@article{6d47ac526527464283ff1f44cf86e007,
title = "Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges",
abstract = "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.",
keywords = "Crohn's disease, bipolar disorder, exomes, machine learning, phenotype prediction, warfarin",
author = "Roxana Daneshjou and Yanran Wang and Yana Bromberg and Samuele Bovo and Martelli, {Pier L.} and Giulia Babbi and Lena, {Pietro Di} and Rita Casadio and Matthew Edwards and David Gifford and Jones, {David T.} and Laksshman Sundaram and Bhat, {Rajendra Rana} and Xiaolin Li and Pal, {Lipika R.} and Kunal Kundu and Yizhou Yin and John Moult and Yuxiang Jiang and Vikas Pejaver and Pagel, {Kymberleigh A.} and Biao Li and Mooney, {Sean D.} and Predrag Radivojac and Sohela Shah and Marco Carraro and Alessandra Gasparini and Emanuela Leonardi and Manuel Giollo and Carlo Ferrari and Tosatto, {Silvio C.E.} and Eran Bachar and Azaria, {Johnathan R.} and Yanay Ofran and Ron Unger and Abhishek Niroula and Mauno Vihinen and Billy Chang and Wang, {Maggie H.} and Andre Franke and Petersen, {Britt Sabina} and Mehdi Pirooznia and Peter Zandi and Richard McCombie and Potash, {James B.} and Altman, {Russ B.} and Klein, {Teri E.} and Hoskins, {Roger A.} and Susanna Repo and Brenner, {Steven E.} and Morgan, {Alexander A.}",
note = "Funding Information: We would like to thank and acknowledge the CAGI planning committee, as well as all data providers and participants. R.M. has participated in Illumina-sponsored meetings over the last 4 years and received travel reimbursement and an honorarium for presenting at these events. Illumina had no role in decisions relating to the study/work to be published, data collection, and analysis of data and the decision to publish. R.M. has participated in Pacific Biosciences-sponsored meetings over the last 3 years and received travel reimbursement for presenting at these events. R.M. is a founder and shared holder of Orion Genomics, which focuses on plant genomics and cancer genetics. R.M. is a SAB member for RainDance Technologies, Inc. All the other authors have no conflict of interest to declare. Publisher Copyright: {\textcopyright} 2017 Wiley Periodicals, Inc.",
year = "2017",
month = sep,
doi = "10.1002/humu.23280",
language = "English (US)",
volume = "38",
pages = "1182--1192",
journal = "Human mutation",
issn = "1059-7794",
publisher = "Wiley-Liss Inc.",
number = "9",
}