Dataset Information

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

ABSTRACT: The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.

SUBMITTER: Cai B

PROVIDER: S-EPMC5645203 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Cai Binghuang B Li Biao B Kiga Nikki N Thusberg Janita J Bergquist Timothy T Chen Yun-Ching YC Niknafs Noushin N Carter Hannah H Tokheim Collin C Beleva-Guthrie Violeta V Douville Christopher C Bhattacharya Rohit R Yeo Hui Ting Grace HTG Fan Jean J Sengupta Sohini S Kim Dewey D Cline Melissa M Turner Tychele T Diekhans Mark M Zaucha Jan J Pal Lipika R LR Cao Chen C Yu Chen-Hsin CH Yin Yizhou Y Carraro Marco M Giollo Manuel M Ferrari Carlo C Leonardi Emanuela E Tosatto Silvio C E SCE Bobe Jason J Ball Madeleine M Hoskins Roger A RA Repo Susanna S Church George G Brenner Steven E SE Moult John J Gough Julian J Stanke Mario M Karchin Rachel R Mooney Sean D SD

Human mutation 20170619 9

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genome ...[more]

PMID: 28544481

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Project description:BACKGROUND:Historical changes in the nature of sedentary activities have been observed in other countries, but it is not clear if similar trends exist in Canada. It is also unclear how changes in the measurement of sedentary behaviour affects national estimates. Our objective is to document all sources and measures of sedentary behaviour from Canadian, nationally representative surveys, and report on selected estimates of time spent in sedentary activities. Lessons learned can benefit the wider international surveillance community. METHODS:We describe and document all data sources of sedentary behaviour at the national level in Canada, and report on selected prevalence data from repeated cross-sectional surveys. We summarize amounts of total device-assessed sedentary time and self-reported sedentary activities (e.g., passive travel, leisure television, computer, video games, screen, and reading) by age group over time. RESULTS:Nineteen national surveys were identified. Changes in questions and/or response categories precluded direct assessment of trends over time for some measures; however, certain trends were observed. Accelerometer-measured sedentary time, leisure reading (among those < 50 years) and television/video viewing in younger age groups have remained relatively stable (with a possible slight decline in television/video viewing). Time spent in passive travel and leisure computer and electronic device use appears to have increased. Television and video viewing appears to have increased in older adults while their leisure reading appears to have fallen. CONCLUSIONS:Changes in measurement of sedentary behaviour can affect estimates and reduce comparability over time. Total leisure screen use appears to have increased over time, reflecting the ways in which Canadians spend their free time and technological advances. The main public health message is the need for continued efforts to reduce leisure screen use, especially among youth and older adults.

Project description:BackgroundClinical trials management can be studied using project management theory. The CYCLE pilot randomized controlled trial (RCT) was conducted to determine the feasibility of a future rehabilitation trial of early in-bed cycling in the intensive care unit (ICU). In-bed cycling is a novel intervention, not typically available in ICUs. Implementation of this intervention requires personnel with specialized clinical expertise caring for critically ill patients and use of the in-bed cycle. Our objective was to describe the implementation and conduct of our pilot RCT using a project management approach.MethodsWe retrospectively reviewed activities, timelines, and personnel involved in the trial. We organized activities into four project management phases: initiation, planning, execution, and monitoring and controlling. Data sources included Methods Centre documents used for trial coordination and conduct, and the trial data set. We report descriptive statistics as counts and proportions and also medians and quartiles, and we summarize the lessons learned.ResultsSeven ICUs in Canada participated in the trial. Time from research ethics board and contracts submission to first enrolment was a median (first quartile, third quartile) of 185 (146, 209) and 162 (114, 181) days, respectively. We trained 128 personnel on the CYCLE pilot RCT protocol, and 80 (63%) completed trial-related activities. Four sites required additional training after start-up due to staff turnover and leaves of absence. Over 15 months, we screened 864 patients: 256 were eligible and 66 were enrolled. Despite an 85% consent rate, 74% (190/256) of eligible patients were not randomized, largely (80% [152/190]) due to physiotherapist availability. Thirteen percent of recruitment weeks were lost due to physiotherapist staffing shortages. We highlight five key lessons learned: (1) prepare and anticipate site needs; (2) communicate regularly; (3) proactively analyse and act on process measure data; (4) develop contingency plans; (5) express appreciation to participating sites.ConclusionsOur analysis highlights the scope of relevant activities, rigorous training and monitoring, number and types of required personnel, and time required to conduct a multicentre ICU rehabilitation intervention trial. Our lessons learned can help others interested in implementing complex intervention trials, such as rehabilitation.Trial registrationClinicalTrials.gov, NCT02377830 . Registered prospectively on 4 March 2015.

Dataset Information

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Publications

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

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