics and humanities at the University of Washington, in Seattle
| | - Theodore G Ganiats
- Theodore G. Ganiats is director of the National Center for Excellence in Primary Care Research, Agency for Healthcare Research and Quality, in Rockville, Maryland
| | - Ridgely Fisk Green
- Ridgely Fisk Green is a Carter Consulting, Inc., contractor in the Office of Public Health Genomics, CDC, and at Carter Consulting, in Atlanta
| | - Georgia M Hurst
- Georgia M. Hurst is the director of ihavelynchsyndrome.org, in Evanston, Illinois
| | - Alisdair R Philp
- Alisdair R. Philp is a genetic counselor and a clinical assistant professor at the University of Kansas Hospitals and Clinics, in Westwood
| | - Charité N Ricker
- Charité N. Ricker is a genetic counselor and clinical instructor at the University of Southern California, in Los Angeles
| | - Amy C Sturm
- Amy C. Sturm is a professor at the Genomic Medicine Institute, Geisinger, in Danville, Pennsylvania
| | - Angela M Trepanier
- Angela M. Trepanier is an associate professor (clinician educator) at the Center for Molecular Medicine and Genetics, Wayne State University, in Detroit, Michigan
| | - Janet L Williams
- Janet L. Williams is director, Research Genetic Counselors, at the Genomic Medicine Institute, Geisinger, in Danville, Pennsylvania
| | - Heather A Zierhut
- Heather A. Zierhut is an assistant professor in genetics, cell biology, and development at the College of Biological Sciences, University of Minnesota Twin Cities, in Minneapolis
| | - Katherine A Wilemon
- Katherine A. Wilemon is CEO of the Familial Hypercholesterolemia Foundation, in Pasadena, California
| | - Heather Hampel
- Heather Hampel is associate director of the Division of Human Genetics and of biospecimen research, and a professor of internal medicine, all at the Ohio State University Comprehensive Cancer Center, in Columbus
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7
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Khoury MJ, Bowen MS, Clyne M, Dotson WD, Gwinn ML, Green RF, Kolor K, Rodriguez JL, Wulf A, Yu W. From public health genomics to precision public health: a 20-year journey. Genet Med 2017; 20:574-582. [PMID: 29240076 DOI: 10.1038/gim.2017.211] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 10/20/2017] [Indexed: 12/20/2022] Open
Abstract
In this paper, we review the evolution of the field of public health genomics in the United States in the past two decades. Public health genomics focuses on effective and responsible translation of genomic science into population health benefits. We discuss the relationship of the field to the core public health functions and essential services, review its evidentiary foundation, and provide examples of current US public health priorities and applications. We cite examples of publications to illustrate how Genetics in Medicine reflected the evolution of the field. We also reflect on how public-health genomics is contributing to the emergence of "precision public health" with near-term opportunities offered by the US Precision Medicine (AllofUs) Initiative.
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Affiliation(s)
- Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Scott Bowen
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mindy Clyne
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, Maryland, USA
| | - W David Dotson
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marta L Gwinn
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ridgely Fisk Green
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine Kolor
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Juan L Rodriguez
- Division of Cancer Prevention and Control, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anja Wulf
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wei Yu
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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Kolor K, Chen Z, Grosse SD, Rodriguez JL, Green RF, Dotson WD, Bowen MS, Lynch JA, Khoury MJ. BRCA Genetic Testing and Receipt of Preventive Interventions Among Women Aged 18-64 Years with Employer-Sponsored Health Insurance in Nonmetropolitan and Metropolitan Areas - United States, 2009-2014. MMWR Surveill Summ 2017; 66:1-11. [PMID: 28880857 PMCID: PMC5879728 DOI: 10.15585/mmwr.ss6615a1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
PROBLEM/CONDITION Genetic testing for breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) gene mutations can identify women at increased risk for breast and ovarian cancer. These testing results can be used to select preventive interventions and guide treatment. Differences between nonmetropolitan and metropolitan populations in rates of BRCA testing and receipt of preventive interventions after testing have not previously been examined. PERIOD COVERED 2009-2014. DESCRIPTION OF SYSTEM Medical claims data from Truven Health Analytics MarketScan Commercial Claims and Encounters databases were used to estimate rates of BRCA testing and receipt of preventive interventions after BRCA testing among women aged 18-64 years with employer-sponsored health insurance in metropolitan and nonmetropolitan areas of the United States, both nationally and regionally. RESULTS From 2009 to 2014, BRCA testing rates per 100,000 women aged 18-64 years with employer-sponsored health insurance increased 2.3 times (102.7 to 237.8) in metropolitan areas and 3.0 times (64.8 to 191.3) in nonmetropolitan areas. The relative difference in BRCA testing rates between metropolitan and nonmetropolitan areas decreased