Public Health Genomics Program Review
4.0 Scientific Highlights in FY2008
EGAPP™ Recommendation Statements
In December 2007, the CDC-supported independent EGAPP™ Working Group released its first recommendation statement, which addresses the use of cytochrome P450 (CYP450) testing in adults with depression beginning treatment with a widely prescribed class of antidepressants. The EGAPP™ Working Group did not find sufficient evidence to support the use of CYP450 testing in adults beginning treatment with selective serotonin reuptake inhibitors (SSRI) in patients with non-psychotic depression. EGAPP™ discourages the use of CYP450 testing for patients beginning SSRI treatment until more research is completed. This recommendation statement was published in Genetics in Medicine and can be accessed free of charge at: www.geneticsinmedicine.org/pt/re/gim/fulltext.00125817-200712000-00004.htm. OPHG is conducting an evaluation to assess awareness and use of this EGAPP™ recommendation among health care providers, health plans and payers, policy makers, and consumer groups.
EGAPP™ efforts in FY2008 were primarily focused on the development of evidence-based products that address the following:
- the use of UGT1A1 genotyping in metastatic colorectal cancer patients treated with irinotecan
- identifying DNA testing strategies that can reduce morbidity and mortality from Lynch Syndrome
- the use of tumor gene expression profiling in breast cancer patients
Another important paper that appeared in the January 2009 issue of Genetics in Medicine, entitled The Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) initiative: methods of the EGAPP™ Working Group, was originally published in an online ahead of print format in 2008. The paper is important in that it provides in-depth coverage and detailed descriptions of EGAPP™ methods and processes, while promoting transparency and dissemination of knowledge. This paper, as well at the three most recent EGAPP™ recommendation statements can be accessed free of charge at: http://www.geneticsinmedicine.org/pt/re/gim/toc.00125817-200901000-00000.htm.
EGAPP™ Evidence Reports
In FY2008, OPHG funded an evidence-based practice center, through an interagency agreement with the Agency for Healthcare Research and Quality, to develop the following evidence-based report: Impact of Gene Expression Profiling Tests on Breast Cancer Outcomes. This report is available free of charge at: www.ahrq.gov/clinic/tp/brcgenetp.htm.
EGAPP™ Stakeholders Group
In January 2008, the CDC-supported EGAPP™ Stakeholders Group (ESG) held its first meeting in Houston, Texas. Of the 35 stakeholders, 32 attended this meeting as well as an EGAPP™ Working Group member, CDC staff, and EGAPP™ consultants. The meeting focused on understanding EGAPP™; understanding challenges associated with evaluating genetic tests and how the EGAPP™ Working Group functions and develops recommendations; developing approaches for communicating to key audiences and other stakeholders and ways to interface with EGAPP™; and defining plans to move forward.
In July 2008, the ESG held its second meeting in Seattle, Washington. The meeting was sponsored and hosted by the Center for Genomics and Public Health at the University of Washington. More than 30 participants attended the meeting, including 24 stakeholders, CDC staff, and EGAPP™ consultants. The meeting focused on further clarifying how the ESG and the EGAPP™ Working Group would interact, defining the work of the ESG subcommittees for Topics, Communication, and Information Technology, and outlining how the ESG could increase awareness of EGAPP™ and facilitate dissemination of EGAPP™ reports and recommendations.
Evaluation Study of the Family Healthware™
In October 2007, three OPHG-sponsored research centers at the University of Michigan School of Medicine, Evanston Northwestern Healthcare Research Institute, and Case Western Reserve University School of Medicine completed data collection for an evaluation study of the Family Healthware tool. This Web-based tool provides users with a familial risk assessment for six chronic conditions (breast, colorectal, and ovarian cancer, coronary heart disease, diabetes, and stroke) and a “prevention plan” containing personalized recommendations for lifestyle changes and screening recommendations.
