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1.  A Review of NCI’s Extramural Grant Portfolio: Identifying Opportunities for Future Research in Genes and Environment in Cancer 
Background
Genetic and environmental factors jointly influence cancer risk. The National Institutes of Health (NIH) has made the study of gene-environment (GxE) interactions a research priority since the year 2000.
Methods
To assess the current status of GxE research in cancer, we analyzed the extramural grant portfolio of the National Cancer Institute (NCI) from Fiscal Years 2007 to 2009. Publications attributed to selected grants were also evaluated.
Results
From the 1,106 research grants identified in our portfolio analysis, a random sample of 450 grants (40%) was selected for data abstraction; of these, 147 (33%) were considered relevant. The most common cancer type was breast (20%, n=29), followed by lymphoproliferative (10%, n=14), colorectal (9%, n=13), melanoma/other skin (9%, n=13), and lung/upper aero-digestive tract (8%, n=12) cancers. The majority of grants were studies of candidate genes (68%, n=100) compared to genome-wide association studies (GWAS) (8%, n=12). Approximately one third studied environmental exposures categorized as energy balance (37%, n=54) or drugs/treatment (29%, n=43). From the 147 relevant grants, 108 publications classified as GxE or pharmacogenomic were identified. These publications were linked to 37 of the 147 grant applications (25%).
Conclusion
The findings from our portfolio analysis suggest that GxE studies are concentrated in specific areas. There is room for investments in other aspects of GxE research, including, but not limited to developing alternative approaches to exposure assessment, broadening the spectrum of cancer types investigated, and performing GxE within GWAS.
Impact
This portfolio analysis provides a cross-sectional review of NCI support for GxE research in cancer.
doi:10.1158/1055-9965.EPI-13-0156
PMCID: PMC3617050  PMID: 23462918
Gene-Environment Interaction; Grants
2.  How do researchers manage genetic results in practice? The experience of the multinational Colon Cancer Family Registry 
Journal of Community Genetics  2013;5(2):99-108.
There is consensus internationally that research participants should be offered the opportunity to receive clinically relevant genetic information identified through research, but there is little empirical peer-reviewed work documenting this process. We report the experience of conducting genetic research with nearly 35,000 participants in the Colon Cancer Family Registry, based in the USA, Canada, Australia, and New Zealand. Investigators from six multinational sites provided information about disclosure protocols, implementation, and uptake of genetic results and made suggestions to inform practice. Across 5 of the 6 registry sites, 1,634 participants in families with mismatch repair or MutYH gene mutations have been offered results. Participant uptake ranged from 56 to 86 %. Researchers faced significant challenges in the effort to return results. We offer suggestions in five key areas: (1) planning for the disclosure process, (2) participant information, (3) autonomy of participants, (4) monitoring scientific progress, and (5) involvement of stakeholders. Despite increasing discussion of the importance of returning incidental findings from genetic research, this paper highlights the considerable diversity, challenges, and costs faced in practice when returning expected findings with established utility and validity. We argue that more work is needed to ensure that genetic results in research are optimally managed.
doi:10.1007/s12687-013-0148-y
PMCID: PMC3955463  PMID: 23703702
Colorectal neoplasms; Genetic predisposition testing; Hereditary nonpolyposis; Disclosure of research results
3.  Translation of Genetics Research to Clinical Medicine: the NHLBI Perspective 
The National Heart, Lung and Blood Institute (NHLBI) is firmly committed to advancing translational research, especially in the field of genetics. An evaluation of the NHLBI’s extramural research grants funded in FY2008 and FY2011 was conducted to establish a baseline from which to assess progress in translational research, to assess current commitments and initial progress, and to identify putative gaps, barriers, and opportunities in the Institute’s human genetics research portfolios.