from 37% in 2009 (102.7 versus 64.8) to 20% in 2014 (237.8 versus 191.3). The relative difference in BRCA testing rates between metropolitan and nonmetropolitan areas decreased more over time in younger women than in older women and decreased in all regions except the West. Receipt of preventive services 90 days after BRCA testing in metropolitan versus nonmetropolitan areas throughout the period varied by service: the percentage of women who received a mastectomy was similar, the percentage of women who received magnetic resonance imaging of the breast was lower in nonmetropolitan areas (as low as 5.8% in 2014 to as high as 8.2% in 2011) than metropolitan areas (as low as 7.3% in 2014 to as high as 10.3% in 2011), and the percentage of women who received mammography was lower in nonmetropolitan areas in earlier years but was similar in later years. INTERPRETATION Possible explanations for the 47% decrease in the relative difference in BRCA testing rates over the study period include increased access to genetic services in nonmetropolitan areas and increased demand nationally as a result of publicity. The relative differences in metropolitan and nonmetropolitan BRCA testing rates were smaller among women at younger ages compared with older ages. PUBLIC HEALTH ACTION Improved data sources and surveillance tools are needed to gather comprehensive data on BRCA testing in the United States, monitor adherence to evidence-based guidelines for BRCA testing, and assess receipt of preventive interventions for women with BRCA mutations. Programs can build on the recent decrease in geographic disparities in receipt of BRCA testing while simultaneously educating the public and health care providers about U.S. Preventive Services Task Force recommendations and other clinical guidelines for BRCA testing and counseling.
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Affiliation(s)
- Katherine Kolor
- Office of Public Health Genomics, Division of Public Health Information Dissemination, Center for Surveillance, Epidemiology, and Laboratory Services, CDC, Atlanta, Georgia
| | - Zhuo Chen
- Office of Public Health Genomics, Division of Public Health Information Dissemination, Center for Surveillance, Epidemiology, and Laboratory Services, CDC, Atlanta, Georgia.,CFO Leasing, Inc., Atlanta, Georgia.,Department of Health Policy and Management, College of Public Health, University of Georgia, Athens, Georgia
| | - Scott D Grosse
- National Center on Birth Defects and Developmental Disabilities, CDC, Atlanta, Georgia
| | - Juan L Rodriguez
- Division of Cancer Prevention and Control, National Center for Chronic Disease Prevention and Health Promotion, CDC, Atlanta, Georgia
| | - Ridgely Fisk Green
- Office of Public Health Genomics, Division of Public Health Information Dissemination, Center for Surveillance, Epidemiology, and Laboratory Services, CDC, Atlanta, Georgia.,Carter Consulting, Inc., Atlanta, Georgia
| | - W David Dotson
- Office of Public Health Genomics, Division of Public Health Information Dissemination, Center for Surveillance, Epidemiology, and Laboratory Services, CDC, Atlanta, Georgia
| | - M Scott Bowen
- Office of Public Health Genomics, Division of Public Health Information Dissemination, Center for Surveillance, Epidemiology, and Laboratory Services, CDC, Atlanta, Georgia
| | - Julie A Lynch
- US Department of Veterans Affairs Salt Lake City Healthcare System, Salt Lake City, Utah
| | - Muin J Khoury
- Office of Public Health Genomics, Division of Public Health Information Dissemination, Center for Surveillance, Epidemiology, and Laboratory Services, CDC, Atlanta, Georgia
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9
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Lynch JA, Berse B, Dotson WD, Khoury MJ, Coomer N, Kautter J. Utilization of genetic tests: analysis of gene-specific billing in Medicare claims data. Genet Med 2017; 19:890-899. [PMID: 28125086 DOI: 10.1038/gim.2016.209] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/17/2016] [Indexed: 02/06/2023] Open
Abstract
PURPOSE We examined the utilization of precision medicine tests among Medicare beneficiaries through analysis of gene-specific tier 1 and 2 billing codes developed by the American Medical Association in 2012. METHODS We conducted a retrospective cross-sectional study. The primary source of data was 2013 Medicare 100% fee-for-service claims. We identified claims billed for each laboratory test, the number of patients tested, expenditures, and the diagnostic codes indicated for testing. We analyzed variations in testing by patient demographics and region of the country. RESULTS Pharmacogenetic tests were billed most frequently, accounting for 48% of the expenditures for new codes. The most common indications for testing were breast cancer, long-term use of medications, and disorders of lipid metabolism. There was underutilization of guideline-recommended tumor mutation tests (e.g., epidermal growth factor receptor) and substantial overutilization of a test discouraged by guidelines (methylenetetrahydrofolate reductase). Methodology-based tier 2 codes represented 15% of all claims billed with the new codes. The highest rate of testing per beneficiary was in Mississippi and the lowest rate was in Alaska. CONCLUSIONS Gene-specific billing codes significantly improved our ability to conduct population-level research of precision medicine. Analysis of these data in conjunction with clinical records should be conducted to validate findings.Genet Med advance online publication 26 January 2017.
