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Grant Details

Grant Number: 5R13HG006650-05 Interpret this number
Primary Investigator: Brenner, Steven
Organization: University Of California Berkeley
Project Title: Critical Assessment of Genome Interpretation Conference
Fiscal Year: 2018
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Abstract

We propose to organize two further Critical Assessment of Genome Interpretation (CAGI) conferences, in 2017 and 2018. The CAGI experiments and conferences are providing the primary independent assessment of the state of the art of variation interpretation. In the CAGI experiments participants are provided genetic variants and make blinded predictions of resulting molecular, cellular, organismal, or clinical phenotypes. The new experiments will build on extensive and informative results obtained in the first four rounds. Datasets will include rare disease, common diseases, and germline and somatic cancer variation, from both research and clinical sources. Data types will include complete genomes and exomes, as well as single base changes affecting coding sequence, gene expression, and RNA splicing. Independent assessors will evaluate the predictions against experimentally characterized phenotypes. A CAGI Conference is held at the end of each experiment. The specific goals of the conferences are: (1) to assess the quality of current computational methods for interpreting genomic data, and highlight innovations and progress; (2) to guide future research efforts in computational genome interpretation and build a strong community for collaboration and interaction; and (3) to disseminate results both amongst key members of the variant-phenotype prediction community at the meeting and to a broader audience via publication of results in peer-reviewed journals. The new CAGI experiments will continue the process already established over four rounds, starting in 2010 and with the latest meeting in March 2016. The 2016 experiment yielded 174 submissions on 11 challenges, by 37 groups from 13 countries. 57 people attended the meeting, and we are disseminating results via open access publications and conference presentations. Once again, the participating community was overwhelmingly of the opinion that this experiment is necessary and should be organized again on an ongoing basis. The organizers will continue to encourage the participation of women and underrepresented minorities, and broad participation of trainees and senior scientists at the CAGI conferences. Funding is requested for awarding 17 trainee fellowships for students and postdoctoral researchers to cover registration and approximately 2/3 of their other participation costs. In addition, we seek funding to subsidize registration and approximately half of meeting costs of the independent assessors, some data providers, and the organizers of the CAGI experiments.