A search of the category of Genetics using the NIH Research, Condition, and Disease Categorization (RCDC) system was conducted to identify human genetics research project grants in the NHLBI’s genetics research portfolio. The NHLBI genetics portfolios were evaluated using a multidisciplinary research framework continuum that comprises five categories: discovery (T0); characterization (T1); clinical utility (T2); implementation, dissemination and diffusion (T3); and population health impact (T4). The abstracts for the grants were evaluated independently by two reviewers with an adjudicator for discrepancies in coding. The majority of the grants in 2008 and 2011 were classified as T0 and T1 research, with only four grants classified as T2 and beyond.
The majority of genetics grants funded in 2008 and 2011 were in the T0 and T1 categories, although the proportion of grants in T0 actually increased in that period. NHLBI-initiated programs to address this inability to move beyond T1 translation research have yet to have an impact on grant-funded translational genetic research. Future genetics studies should be designed with an eye towards translation to help overcome this barrier.
doi:10.1161/CIRCGENETICS.113.000227
PMCID: PMC3957221  PMID: 24347619
genetics; translational medicine; NHLBI/NIH
4.  “Drivers” of Translational Cancer Epidemiology in the 21st Century: Needs and Opportunities 
Cancer epidemiology is at the cusp of a paradigm shift--propelled by an urgent need to accelerate the pace of translating scientific discoveries into healthcare and population health benefits. As part of a strategic planning process for cancer epidemiologic research, the Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is leading a “longitudinal” meeting with members of the research community to engage in an on-going dialogue to help shape and invigorate the field. Here, we review a translational framework influenced by “drivers” that we believe have begun guiding cancer epidemiology towards translation in the past few years and are most likely to drive the field further in the next decade. The drivers include: (1) collaboration and team science; (2) technology; (3) multi-level analyses and interventions; and (4) knowledge integration from basic, clinical and population sciences. Using the global prevention of cervical cancer as an example of a public health endeavor to anchor the conversation, we discuss how these drivers can guide epidemiology from discovery to population health impact, along the translational research continuum.
doi:10.1158/1055-9965.EPI-12-1262
PMCID: PMC3565029  PMID: 23322363
cancer; epidemiology; medicine; public health; translational research
5.  Frontiers in Cancer Epidemiology: A Challenge to the Research Community from the Epidemiology and Genomics Research Program at the National Cancer Institute 
The Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is develop scientific priorities for cancer epidemiology research in the next decade. We would like to engage the research community and other stakeholders in a planning effort that will include a workshop, in December, 2012, to help shape new foci for cancer epidemiology research. To facilitate the process of defining the future of cancer epidemiology, we invite the research community to join in an ongoing Web-based conversation at http://blog-epi.grants.cancer.gov/ to develop priorities and the next generation of high-impact studies.
doi:10.1158/1055-9965.EPI-12-0525
PMCID: PMC3392448  PMID: 22665580
6.  Multilevel Research and the Challenges of Implementing Genomic Medicine 
Advances in genomics and related fields promise a new era of personalized medicine in the cancer care continuum. Nevertheless, there are fundamental challenges in integrating genomic medicine into cancer practice. We explore how multilevel research can contribute to implementation of genomic medicine. We first review the rapidly developing scientific discoveries in this field and the paucity of current applications that are ready for implementation in clinical and public health programs. We then define a multidisciplinary translational research agenda for successful integration of genomic medicine into policy and practice and consider challenges for successful implementation. We illustrate the agenda using the example of Lynch syndrome testing in newly diagnosed cases of colorectal cancer and cascade testing in relatives. We synthesize existing information in a framework for future multilevel research for integrating genomic medicine into the cancer care continuum.
doi:10.1093/jncimonographs/lgs003
PMCID: PMC3482965  PMID: 22623603
7.  Building the Evidence Base for Decision-making in Cancer Genomic Medicine Using Comparative Effectiveness Research 
Background
The clinical utility is uncertain for many cancer genomic applications. Comparative effectiveness research (CER) can provide evidence to clarify this uncertainty.
