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Title: Lessons from the CAGI-4 Hopkins clinical panel challenge

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [5];  [4];  [6];  [7];  [8];  [9];  [4];  [10]; ORCiD logo [11];  [12];  [13];  [8];  [14]; ORCiD logo [15];  [9];  [5]
  1. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley California
  2. Department of Plant and Microbial Biology, University of California, Berkeley California
  3. Department of Biomedical Sciences, University of Padova, Padova Italy
  4. Roche Sequencing Solutions, Belmont California
  5. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore Maryland
  6. Department of Biomedical Sciences, University of Padova, Padova Italy, Department of Women's and Children's Health, University of Padova, Padova Italy
  7. Department of Computer Science, University College London, London United Kingdom
  8. Qiagen Bioinformatics, Redwood City California
  9. Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville Maryland, Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park Maryland
  10. Department of Women's and Children's Health, University of Padova, Padova Italy
  11. Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville Maryland, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park Maryland
  12. Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville Maryland
  13. Independent Consultant, Philadelphia Pennsylvania
  14. Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston Massachusetts, Department of Biomedical Informatics, Harvard Medical School, Boston Massachusetts
  15. Department of Biomedical Sciences, University of Padova, Padova Italy, CNR Institute of Neuroscience, Padova Italy
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1375505
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Human Mutation
Additional Journal Information:
Journal Name: Human Mutation Journal Volume: 38 Journal Issue: 9; Journal ID: ISSN 1059-7794
Publisher:
Wiley
Country of Publication:
United States
Language:
English

Citation Formats

Chandonia, John-Marc, Adhikari, Aashish, Carraro, Marco, Chhibber, Aparna, Cutting, Garry R., Fu, Yao, Gasparini, Alessandra, Jones, David T., Kramer, Andreas, Kundu, Kunal, Lam, Hugo Y. K., Leonardi, Emanuela, Moult, John, Pal, Lipika R., Searls, David B., Shah, Sohela, Sunyaev, Shamil, Tosatto, Silvio C. E., Yin, Yizhou, and Buckley, Bethany A. Lessons from the CAGI-4 Hopkins clinical panel challenge. United States: N. p., 2017. Web. doi:10.1002/humu.23225.
Chandonia, John-Marc, Adhikari, Aashish, Carraro, Marco, Chhibber, Aparna, Cutting, Garry R., Fu, