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A public resource facilitating clinical use of genomes.

ABSTRACT: Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved "open consent" process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain-we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research.

SUBMITTER: Ball MP

PROVIDER: S-EPMC3409785 | biostudies-other | 2012 Jul

REPOSITORIES: biostudies-other

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A public resource facilitating clinical use of genomes.

Ball Madeleine P MP Thakuria Joseph V JV Zaranek Alexander Wait AW Clegg Tom T Rosenbaum Abraham M AM Wu Xiaodi X Angrist Misha M Bhak Jong J Bobe Jason J Callow Matthew J MJ Cano Carlos C Chou Michael F MF Chung Wendy K WK Douglas Shawn M SM Estep Preston W PW Gore Athurva A Hulick Peter P Labarga Alberto A Lee Je-Hyuk JH Lunshof Jeantine E JE Kim Byung Chul BC Kim Jong-Il JI Li Zhe Z Murray Michael F MF Nilsen Geoffrey B GB Peters Brock A BA Raman Anugraha M AM Rienhoff Hugh Y HY Robasky Kimberly K Wheeler Matthew T MT Vandewege Ward W Vorhaus Daniel B DB Yang Joyce L JL Yang Luhan L Aach John J Ashley Euan A EA Drmanac Radoje R Kim Seong-Jin SJ Li Jin Billy JB Peshkin Leonid L Seidman Christine E CE Seo Jeong-Sun JS Zhang Kun K Rehm Heidi L HL Church George M GM

Proceedings of the National Academy of Sciences of the United States of America 20120713 30

Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved "open consent" process. The contribution of public data and samples facilitates both scientific discovery and stan ...[more]

PMID: 22797899

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Project description:AimsThe aims of this study were to describe patient characteristics of the adult chronic heart failure (HF) population and to estimate the prevalence, incidence, healthcare resource utilization (HCRU), and mortality associated with HF in Southwest Finland.Methods and resultsThis was a retrospective biobank and clinical registry study. Adult patients with an HF diagnosis (International Statistical Classification of Diseases and Related Health Problems (ICD) code I50) during 2004-2013 in secondary care were included in the study and compared with age-matched and gender-matched control patients without an I50 diagnosis. HF patients were stratified in groups by left ventricular ejection fraction (LVEF) as follows: LVEF < 40% [HF with reduced ejection fraction (HFrEF)]; LVEF ≥ 40% [HF with preserved ejection fraction (HFpEF)]; or unknown (LVEF unknown). HCRU was stratified by inpatient, outpatient, and emergency room visits. In 2013, the incidence of HF was 3.2/1000, and the prevalence was 13.9/1000 inhabitants (n = 15 594). In the stratified analysis of HF patients (n = 8833, average ± SD age 77.1 ± 11.2), 1115 (12.6%) patients had HFrEF (female 31.3%), 1449 (16.4%) had HFpEF (female 50.9%), and 6269 (71%) had unknown LVEF (female 52.1%). The most common co-morbidities were essential hypertension (58%), chronic elevated serum creatinine (57.3%), atrial fibrillation and flutter (55.1%), and chronic ischaemic heart disease (46.4%). Patients with HF diagnosis had higher HCRU compared with that of age-matched and gender-matched controls (3.7 more days per year at the hospital for HF patients compared with the controls). The total 5 year mortality was 62.6% for HF patients and 28.3% for controls, with higher age being the strongest predictor of mortality. Moreover, multivariable Cox regression analysis showed that patients with HFrEF had a 13% (95% confidence interval 2.7-25%) increased risk of mortality compared with HFpEF patients.ConclusionsThe high mortality rate and HCRU among the studied HF patients highlight the severity of the disease and the economic and social burden on both patients and society. This calls for improved methods of care for this large patient population.

Project description:BackgroundIn Ethiopia, public hospitals deal with a persistent human resource crisis, even by Sub-Saharan Africa (SSA) standards. Policy and hospital reforms, however, have thus far resulted in limited progress towards addressing the strategic human resource management (SHRM) challenges Ethiopia's public hospitals face.MethodsTo explore the contextual factors influencing these SHRM challenges of Ethiopian public hospitals, we conducted a qualitative study based on the Contextual SHRM framework of Paauwe. A total of 19 structured interviews were conducted with Chief Executive Officers (CEOs) and HR managers from a purposive sample of 15 hospitals across Ethiopia. An additional four focus groups were held with professionals and managers.ResultsThe study found that hospitals compete on the supply side for scarce resources, including skilled professionals. There was little reporting on demand-side competition for health services provided, service quality, and service innovation. Governmental regulations were the main institutional mechanism in place. These regulations also emphasized human resources and were perceived to tightly regulate employee numbers, salaries, and employment arrangements at detailed levels. These regulations were perceived to restrict the autonomy of hospitals regarding SHRM. Regulation-induced differences in allowances and external employment arrangements were among the concerns that decreased motivation and job satisfaction and caused employees to leave. The mismatch between regulation and workforce demands posed challenges for leadership and caused leaders to be perceived as incompetent and unable when they could not successfully address workforce needs.ConclusionsBottom-up involvement in SHRM may help resolve the aforementioned persistent problems. The Ethiopian government might better loosen regulations and provide more autonomy to hospitals to develop SHRM and implement mechanisms that emphasize the quality of the health services demanded rather than the quantity of human resources supplied.

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A public resource facilitating clinical use of genomes.

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A public resource facilitating clinical use of genomes.

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