Objectives
To identify approaches to help stakeholders make evidence-based decisions, and to describe potential challenges and opportunities using CER to produce evidence-based guidance.
Methods
We identified general CER approaches for genomic applications through literature review, the authors’ experiences, and lessons learned from a recent, seven-site CER initiative in cancer genomic medicine. Case studies illustrate the use of CER approaches.
Results
Evidence generation and synthesis approaches include comparative observational and randomized trials, patient reported outcomes, decision modeling, and economic analysis. We identified significant challenges to conducting CER in cancer genomics: the rapid pace of innovation, the lack of regulation, the limited evidence for clinical utility, and the beliefs that genomic tests could have personal utility without having clinical utility. Opportunities to capitalize on CER methods in cancer genomics include improvements in the conduct of evidence synthesis, stakeholder engagement, increasing the number of comparative studies, and developing approaches to inform clinical guidelines and research prioritization.
Conclusions
CER offers a variety of methodological approaches to address stakeholders’ needs. Innovative approaches are needed to ensure an effective translation of genomic discoveries.
doi:10.1038/gim.2012.16
PMCID: PMC3632438  PMID: 22516979
evidence synthesis; evidence generation; stakeholder; clinical utility
8.  Population Sciences, Translational Research and the Opportunities and Challenges for Genomics to Reduce the Burden of Cancer in the 21st Century 
Advances in genomics and related fields are promising tools for risk assessment, early detection, and targeted therapies across the entire cancer care continuum. In this commentary, we submit that this promise cannot be fulfilled without an enhanced translational genomics research agenda firmly rooted in the population sciences. Population sciences include multiple disciplines that are needed throughout the translational research continuum. For example, epidemiologic studies are needed not only to accelerate genomic discoveries and new biological insights into cancer etiology and pathogenesis, but to characterize and critically evaluate these discoveries in well defined populations for their potential for cancer prediction, prevention and response to treatments. Behavioral, social and communication sciences are needed to explore genomic-modulated responses to old and new behavioral interventions, adherence to therapies, decision-making across the continuum, and effective use in health care. Implementation science, health services, outcomes research, comparative effectiveness research and regulatory science are needed for moving validated genomic applications into practice and for measuring their effectiveness, cost effectiveness and unintended consequences. Knowledge synthesis, evidence reviews and economic modeling of the effects of promising genomic applications will facilitate policy decisions, and evidence-based recommendations. Several independent and multidisciplinary panels have recently made specific recommendations for enhanced research and policy infrastructure to inform clinical and population research for moving genomic innovations into the cancer care continuum. An enhanced translational genomics and population sciences agenda is urgently needed to fulfill the promise of genomics in reducing the burden of cancer.
doi:10.1158/1055-9965.EPI-11-0481
PMCID: PMC3189274  PMID: 21795499
cancer; genetics; genomics; medicine; population sciences; public health; translation
9.  Cancer GAMAdb: database of cancer genetic associations from meta-analyses and genome-wide association studies 
In the field of cancer, genetic association studies are among the most active and well-funded research areas, and have produced hundreds of genetic associations, especially in the genome-wide association studies (GWAS) era. Knowledge synthesis of these discoveries is the first critical step in translating the rapidly emerging data from cancer genetic association research into potential applications for clinical practice. To facilitate the effort of translational research on cancer genetics, we have developed a continually updated database named Cancer Genome-wide Association and Meta Analyses database that contains key descriptive characteristics of each genetic association extracted from published GWAS and meta-analyses relevant to cancer risk. Here we describe the design and development of this tool with the aim of aiding the cancer research community to quickly obtain the current updated status in cancer genetic association studies.
doi:10.1038/ejhg.2011.53
PMCID: PMC3172934  PMID: 21487441
cancer; meta-analyses; pooled analyses; GWAS
10.  The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention Multidisciplinary Workshop 
The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed.