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Affiliation(s)
- Julie A Lynch
- RTI International, Waltham, Massachusetts, USA.,Department of Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA
| | - Brygida Berse
- RTI International, Waltham, Massachusetts, USA.,Boston University School of Medicine, Boston, Massachusetts, USA.,Veterans Health Administration, Bedford, Massachusetts, USA
| | - W David Dotson
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Muin J Khoury
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nicole Coomer
- RTI International, Research Triangle Park, North Carolina, USA
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10
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Yu W, Gwinn M, Dotson WD, Green RF, Clyne M, Wulf A, Bowen S, Kolor K, Khoury MJ. A knowledge base for tracking the impact of genomics on population health. Genet Med 2016; 18:1312-1314. [PMID: 27280867 DOI: 10.1038/gim.2016.63] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/06/2016] [Indexed: 01/08/2023] Open
Abstract
PURPOSE We created an online knowledge base (the Public Health Genomics Knowledge Base (PHGKB)) to provide systematically curated and updated information that bridges population-based research on genomics with clinical and public health applications. METHODS Weekly horizon scanning of a wide variety of online resources is used to retrieve relevant scientific publications, guidelines, and commentaries. After curation by domain experts, links are deposited into Web-based databases. RESULTS PHGKB currently consists of nine component databases. Users can search the entire knowledge base or search one or more component databases directly and choose options for customizing the display of their search results. CONCLUSION PHGKB offers researchers, policy makers, practitioners, and the general public a way to find information they need to understand the complicated landscape of genomics and population health.Genet Med 18 12, 1312-1314.
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Affiliation(s)
- Wei Yu
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marta Gwinn
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,McKing Consulting Corporation, Atlanta, Georgia, USA
| | - W David Dotson
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ridgely Fisk Green
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Carter Consulting, Inc., Atlanta, Georgia, USA
| | - Mindy Clyne
- Epidemiology and Genomics Research Program, National Cancer Institute, Bethesda, Maryland, USA.,Kelly Services, Troy, Michigan, USA
| | - Anja Wulf
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Cadence Group, Atlanta, Georgia, USA
| | - Scott Bowen
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine Kolor
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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11
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Fisk Green R, Dotson WD, Bowen S, Kolor K, Khoury MJ. Genomics in Public Health: Perspective from the Office of Public Health Genomics at the Centers for Disease Control and Prevention (CDC). Healthcare (Basel) 2015; 3:830-7. [PMID: 26636032 PMCID: PMC4666313 DOI: 10.3390/healthcare3030830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/08/2015] [Indexed: 12/19/2022] Open
Abstract
The national effort to use genomic knowledge to save lives is gaining momentum, as illustrated by the inclusion of genomics in key public health initiatives, including Healthy People 2020, and the recent launch of the precision medicine initiative. The Office of Public Health Genomics (OPHG) at the Centers for Disease Control and Prevention (CDC) partners with state public health departments and others to advance the translation of genome-based discoveries into disease prevention and population health. To do this, OPHG has adopted an "identify, inform, and integrate" model: identify evidence-based genomic applications ready for implementation, inform stakeholders about these applications, and integrate these applications into public health at the local, state, and national level. This paper addresses current and future work at OPHG for integrating genomics into public health programs.