Approximately 3,600 participants and 190 clinicians from 13 states participated in this study. Approximately 82% of the participants showed a moderate to high familial risk for at least one of the six diseases included in the tool.
- Awareness and Behavior Change Preliminary Findings:
Most study participants were aware of their familial risk and were also accurate in evaluating their risk level. However, participants in the high risk category tended to underestimate their familial risk.
Participants who were aware of their elevated familial risk for specific diseases were not more likely to undertake screening tests for the diseases involved.
Participants who were informed of their familial risk and advised to take measures according to their risk were more likely to talk to their primary care physician about this risk in their next appointment. They were also more likely to collect additional family history information from their relatives.
The Family History Impact Trial (FHITr) working group, which was formed to evaluate the study results, will be publishing a series of papers throughout FY2009 based on these investigations. This study appeared to indicate that, among people with access to primary healthcare and preventive services, it might be possible to induce some positive changes using family history. It also appeared to indicate that family history could be an essential component of public health prevention strategies for the six chronic conditions studied, as it can help identify groups at risk for these conditions and could also help health providers make decisions about screening and early testing for some diseases, which can lead to detection of early signs of disease among those with high familial risk.
New U.S. Surgeon General’s My Family Health Portrait Tool
OPHG is a member of the HHS American Health Information Community (AHIC) Family History working group, which is part of the HHS Initiative on Personalized Health Care. This working group helps to set the standards for collecting family history and is working to update and improve the U.S. Surgeon General’s My Family Health Portrait tool (https://familyhistory.hhs.gov/fhh-web/home.action). OPHG is helping to develop a plan to enable consumers to share their family health history information electronically and securely with family members and healthcare providers, and ultimately, to allow this information to become part of the consumer’s electronic health record (EHR).
OPHG is also working with the National Institute of Genomic Medicine of Mexico, in order to create a Spanish version of the new My Family Health Portrait tool that will be linked to electronic medical records. Other collaborative activities focus on integrating English versions of the new My Family Health Portrait tool into the electronic medical records system of the Veterans Administration (VA) and the Indian Health Service (IHS).
Family Matters Workshop
In June 2008, OPHG held the Family Matters Workshop: Developing a Portrait of Your Family Health History. This workshop provided an opportunity for CDC staff to learn about what family health history is and why it is important for health, how to collect their family health history and check for signs of elevated health risks, and resources available for collecting family health history. A total of 23 participants attended the event, and numerous individuals participated remotely from Alaska, Massachusetts, Pennsylvania, New Jersey, Washington DC, West Virginia, and Colorado.
Family History Publications in FY2008
- Scheuner MT and Yoon PW. The use of family history in clinical medicine and public health. In: Handbook of Genomic Medicine. Willard H, Ginsburg G, eds. New York: ELSEVIER (in press).
Robitaille J, Yoon PW, Irizarry-Delacruz M, Liu T, Moore CA, Looker AC, Khoury MJ. Prevalence, Family History, and Prevention of Reported Osteoporosis in U.S. Women. Am J Prev Med. July 2008; 35(1):47-54
Ghosh A, Liu T, Khoury MJ, Valdez R. Family History of Diabetes and Prevalence of the Metabolic Syndrome in U.S. Adults without Diabetes: 6-year results from the National Health and Nutrition Examination Survey (1999-2004). [in clearance]
Liu T, Valdez R, Yoon P, Crocker D, Moonesinghe R, Khoury MJ. The association between family history of asthma and the prevalence of asthma among US adults: National Health and Nutrition Examination Survey, 1999–2004. [in press]
Kim C, Liu T, Valdez R, Beckles G. Family history among parous women with histories of gestational diabetes mellitus only and diagnosed diabetes mellitus in the Third National Health and Nutrition Examination Survey. [draft]
Mvundura M, Henraya McGruder, Muin J. Khoury, Rodolfo Valdez, Paula W. Yoon. Family History as a Risk Factor for Early-Onset Stroke / Transient Ischemic Attack Among U.S. Adults. Public Health Genomics. 2009 Mar 23. [Epub ahead of print]
Epidemiologic approaches to the use of family history in public health practice. Authors: Rodolfo Valdez, Muin J. Khoury, Paula W. Yoon [draft of book chapter]
In September 2007, OPHG launched HuGE Navigator (http://www.hugenavigator.net), which is an up-to-date knowledge base in human genome epidemiology, with information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene-environment interactions, and evalua¬tion of genetic tests. In FY2008, OPHG added approximately 8,000 scientific articles on human genome epidemiol¬ogy were added to the HuGE Navigator. By the end of December 2008, the HuGE Navigator contained about 40,000 scientific articles (>80% genetic association studies), indexed by gene, study type, category and MeSH terms from PubMed.