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Publications

Stratified polygenic risk prediction model with application to CAGI bipolar disorder sequencing data.
Authors: Wang M.H. , Chang B. , Sun R. , Hu I. , Xia X. , Wu W.K.K. , Chong K.C. , Zee B.C. .
Source: Human Mutation, 2017 Sep; 38(9), p. 1235-1239.
EPub date: 2017-06-13 00:00:00.0.
PMID: 28419606
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Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge.
Authors: Kundu K. , Pal L.R. , Yin Y. , Moult J. .
Source: Human Mutation, 2017 Sep; 38(9), p. 1201-1216.
EPub date: 2017-06-27 00:00:00.0.
PMID: 28497567
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Reports from CAGI: The Critical Assessment of Genome Interpretation.
Authors: Hoskins R.A. , Repo S. , Barsky D. , Andreoletti G. , Moult J. , Brenner S.E. .
Source: Human Mutation, 2017 Sep; 38(9), p. 1039-1041.
PMID: 28817245
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Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I.
Authors: Zhang J. , Kinch L.N. , Cong Q. , Weile J. , Sun S. , Cote A.G. , Roth F.P. , Grishin N.V. .
Source: Human Mutation, 2017 Sep; 38(9), p. 1051-1063.
PMID: 28817247
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Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Authors: Daneshjou R. , Wang Y. , Bromberg Y. , Bovo S. , Martelli P.L. , Babbi G. , Lena P.D. , Casadio R. , Edwards M. , Gifford D. , et al. .
Source: Human Mutation, 2017-06-21 00:00:00.0; , .
EPub date: 2017-06-21 00:00:00.0.
PMID: 28634997
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Deep bipolar: Identifying genomic mutations for bipolar disorder via deep learning.
Authors: Laksshman S. , Bhat R.R. , Viswanath V. , Li X. .
Source: Human Mutation, 2017-06-10 00:00:00.0; , .
EPub date: 2017-06-10 00:00:00.0.
PMID: 28600868
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Ensemble variant interpretation methods to predict enzyme activity and assign pathogenicity in the CAGI4 NAGLU (Human N-acetyl-glucosaminidase) and UBE2I (Human SUMO-ligase) challenges.
Authors: Yin Y. , Kundu K. , Pal L.R. , Moult J. .
Source: Human Mutation, 2017-05-24 00:00:00.0; , .
EPub date: 2017-05-24 00:00:00.0.
PMID: 28544272
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Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests.
Authors: Katsonis P. , Lichtarge O. .
Source: Human Mutation, 2017-05-23 00:00:00.0; , .
EPub date: 2017-05-23 00:00:00.0.
PMID: 28544059
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Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.
Authors: Cai B. , Li B. , Kiga N. , Thusberg J. , Bergquist T. , Chen Y.C. , Niknafs N. , Carter H. , Tokheim C. , Beleva-Guthrie V. , et al. .
Source: Human Mutation, 2017-05-23 00:00:00.0; , .
EPub date: 2017-05-23 00:00:00.0.
PMID: 28544481
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Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges.
Authors: Pejaver V. , Mooney S.D. , Radivojac P. .
Source: Human Mutation, 2017-05-16 00:00:00.0; , .
EPub date: 2017-05-16 00:00:00.0.
PMID: 28508593
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CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants.
Authors: Pal L.R. , Kundu K. , Yin Y. , Moult J. .
Source: Human Mutation, 2017-05-16 00:00:00.0; , .
EPub date: 2017-05-16 00:00:00.0.
PMID: 28512736
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CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease.
Authors: Pal L.R. , Kundu K. , Yin Y. , Moult J. .
Source: Human Mutation, 2017-05-16 00:00:00.0; , .
EPub date: 2017-05-16 00:00:00.0.
PMID: 28512778
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Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.
Authors: Carraro M. , Minervini G. , Giollo M. , Bromberg Y. , Capriotti E. , Casadio R. , Dunbrack R. , Elefanti L. , Fariselli P. , Ferrari C. , et al. .
Source: Human Mutation, 2017-04-25 00:00:00.0; , .
EPub date: 2017-04-25 00:00:00.0.
PMID: 28440912
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Lessons from the CAGI-4 Hopkins clinical panel challenge.
Authors: Chandonia J.M. , Adhikari A. , Carraro M. , Chhibber A. , Cutting G.R. , Fu Y. , Gasparini A. , Jones D.T. , Kramer A. , Kundu K. , et al. .
Source: Human Mutation, 2017-04-11 00:00:00.0; , .
EPub date: 2017-04-11 00:00:00.0.
PMID: 28397312
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Benchmarking Predictions Of Allostery In Liver Pyruvate Kinase In Cagi4
Authors: Xu Q. , Tang Q. , Katsonis P. , Lichtarge O. , Jones D. , Bovo S. , Babbi G. , Martelli P.L. , Casadio R. , Lee G.R. , et al. .
Source: Human Mutation, 2017-03-29 00:00:00.0; , .
PMID: 28370845
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Pon-p And Pon-p2 Predictor Performance In Cagi Challenges: Lessons Learned
Authors: Niroula A. , Vihinen M. .
Source: Human Mutation, 2017-02-22 00:00:00.0; , .
PMID: 28224672
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Predicting Gene Expression In Massively Parallel Reporter Assays: A Comparative Study
Authors: Kreimer A. , Zeng H. , Edwards M.D. , Guo Y. , Tian K. , Shin S. , Welch R. , Wainberg M. , Mohan R. , Sinnott-Armstrong N.A. , et al. .
Source: Human Mutation, 2017-02-21 00:00:00.0; , .
PMID: 28220625
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Accurate Eqtl Prioritization With An Ensemble-based Framework
Authors: Zeng H. , Edwards M.D. , Guo Y. , Gifford D.K. .
Source: Human Mutation, 2017-02-21 00:00:00.0; , .
PMID: 28224684
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Predicting Enhancer Activity And Variant Impact Using Gkm-svm
Authors: Beer M.A. .
Source: Human Mutation, 2017-01-25 00:00:00.0; , .
PMID: 28120510
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Blind prediction of deleterious amino acid variations with SNPs&GO.
Authors: Capriotti E. , Martelli P.L. , Fariselli P. , Casadio R. .
Source: Human Mutation, 2017-01-19 00:00:00.0; , .
EPub date: 2017-01-19 00:00:00.0.
PMID: 28102005
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Crohn Disease Risk Prediction-best Practices And Pitfalls With Exome Data
Authors: Giollo M. , Jones D.T. , Carraro M. , Leonardi E. , Ferrari C. , Tosatto S.C. .
Source: Human Mutation, 2017-01-13 00:00:00.0; , .
PMID: 28087895
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Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
Authors: Dudley J.T. , Listgarten J. , Stegle O. , Brenner S.E. , Parts L. .
Source: Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing, 2015; , p. 342-6.
PMID: 25592594
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Personalized Medicine: From Genotypes And Molecular Phenotypes Towards Therapy- Session Introduction
Authors: Listgarten J. , Stegle O. , Morris Q. , Brenner S.E. , Parts L. .
Source: Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing, 2014; 19, p. 224-8.
PMID: 24297549
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PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.
Authors: Stegle O. , Brenner S.E. , Morris Q. , Listgarten J. .
Source: Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing, 2013; 18, p. 171-174.
PMID: 23424122
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The future of genome-based medicine.
Authors: Morris Q. , Brenner S.E. , Listgarten J. , Stegle O. .
Source: Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing, 2013; , p. 456-8.
PMID: 23424151
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