doi:10.1097/GIM.0b013e3181b13a6c
PMCID: PMC2936269  PMID: 19617843
behavioral sciences; epidemiologic methods; evidence-based medicine; genetics; genetic testing; genomics; medicine; public health
11.  Transforming Epidemiology for 21st Century Medicine and Public Health 
In 2012, the National Cancer Institute (NCI) engaged the scientific community to provide a vision for cancer epidemiology in the 21st century. Eight overarching thematic recommendations, with proposed corresponding actions for consideration by funding agencies, professional societies, and the research community emerged from the collective intellectual discourse. The themes are (i) extending the reach of epidemiology beyond discovery and etiologic research to include multilevel analysis, intervention evaluation, implementation, and outcomes research; (ii) transforming the practice of epidemiology by moving towards more access and sharing of protocols, data, metadata, and specimens to foster collaboration, to ensure reproducibility and replication, and accelerate translation; (iii) expanding cohort studies to collect exposure, clinical and other information across the life course and examining multiple health-related endpoints; (iv) developing and validating reliable methods and technologies to quantify exposures and outcomes on a massive scale, and to assess concomitantly the role of multiple factors in complex diseases; (v) integrating “big data” science into the practice of epidemiology; (vi) expanding knowledge integration to drive research, policy and practice; (vii) transforming training of 21st century epidemiologists to address interdisciplinary and translational research; and (viii) optimizing the use of resources and infrastructure for epidemiologic studies. These recommendations can transform cancer epidemiology and the field of epidemiology in general, by enhancing transparency, interdisciplinary collaboration, and strategic applications of new technologies. They should lay a strong scientific foundation for accelerated translation of scientific discoveries into individual and population health benefits.
doi:10.1158/1055-9965.EPI-13-0146
PMCID: PMC3625652  PMID: 23462917
big data; clinical trials; cohort studies; epidemiology; genomics; medicine; public health; technologies; training; translational research
12.  Implementing screening for Lynch syndrome among patients with newly diagnosed colorectal cancer: summary of a public health/clinical collaborative meeting 
Lynch syndrome is the most common cause of inherited colorectal cancer, accounting for approximately 3% of all colorectal cancer cases in the United States. In 2009, an evidence-based review process conducted by the independent Evaluation of Genomic Applications in Practice and Prevention Working Group resulted in a recommendation to offer genetic testing for Lynch syndrome to all individuals with newly diagnosed colorectal cancer, with the intent of reducing morbidity and mortality in family members. To explore issues surrounding implementation of this recommendation, the Centers for Disease Control and Prevention convened a multidisciplinary working group meeting in September 2010. This article reviews background information regarding screening for Lynch syndrome and summarizes existing clinical paradigms, potential implementation strategies, and conclusions which emerged from the meeting. It was recognized that widespread implementation will present substantial challenges, and additional data from pilot studies will be needed. However, evidence of feasibility and population health benefits and the advantages of considering a public health approach were acknowledged. Lynch syndrome can potentially serve as a model to facilitate the development and implementation of population-level programs for evidence-based genomic medicine applications involving follow-up testing of at-risk relatives. Such endeavors will require multilevel and multidisciplinary approaches building on collaborative public health and clinical partnerships.
doi:10.1038/gim.0b013e31823375ea
PMCID: PMC3762677  PMID: 22237445
colorectal cancer; genetic screening; genetic testing; HNPCC; Lynch syndrome
13.  The Geometric Increase in Meta-Analyses from China in the Genomic Era 
PLoS ONE  2013;8(6):e65602.