- HuGE Reviews are systematic reviews of research findings on particular gene-disease associations, which are published in partnership with 10 scientific journals. These reviews typically point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. In FY2008, 10 HuGE reviews were published. Thirteen HuGE reviews are anticipated in 2009 on genetic risk factors and pregnancy and childbirth, mental disorders and epilepsy, lung cancer, and general cancer risk.
Angiotensin II type 1 receptor polymorphisms and susceptibility to hypertension: a HuGE review. Genet Med. 2008 Aug.
Meta-analysis and pooled analysis of GSTM1 and CYP1A1 polymorphisms and oral and pharyngeal cancers: a HuGE-GSEC review. Genet Med. 2008 Jun
Association study between interleukin 1 beta gene and epileptic disorders: a HuGe review and meta-analysis. Genet Med. 2008 Feb
Genetic risk factors for placental abruption: a HuGE review and meta-analysis. Epidemiology. 2008 Mar.
Glutathione S-transferase M1 (GSTM1) polymorphisms and lung cancer: a literature-based systematic HuGE review and meta-analysis. Am J Epidemiol. 2008 Apr
Meta- and pooled analyses of the methylenetetrahydrofolate reductase C677T and A1298C polymorphisms and gastric cancer risk: a huge-GSEC review. Am J Epidemiol. 2008 Mar.
Genetic variants of glutathione S-transferase as possible risk factors for hepatocellular carcinoma: a HuGE systematic review and meta-analysis. Am J Epidemiol. 2008 Feb.
Meta-analysis of the association of the Taq1A polymorphism with the risk of alcohol dependency: a HuGE gene-disease association review. Am J Epidemiol. 2008 Jan.
The E-cadherin gene polymorphism 160C->A and cancer risk: A HuGE review and meta-analysis of 26 case-control studies. Am J Epidemiol. 2008 Jan.
Joint effects of the N-acetyltransferase 1 and 2 (NAT1 and NAT2) genes and smoking on bladder carcinogenesis: a literature-based systematic HuGE review and evidence synthesis. Am J Epidemiol. 2007 Oct.
In August and September 2008, OPHG conducted two CDC workshops entitled “HuGE Navigator – Human Genome Epidemiology and Public Health Research.” These workshops provided an opportunity for CDC researchers and health professionals to learn basic concepts of human genome epidemiology and how to use the HuGE Navigator for conducting scientific literature searches about gene, disease, and environment interactions. A total of 33 attendees participated in each workshop. Attendees were from the following CDC divisions and offices: COTPER, NCCDPHP, NCBDDD, NCZVED, NCPDCID, OSI, NCHHSTP, NCIRD, NCEH, CHAPS, DHAP, ATSDR, and NCPHI.
- In January 2008, OPHG conducted a two-day meeting entitled “Networks, Genome-Wide Association Studies, and the Knowledge Base on Genetic Variation and Human Health.” Fifty five participants from a variety of research organizations and universities in the United States and globally, including 29 members of the HuGE Working Group attended this meeting. The participants discussed approaches for developing the knowledge base on genetic variation and human health, focusing on “field synopses” that summarize genetic associations with specific diseases and a proposal for an online encyclopedia. Key themes and discussion topics included:
interim cumulative evidence on genetic associations: applying interim “Venice criteria”;
field synopses: reviewing results of pilot studies;
genome-wide association studies: integrating evidence into field synopses;
distributed online knowledge base: connecting the dots; and
linking field synopses with data collections through networks and biobanks.
