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PS3-16: Access and Collaboration with the Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH).

ABSTRACT: Background/AimsThe Kaiser Permanente Northern California (KPNC) Research Program on Genes, Environment, and Health (RPGEH) provides a research resource to support investigations of environmental and genetic factors in the development of a wide variety of conditions. While the resource is still evolving with new data collection, it consists of data from surveys and electronic medical records on over 400,000 adult members of KPNC; biospecimens collected and stored on ~200,000 of these individuals; and data from genome-wide and telomere-length assays on ~110,000 of those who have contributed biospecimens; and linkage of these members to environmental, area-level databases.MethodsThe RPGEH was developed in part with the understanding that it would be made available to the scientific community for appropriate studies. An Access and Collaborations Core has developed procedures for submission of applications for research studies, their review, and decisions on approval and support. Review of proposals by an Applications Review Committee follows a two-step process, with a pre-application to assess feasibility (e.g., adequate numbers of the phenotype: availability of appropriate data, given inclusion criteria) and a full application to assess appropriateness of the study in the RPGEH context. Scientific merit; alignment with RPGEH guiding principles, including ethical, legal, and social implications; consistency with informed consents; potential overlap with prior approvals; and collaboration with a researcher affiliated with the Division of Research are among the criteria for approval. As an alternative for select analyses, genomic and selected phenotypic data will be available in the NIH database of genotypes and phenotypes (dbGaP) for the substantial subset of RPGEH participants who have consented to dbGaP deposition.ResultsAs of October 31, 2012, the RPGEH has received 74 pre-applications and full applications for the use of its resources; only 6 pre-applications were not approved. In 2011–2012, 13 approved applications were funded by NIH and other agencies. Studies currently underway include genome-wide association studies of prostate cancer, bi-polar disorder, multiple sclerosis, and mammographic density.ConclusionsAccess to the unique and outstanding research resources of the RPGEH balances the mission of promoting research with the need to shepherd finite resources and safeguard member confidentiality.

SUBMITTER: Schaffer D

PROVIDER: S-EPMC3788530 | biostudies-other | 2013 Sep

REPOSITORIES: biostudies-other

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Project description:Background/AimsThe Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort has genotyped data on over 100,000 participants. In order to characterize many health conditions of interest found among respondents for sample-size estimation and GWAS, we sought to extend methodologies that utilized the Electronic Medical Record (EMR) in an automated way to characterize many diseases without the expense and limitation of numerous, complex algorithms specific to individual diseases and conditions.MethodsWe tested a probabilistic approach that scored clinical decisions recorded in the EMR to capture specific diagnostic and treatment domains. We first considered physician diagnosis alone. We assessed sensitivity and specificity against internal registries at the Kaiser Permanente Northern California Division of Research. We also used the methodology to characterize phenotypes for Types 1 and 2 diabetes for GWAS. We tested a single diagnostic domain in a logistic model based on an ICD-9-CM taxonomy and found high sensitivity and specificity when compared with internal registries for breast, lung, colon and prostate cancers; Barrett’s esophagus; HIV; Crohn’s disease; ulcerative colitis, and diabetes. We then assessed a logistic regression model to distinguish among members with Types 1 and 2 diabetes in the genotyped cohort, utilizing the ICD-9 taxonomy, the earliest age at diagnosis available in the EMR or by self-report, and pharmacy prescription utilization of anti-diabetic drugs.ResultsThe model exhibited a sensitivity of 96.3% and specificity of 99.6% for Type 1 diabetes and a sensitivity of 94.0% and specificity of 98.4% for Type 2 diabetes when compared with the gold standard internal diabetes registry. We identified an additional 60 cases of Type 1 diabetes and conducted comparative GWAS.ConclusionsUtilizing diagnostic information in the EMR as independent domains in probabilistic models to accomplish phenotype creation appears to be a reliable approach to facilitate robust characterization for evaluation, analysis and mapping of numerous disease phenotypes. The method is agnostic to input taxonomies as long as the EMR record contains sufficient and reliable atomic detail. It can also be adapted for machine learning given expert user feedback when gold standard databases are not available.

