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Working toward precision medicine : Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Daneshjou, Roxana (author)
Stanford University
Wang, Yanran (author)
Rutgers University: The State University of New Jersey
Bromberg, Yana (author)
Rutgers University: The State University of New Jersey
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Bovo, Samuele (author)
University of Bologna
Martelli, Pier Luigi (author)
University of Bologna
Babbi, Giulia (author)
University of Bologna
Lena, Pietro Di (author)
University of Bologna
Casadio, Rita (author)
University of Bologna
Edwards, Matthew (author)
Massachusetts Institute of Technology
Gifford, David (author)
Massachusetts Institute of Technology
Jones, David T W (author)
Sundaram, Laksshman (author)
Bhat, Rajendra (author)
Li, Xiaolin (author)
Pal, Lipika R. (author)
Kundu, Kunal (author)
Yin, Yizhou (author)
Moult, John (author)
Jiang, Yuxiang (author)
Pejaver, Vikas R. (author)
Pagel, Kymberleigh A. (author)
Li, Biao (author)
Mooney, Sean D. (author)
Radivojac, Predrag (author)
Shah, Sohela (author)
Carraro, Marco (author)
Gasparini, Alessandra (author)
Leonardi, Emanuela (author)
Giollo, Manuel (author)
Ferrari, Carlo (author)
Tosatto, Silvio C.E. (author)
Bachar, Eran (author)
Azaria, Johnathan R. (author)
Ofran, Yanay (author)
Unger, Ron (author)
Niroula, Abhishek (author)
Lund University,Lunds universitet,Proteinbioinformatik,Forskargrupper vid Lunds universitet,Hematogenomics,Protein Bioinformatics,Lund University Research Groups
Vihinen, Mauno (author)
Lund University,Lunds universitet,Proteinbioinformatik,Forskargrupper vid Lunds universitet,Protein Bioinformatics,Lund University Research Groups
Chang, Billy (author)
Wang, Maggie H. (author)
Franke, Andre (author)
Petersen, Britt Sabina (author)
Pirooznia, Mehdi (author)
Zandi, Peter (author)
Mccombie, Richard (author)
Potash, James B. (author)
Altman, Russ B. (author)
Klein, Teri E. (author)
Hoskins, Roger A. (author)
Repo, Susanna (author)
Brenner, Steven E (author)
Morgan, Alexander A. (author)
Stanford University
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 (creator_code:org_t)
2017-07-07
2017
English.
In: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 38:9, s. 1182-1192
Related links:
http://dx.doi.org/10...
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https://lup.lub.lu.s...
https://doi.org/10.1...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Annan medicin och hälsovetenskap -- Övrig annan medicin och hälsovetenskap (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Other Medical and Health Sciences -- Other Medical and Health Sciences not elsewhere specified (hsv//eng)

Keyword

Bipolar disorder
Crohn's disease
Exomes
Machine learning
Phenotype prediction
Warfarin

Publication and Content Type

art (subject category)
ref (subject category)

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