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

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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.

Detaljer

Författare
  • Roxana Daneshjou
  • Yanran Wang
  • Yana Bromberg
  • Samuele Bovo
  • Pier Luigi Martelli
  • Giulia Babbi
  • Pietro Di Lena
  • Rita Casadio
  • Matthew Edwards
  • David Gifford
  • David T W Jones
  • Laksshman Sundaram
  • Rajendra Bhat
  • Xiaolin Li
  • Lipika R. Pal
  • Kunal Kundu
  • Yizhou Yin
  • John Moult
  • Yuxiang Jiang
  • Vikas R. Pejaver
  • Kymberleigh A. Pagel
  • Biao Li
  • Sean D. Mooney
  • Predrag Radivojac
  • Sohela Shah
  • Marco Carraro
  • Alessandra Gasparini
  • Emanuela Leonardi
  • Manuel Giollo
  • Carlo Ferrari
  • Silvio C.E. Tosatto
  • Eran Bachar
  • Johnathan R. Azaria
  • Yanay Ofran
  • Ron Unger
  • Billy Chang
  • Maggie H. Wang
  • Andre Franke
  • Britt Sabina Petersen
  • Mehdi Pirooznia
  • Peter Zandi
  • Richard Mccombie
  • James B. Potash
  • Russ B. Altman
  • Teri E. Klein
  • Roger A. Hoskins
  • Susanna Repo
  • Steven E Brenner
  • Alexander A. Morgan
Enheter & grupper
Externa organisationer
  • Stanford University
  • Rutgers University: The State University of New Jersey
  • University of Bologna
  • Massachusetts Institute of Technology
Forskningsområden

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Övrig annan medicin och hälsovetenskap

Nyckelord

Originalspråkengelska
Sidor (från-till)1182-1192
TidskriftHuman Mutation
Volym38
Utgåva nummer9
StatusPublished - 2017
PublikationskategoriForskning
Peer review utfördJa