Project description:The Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) is a resource developed to facilitate research on genetic and environmental factors on common diseases and healthy aging. The RPGEH resource links biospecimens, health surveys, and comprehensive electronic medical records on broadly consented adult members of Kaiser Permanente Medical Care Plan, Northern California Region (KPNC). KPNC is an integrated health care delivery system with a membership of approximately 3.3 million people in northern California. The membership of KPNC is representative of the general population in the 14 county area in which facilities are located, although extremes of income are underrepresented. At the end of 2013, the RPGEH resource included: (1) demographic and behavioral surveys from over 430,000 participants; (2) biospecimens (DNA, serum, plasma, and/or saliva) from over 204,000 participants, including over 13,000 pregnant women; (3) genome-wide genotype data (70 billion SNP genotypes) on over 100,000 participants, including the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort; and (4) the longitudinal electronic medical records of the participants. The RPGEH was developed beginning in 2005 at the Division of Research of Kaiser Permanente Northern California by Catherine Schaefer (Director), Neil Risch (Co-Director), Lisa Croen, Eric Jorgenson, Lawrence Kushi, Charles Quesenberry, Sarah Rowell, Carol Somkin, Stephen Van den Eeden, Larry Walter, and Rachel Whitmer. Funding of the RPGEH was provided to C. Schaefer (PI) and N. Risch (co-PI) by the Wayne and Gladys Valley Foundation, The Ellison Medical Foundation, the Robert Wood Johnson Foundation, Kaiser Permanente Northern California, and the Kaiser Permanente National and Regional Community Benefit Programs. The GERA cohort was funded by a grant from NIH to RPGEH and UCSF (RC2 AG036607; C. Schaefer and N. Risch, PIs). At the time of the award of the RC2 project in late 2009, the RPGEH had established a cohort of about 140,000 individuals who had answered a detailed survey, provided saliva samples for extraction of DNA, and given broad consent for the use of their data in studies of health and disease. Survey and Cohort Recruitment. Initially, the RPGEH developed electronic disease registries to enable identification of phenotypes, using algorithms applied to EMR data. In 2007, the RPGEH mailed a four page survey to 1.9 million adult (≥ 18 years old) members of KPNC who had been members for two years or more, to obtain data on demographic and behavioral factors complementary to the clinical data in the EMR. The survey materials included a cover letter introducing the RPGEH, a two page list of Frequently Asked Questions, and the survey, which included questions on demographic factors such as education, race-ethnicity, income and marital status, dietary factors, physical activity, smoking, and alcohol consumption, as well as reproductive history and reproductive health. Members whose electronic medical records indicated a preference for written communications in Chinese or Spanish received survey materials both in English and a Chinese or Spanish translation. Approximately 400,000 completed surveys were returned. Saliva Sample Collection. Beginning in July 2008, respondents to the survey were asked to sign and return a consent form and authorization for use and disclosure of protected health information. The consent form authorized broad use of biospecimens, survey data, and data from participants' electronic health records for use in studies of genetic and environmental influences on health and disease. Respondents who returned completed consent forms were mailed (Oragene) saliva collection kits; more than 132,000 saliva samples were collected in two years. Completed saliva kits were scanned and archived in a temporary biorepository at the KPNC Division of Research. In late 2009, the RPGEH began collection of saliva samples from the California Men's Health Study (CMHS), a cohort that had been previously assembled in 2002-2003 and had been excluded from the RPGEH survey mailing with the intent of later adding CMHS participants to the assembled RPGEH cohort. The CMHS was developed to facilitate research on prostate cancer and other conditions in older men; the study protocol is described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/16813653" target="_blank">Enger, et al., 2006</a>. It enrolled and surveyed more than 40,000 men in KPNC, ages 45-69 years, who were members of KPNC during 2002-2003. CMHS men completed two mailed surveys with demographic and behavioral data similar to that of the RPGEH. The data on analogous variables were reconciled and integrated with the data derived from the RPGEH cohort for use in the RPGEH resource. By 2011, RPGEH collected approximately 15,400 saliva samples from men participating in the CMHS. RPGEH Access and Collaborations Website and Procedures. The RPGEH maintains a web portal for inquiries and applications for collaboration and access to data. The url is: <a href="https://rpgehportal.kaiser.org/" target="_blank">https://rpgehportal.kaiser.org/</a>. RPGEH has an application process and an Access Review Committee that reviews applications for collaboration and use. For more information, please contact RPGEH through the website.

Project description:BackgroundIn the last few decades, mobile technologies have been widely adopted in the field of health care services to improve the accessibility to and the quality of health services received. Mobile health (mHealth) has emerged as a field of research with increasing attention being paid to it by scientific researchers and a rapid increase in related literature being reported.ObjectiveThe purpose of this study was to analyze the current state of research, including publication outputs, in the field of mHealth to uncover in-depth collaboration characteristics and topic burst of international mHealth research.MethodsThe authors collected literature that has been published in the last 20 years and indexed by Thomson Reuters Web of Science Core Collection (WoSCC). Various statistical techniques and bibliometric measures were employed, including publication growth analysis; journal distribution; and collaboration network analysis at the author, institution, and country collaboration level. The temporal visualization map of burst terms was drawn, and the co-occurrence matrix of these burst terms was analyzed by hierarchical cluster analysis and social network analysis.ResultsA total of 2704 bibliographic records on mHealth were collected. The earliest paper centered on mHealth was published in 1997, with the number of papers rising continuously since then. A total of 21.28% (2318/10,895) of authors publishing mHealth research were first author, whereas only 1.29% (141/10,895) of authors had published one paper. The total degree of author collaboration was 4.42 (11,958/2704) and there are 266 core authors who have collectively published 53.07% (1435/2704) of the total number of publications, which means that the core group of authors has fundamentally been formed based on the Law of Price. The University of Michigan published the highest number of mHealth-related publications, but less collaboration among institutions exits. The United States is the most productive country in the field and plays a leading role in collaborative research on mHealth. There are 5543 different identified keywords in the cleaned records. The temporal bar graph clearly presents overall topic evolutionary process over time. There are 12 important research directions identified, which are in the imbalanced development. Moreover, the density of the network was 0.007, a relatively low level. These 12 topics can be categorized into 4 areas: (1) patient engagement and patient intervention, (2) health monitoring and self-care, (3) mobile device and mobile computing, and (4) security and privacy.ConclusionsThe collaboration of core authors on mHealth research is not tight and stable. Furthermore, collaboration between institutions mainly occurs in the United States, although country collaboration is seen as relatively scarce. The focus of research topics on mHealth is decentralized. Our study might provide a potential guide for future research in mHealth.

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PS3-16: Access and Collaboration with the Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH).

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