The participants agreed to collaborate on a second edition of Human Genome Epidemiology, which is due to be published as a hardcover text book by Oxford University Press, and also online as part of a new Public Health and Epidemiology module in Oxford Scholarship Online (OSO), a cross-searchable electronic library of key Oxford academic titles, in Fall 2009.
HuGE Publications in FY2008
- Janssens AC, Gwinn M, Bradley LA, Oostra BA, van Duijn CM, Khoury MJ. A critical appraisal of the scientific basis of commercial genomic profiles used to assess health risks and personalize health interventions. Am J Hum Genet 2008 Mar;82(3):593-9.
Janssens AC, Moonesinghe R, Yang Q, Steyerberg EW, van Duijn CM, Khoury MJ.
The impact of genotype frequencies on the clinical validity of genomic profiling
for predicting common chronic diseases. Genet Med. 2007;9(8):528-35.
Moonesinghe R, Khoury MJ, Liu T, Ioannidis JP. Required sample size and nonreplicability thresholds for heterogeneous genetic associations. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):617-22. Epub 2008 Jan 3.
Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ. A navigator for human genome epidemiology. Nat Genet. 2008 Feb;40(2):124-5.
Yu W, Clyne M, Dolan SM, Yesupriya A, Wulf A, Liu T, et al. GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique. BMC Bioinformatics 2008, 9:205 (22 April 2008)
Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, Walsh MC, et al. Reporting of Human Genome Epidemiology (HuGE) association studies: an empirical assessment. BMC Med Res Methodol. 2008 May 20;8(1):31. [Epub ahead of print] PMID: 18492284 [PubMed - as supplied by publisher]
Yesupriya A, Yu W, Clyne M, Gwinn M, Khoury MJ. The continued need to synthesize the results of genetic associations across multiple studies. Genet Med 2008;10:633-5.
Yu W, Wulf A, Yesupriya A, Clyne M, Khoury MJ, Gwinn M. HuGE Watch: tracking trends and patterns of published studies of genetic association and human genome epidemiology in near-real time. Eur J Hum Genet. 2008 May 14. [Epub ahead of print] PMID: 18478035 [PubMed - as supplied by publisher]
Yu W, Yesupriya A, Wulf A, Qu J, Gwinn M, Khoury MJ. An automatic method to generate domain-specific investigator networks using PubMed abstracts. BMC Med Inform Decis Mak 2007; 20:7:17.
Yu W, Yesupriya A, Wulf A, Qu J, Khoury MJ, Gwinn M. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology. BMC bioinformatics 2007;8:436.
U.S. Genome Variation Estimates
In 2008, OPHG reported study results on allele frequency and genotype prevalence estimates of selected candidate gene variants for U.S. population. This study was conducted in collaboration with researchers from across CDC and the National Cancer Institute. The study measured and evaluated 90 variants in 50 candidate genes from DNA collected from 7,159 participants aged 12 years or older in the Third National Health and Nutrition Examination Survey (NHANES III). These variants and genes were selected based on their potential significance to public health. The estimates were calculated by age, sex, and race/ethnicity among non-Hispanic whites, non-Hispanic blacks, and Mexican-Americans. These estimates are the start of a comprehensive databank of human genetic variation in the United States that will serve as an important reference for future investigations into the role genes play in disease. Some possible future investigations using these estimates might explore how genes affect population-level risk for disease and how genetic variants might contribute to health disparities. These estimates are also available online at www.cdc.gov/genomics/population/genvar/.