Meta-analyses are increasingly popular. It is unknown whether this popularity is driven by specific countries and specific meta-analyses types. PubMed was used to identify meta-analyses since 1995 (last update 9/1/2012) and catalogue their types and country of origin. We focused more on meta-analyses from China (the current top producer of meta-analyses) versus the USA (top producer until recently). The annual number of meta-analyses from China increased 40-fold between 2003 and 2011 versus 2.4-fold for the USA. The growth of Chinese meta-analyses was driven by genetics (110-fold increase in 2011 versus 2003). The HuGE Navigator identified 612 meta-analyses of genetic association studies published in 2012 from China versus only 109 from the USA. We compared in-depth 50 genetic association meta-analyses from China versus 50 from USA in 2012. Meta-analyses from China almost always used only literature-based data (92%), and focused on one or two genes (94%) and variants (78%) identified with candidate gene approaches (88%), while many USA meta-analyses used genome-wide approaches and raw data. Both groups usually concluded favorably for the presence of genetic associations (80% versus 74%), but nominal significance (P<0.05) typically sufficed in the China group. Meta-analyses from China typically neglected genome-wide data, and often included candidate gene studies published in Chinese-language journals. Overall, there is an impressive rise of meta-analyses from China, particularly on genetic associations. Since most claimed candidate gene associations are likely false-positives, there is an urgent global need to incorporate genome-wide data and state-of-the art statistical inferences to avoid a flood of false-positive genetic meta-analyses.
doi:10.1371/journal.pone.0065602
PMCID: PMC3680482  PMID: 23776510
14.  Strengthening the Reporting of Genetic Risk Prediction Studies (GRIPS): Explanation and Elaboration 
European journal of epidemiology  2011;26(4):313-337.
The rapid and continuing progress in gene discovery for complex diseases is fuelling interest in the potential application of genetic risk models for clinical and public health practice.The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality.Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction.A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by prior reporting guidelines.These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
doi:10.1007/s10654-011-9551-z
PMCID: PMC3088812  PMID: 21424820
15.  Ethical and Practical Guidelines for Reporting Genetic Research Results To Study Participants: Updated Guidelines from an NHLBI Working Group 
In January 2009 the National Heart, Lung, and Blood Institute (NHLBI) convened a 28-member multidisciplinary Working Group to update the recommendations of a 2004 NHLBI Working Group focused on Guidelines to the Return of Genetic Research Results. Changes in the genetic and societal landscape over the intervening five years raise multiple questions and challenges. The group noted the complex issues arising from the fact that the technologic and bioinformatic progress has made it possible to obtain considerable information on individuals which would not have been possible a decade ago. While unable to reach consensus on a number of issues, the Working Group produced five recommendations. The Working Group offers two recommendations addressing the criteria necessary to determine when genetic results should and may be returned to study participants, respectively. In addition, it suggests that a time limit be established to limit the duration of obligation of investigators to return genetic research results. The Group recommends the creation of a central body, or bodies, to provide guidance on when genetic research results are associated with sufficient risk and have established clinical utility to justify their return to study participants. The final Recommendation urges investigators to engage the broader community when dealing with identifiable communities to advise them on the return of aggregate and individual research results. Creation of an entity charged to provide guidance to IRBs, investigators, research institutions and research sponsors would provide rigorous review of available data, promote standardization of study policies regarding return of genetic research results, and enable investigators and study participants to clarify and share expectations for the handling of this increasingly valuable information with appropriate respect for the rights and needs of participants.
doi:10.1161/CIRCGENETICS.110.958827
PMCID: PMC3090664  PMID: 21156933
consent genetics; ethics; research genetics; risk rediction; single nucleotide polymorphism genetics
16.  Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration 
The rapid and continuing progress in gene discovery for complex diseases is fueling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality. Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by previous reporting guidelines. These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
doi:10.1038/ejhg.2011.27
PMCID: PMC3083630  PMID: 21407270
17.  Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration 
European Journal of Epidemiology  2011;26(4):313-337.
The rapid and continuing progress in gene discovery for complex diseases is fuelling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality. Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by prior reporting guidelines. These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
doi:10.1007/s10654-011-9551-z
PMCID: PMC3088812  PMID: 21424820
Genetic; Risk prediction; Methodology; Guidelines; Reporting

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