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Affiliation(s)
- Ridgely Fisk Green
- Carter Consulting, Inc. and Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - W. David Dotson
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; E-Mails: (W.D.D.); (S.B.); (K.K.); (M.J.K.)
| | - Scott Bowen
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; E-Mails: (W.D.D.); (S.B.); (K.K.); (M.J.K.)
| | - Katherine Kolor
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; E-Mails: (W.D.D.); (S.B.); (K.K.); (M.J.K.)
| | - Muin J. Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; E-Mails: (W.D.D.); (S.B.); (K.K.); (M.J.K.)
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Marrone M, Stewart A, Dotson WD. Clinical utility of gene-expression profiling in women with early breast cancer: an overview of systematic reviews. Genet Med 2014; 17:519-32. [PMID: 25474343 DOI: 10.1038/gim.2014.140] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/02/2014] [Indexed: 01/08/2023] Open
Abstract
PURPOSE This overview systematically evaluates the clinical utility of using Oncotype DX and MammaPrint gene-expression profiling tests to direct treatment decisions in women with breast cancer. The findings are intended to inform an updated recommendation from the Evaluation of Genomic Applications in Practice and Prevention Working Group. METHODS Evidence reported in systematic reviews evaluating the clinical utility of Oncotype DX and MammaPrint, as well as the ability to predict treatment outcomes, change in treatment decisions, and cost-effectiveness, was qualitatively synthesized. RESULTS Five systematic reviews found no direct evidence of clinical utility for either test. Indirect evidence showed Oncotype DX was able to predict treatment effects of adjuvant chemotherapy, whereas no evidence of predictive value was found for MammaPrint. Both tests influenced a change in treatment recommendations in 21 to 74% of participants. The cost-effectiveness of Oncotype DX varied with the alternative compared. For MammaPrint, lack of evidence of the predictive value led to uncertainty in the cost-effectiveness. CONCLUSION No studies were identified that provided direct evidence that using gene-expression profiling tests to direct treatment decisions improved outcomes in women with breast cancer. Three ongoing studies may provide direct evidence for determining the clinical utility of gene-expression profiling testing.
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Affiliation(s)
- Michael Marrone
- 1] McKing Consulting Corporation, Atlanta, Georgia, USA [2] Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison Stewart
- 1] McKing Consulting Corporation, Atlanta, Georgia, USA [2] Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - W David Dotson
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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13
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Dotson WD, Douglas MP, Kolor K, Stewart AC, Bowen MS, Gwinn M, Wulf A, Anders HM, Chang CQ, Clyne M, Lam TK, Schully SD, Marrone M, Feero WG, Khoury MJ. Prioritizing genomic applications for action by level of evidence: a horizon-scanning method. Clin Pharmacol Ther 2014; 95:394-402. [PMID: 24398597 PMCID: PMC4689130 DOI: 10.1038/clpt.2013.226] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [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: 09/12/2013] [Accepted: 11/08/2013] [Indexed: 11/09/2022]
Abstract
As evidence accumulates on the use of genomic tests and other health-related applications of genomic technologies, decision makers may increasingly seek support in identifying which applications have sufficiently robust evidence to suggest they might be considered for action. As an interim working process to provide such support, we developed a horizon-scanning method that assigns genomic applications to tiers defined by availability of synthesized evidence. We illustrate an application of the method to pharmacogenomics tests.