Chang M, Lindegren ML, Butler MA, Chanock SJ, Dowling NF, Gallagher M, et al. Prevalence in the United States of Selected Candidate Gene Variants: Third National Health and Nutrition Examination Survey (NHANES III), 1991-1994. American Journal of Epidemiology 2009 Jan 1;169(1):54-66. Epub 2008 Oct 20.
Beyond Gene Discovery (BGD) Workshop
On March 3, 2008, OPHG hosted the first Beyond Gene Discovery workshop entitled Developing the Genome Profile of the U.S. Population and Assessing the Role of Genetic Variation in Health and Disease to discuss data access issues of the NHANES III DNA bank for public health research purposes and to develop an analytical plan for how these data may be used. The purpose of the workshop was to launch a far-reaching initiative to assess the genome profile of the U.S. population using nationally representative samples and to provide access to research datasets for investigators interested in genotype-phenotype analyses. The workshop convened CDC programs, federal partners, academia, and the private sector to review the Beyond Gene Discovery (BGD) plans, discuss analytic issues and develop solutions regarding models for accessing research datasets that maintain human subjects protections. A major outcome of the workshop was the agreement for the National Center for Health Statistics (NCHS) at CDC to establish and fund the first Remote Data Center in Atlanta, Georgia.
NHANES Publications in FY2008
In addition to the major achievement of the Prevalence in the United States of Selected Candidate Gene Variants: Third National Health and Nutrition Examination Survey (NHANES III), 1991-1994 paper, the following paper based on the NHANES III data was published:
Yang QH, Botto LD, Gallagher M, Friedman JM, Sanders CL, Koontz D, et al. Prevalence and effects of gene-gene and gene-nutrient interactions on serum folate and serum total homocysteine concentrations in the United States: findings from the third National Health and Nutrition Examination Survey DNA Bank. Am J Clin Nutr. 2008 Jul;88(1):232-46.
In 2008, OPHG awarded seed funding for five new CDC projects to integrate genomics into existing public health research and programs. Priority was given to those projects with potential to demonstrate health impact within a two-year period. Descriptions of these projects can be found at: http://www.cdc.gov/genomics/population/fund2008.htm.
10th Anniversary Meeting of Public Health Genomics at CDC
In January 2008, OPHG hosted a meeting to highlight progress and achievements in genomics and to discuss future directions. Richard Campanelli of the U.S. Department of Health and Human Services, Julie Gerberding, MD, MPH, director of CDC, and other CDC directors gave welcoming remarks. National and international public health and genomics experts presented on emerging topics, including genome-wide association, human genome epidemiology, family history, genetic testing, and genomics translation research. A scientific poster session showcased a broad scope of more than 70 genomics projects currently being done or recently completed by CDC programs and partners, and other organizations. About 170 scientists and professionals from across CDC and partners from other federal agencies, state health departments, academic and research institutions, and nonprofit organizations attended the event.
- OPHG achievements during the last 10 years are described in the following publications:
10 Years of Public Health Genomics at CDC 1997-2007 (www.cdc.gov/genomics/about/file/print/2007-12_10yr_web.pdf[PDF 3.9MB])
Khoury MJ, Bowen S, Bradley LA, Coates R, Dowling NF, Gwinn M, et al. A Decade of Public Health Genomics in the United States: Centers for Disease Control and Prevention 1997-2007. Public Health Genomics. 2008 Sep 3. [Epub ahead of print]
National Surveys of Direct-To-Consumer Nutrigenomic Tests
In 2008, OPHG utilized two national surveys (HealthStyles and DocStyles) to assess awareness and use of direct-to-consumer personal genome scans among U.S. consumers as well as knowledge of and experiences with these scans among U.S. physicians. OPHG also assessed knowledge of and exposure to EGAPP™ recommendations among U.S. physicians. Preliminary analyses of these data indicate that one in five consumers surveyed were aware of these personal genome scans, but very few had actually used them. OPHG also worked with three state health departments to assess U.S. consumer awareness and use of these scans using the 2009 Behavioral Risk Factor Surveillance System.