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Affiliation(s)
- WD Dotson
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - MP Douglas
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- McKing Consulting Corporation, Atlanta, Georgia, USA
| | - K Kolor
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - AC Stewart
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- McKing Consulting Corporation, Atlanta, Georgia, USA
| | - MS Bowen
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Gwinn
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- McKing Consulting Corporation, Atlanta, Georgia, USA
| | - A Wulf
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Cadence Group, Atlanta, Georgia, USA
| | - HM Anders
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- McKing Consulting Corporation, Atlanta, Georgia, USA
| | - CQ Chang
- Epidemiology and Genomics Research Program, National Cancer Institute, Bethesda, Maryland, USA
| | - M Clyne
- Epidemiology and Genomics Research Program, National Cancer Institute, Bethesda, Maryland, USA
- Kelly Services, Troy, Michigan, USA
| | - TK Lam
- Epidemiology and Genomics Research Program, National Cancer Institute, Bethesda, Maryland, USA
| | - SD Schully
- Epidemiology and Genomics Research Program, National Cancer Institute, Bethesda, Maryland, USA
| | - M Marrone
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - WG Feero
- Maine Dartmouth Family Medicine Residency Program, Augusta, Maine, USA
| | - MJ Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemiology and Genomics Research Program, National Cancer Institute, Bethesda, Maryland, USA
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14
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Bowen MS, Kolor K, Dotson WD, Ned RM, Khoury MJ. Public health action in genomics is now needed beyond newborn screening. Public Health Genomics 2012; 15:327-34. [PMID: 22986915 PMCID: PMC4748713 DOI: 10.1159/000341889] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [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: 05/08/2012] [Accepted: 07/09/2012] [Indexed: 01/09/2023] Open
Abstract
For decades, newborn screening was the only public health program in the US focused on reducing morbidity, mortality and disability in people affected by genetic conditions. The landscape has changed, however, as evidence-based recommendations are now available for several other genomic applications that can save lives now in the US. Many more such applications are expected to emerge in the next decade. An action plan, based on evidence, provides the impetus for a new paradigm for public health practice in genomics across the lifespan using established multilevel processes as a guide. These include policy interventions, education, clinical interventions, and surveillance. Applying what we know today in hereditary breast/ovarian cancer, Lynch syndrome and familial hypercholesterolemia has the potential to affect thousands of people in the US population every year. Enhanced partnerships between genetic and nongenetic providers of clinical medicine and public health are needed to overcome the challenges for implementing genomic medicine applications both now and in the future.
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Affiliation(s)
- M S Bowen
- Centers for Disease Control and Prevention, Department of Health and Human Services, Atlanta, GA, USA.
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15
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Abstract
Three articles in this issue of Genetics in Medicine describe examples of "knowledge integration," involving methods for generating and synthesizing rapidly emerging information on health-related genomic technologies and engaging stakeholders around the evidence. Knowledge integration, the central process in translating genomic research, involves three closely related, iterative components: knowledge management, knowledge synthesis, and knowledge translation. Knowledge management is the ongoing process of obtaining, organizing, and displaying evolving evidence. For example, horizon scanning and "infoveillance" use emerging technologies to scan databases, registries, publications, and cyberspace for information on genomic applications. Knowledge synthesis is the process of conducting systematic reviews using a priori rules of evidence. For example, methods including meta-analysis, decision analysis, and modeling can be used to combine information from basic, clinical, and population research. Knowledge translation refers to stakeholder engagement and brokering to influence policy, guidelines and recommendations, as well as the research agenda to close knowledge gaps. The ultrarapid production of information requires adequate public and private resources for knowledge integration to support the evidence-based development of genomic medicine.
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Affiliation(s)
- Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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16
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Abstract
A decade after the sequencing of the human genome, the National Human Genome Research Institute announced a strategic plan for genomic medicine. It calls for evaluating the structure and biology of genomes, understanding the biology of disease, advancing the science of medicine, and improving the effectiveness of health care. Fulfilling the promise of genomics urgently requires a population perspective to complement the bench-to-bedside model of translation. A population approach should assess the contribution of genomics to health in the context of social and environmental determinants of disease; evaluate genomic applications that may improve health care; design strategies for integrating genomics into practice; address ethical, legal, and social issues; and measure the population health impact of new technologies.
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Affiliation(s)
- Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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17
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Bellcross C, Dotson WD. Tumor gene expression profiling in women with breast cancer. Test category: prognostic. PLoS Curr 2010; 2:k/-/-/39jrm5yo7vhua/4. [PMID: 20877449 PMCID: PMC2940139 DOI: 10.1371/currents.rrn1178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2010] [Indexed: 11/26/2022]
Abstract
Differences in the expression of specific genes within breast tumors have been associated with risk of recurrence after treatment. Most women with Stage I or II node-negative breast cancer (especially when estrogen-receptor positive and treated with tamoxifen) remain disease-free at 10 years. Information on risk of recurrence could help identify women most likely to benefit from chemotherapy. Several clinically available gene expression profiles (GEP) provide “recurrence risk scores” that are intended to supplement information used by clinicians and patients in treatment decision-making.
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Teutsch SM, Bradley LA, Palomaki GE, Haddow JE, Piper M, Calonge N, Dotson WD, Douglas MP, Berg AO. The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Initiative: methods of the EGAPP Working Group. Genet Med 2009; 11:3-14. [PMID: 18813139 PMCID: PMC2743609 DOI: 10.1097/gim.0b013e318184137c] [Citation(s) in RCA: 460] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Initiative, established by the National Office of Public Health Genomics at the Centers for Disease Control and Prevention, supports the development and implementation of a rigorous, evidence-based process for evaluating genetic tests and other genomic applications for clinical and public health practice in the United States. An independent, non-federal EGAPP Working Group (EWG), a multidisciplinary expert panel selects topics, oversees the systematic review of evidence, and makes recommendations based on that evidence. This article describes the EGAPP processes and details the specific methods and approaches used by the EWG.
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Affiliation(s)
| | - Linda A. Bradley
- National Office of Public Health Genomics, CDC, Atlanta, Georgia
| | - Glenn E. Palomaki
- Department of Pathology and Laboratory Medicine (Research), The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - James E. Haddow
- Department of Pathology and Laboratory Medicine (Research), The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Margaret Piper
- Blue Cross/Blue Shield Association Technology Evaluation Center, Chicago, Illinois
| | - Ned Calonge
- Colorado Department of Public Health and Environment, Denver, Colorado
| | - W. David Dotson
- National Office of Public Health Genomics, CDC, Atlanta, Georgia
- McKing Consulting Corp., Atlanta, Georgia and
| | - Michael P. Douglas
- National Office of Public Health Genomics, CDC, Atlanta, Georgia
- McKing Consulting Corp., Atlanta, Georgia and
| | - Alfred O. Berg
- Department of Family Medicine, University of Washington, Seattle, Washington
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Abstract
Saccharomyces cerevisiae normally will not take up sterols from the environment under aerobic conditions. A specific mutant, upc2-1, of the predicted transcriptional activator UPC2 (YDR213w) has been recognized as a strain that allows a high level of aerobic sterol uptake. Another predicted transcriptional activator, the YLR228c gene product, is highly homologous to Upc2p. In fact, at the carboxy terminus 130 of the last 139 amino acids are similar between the two proteins. Since these proteins are very similar, the effect of mutations in the YLR228c open reading frame (ORF) was compared with like alterations in UPC2. First, the YLR228c ORF was insertionally inactivated and crossed with various UPC2 constructs. Deletion of YLR228c and UPC2 in combination resulted in nonviability, suggesting that the two proteins have some essential overlapping function. The upc2-1 point mutation responsible for aerobic sterol uptake was duplicated in the homologous carboxy region of the YLR228c ORF using site-directed mutagenesis. This mutation on a high-copy vector resulted in an increase in sterol uptake compared to an isogenic wild-type strain. The combination of both point mutations resulted in the greatest level of aerobic sterol uptake. When the YLR228c point mutation was expressed from a low-copy vector there was little if any effect on sterol uptake. Gas chromatographic analysis of the nonsaponifiable fractions of the various strains showed that the major sterol for all YLR228c and UPC2 combinations was ergosterol, the consensus yeast sterol.
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Affiliation(s)
- K V Shianna
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA
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Abstract
Phytophthora species are eukaryotic sterol auxotrophs that possess the ability to grow, albeit poorly, in the complete absence of sterols. Growth of Phytophthora is often improved substantially when an exogenous source of sterol is provided. Additionally, sterols may be required for sexual and asexual sporulation in Phytophthora. Our research has been focused on identifying and characterizing the immediate physiological effects following sterol addition to cultures of P. parasitica. Through gas chromatographic analysis of extracts from P. parasitica cultures that were fed various sterols, we have obtained evidence for sterol C5 desaturase and delta7 reductase activities in this organism. Zoo blots were probed with DNA sequences encoding these enzymes, from Saccharomyces cerevisiae and Arabidopsis thaliana. Hybridization of a S. cerevisiae ERG3 probe to P. parasitica DNA was observed, implicating sequence similarity between the sterol C5 desaturase encoding genes. Differential display experiments, using RNA from P. parasitica, have demonstrated a pattern of altered gene expression between cultures grown in the presence and absence of sitosterol. Characterization of sterol-related metabolic effects and sterol functions in Phytophthora should lead to improved measures for control of this important group of plant pathogens.
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Affiliation(s)
- W D Dotson
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615, USA
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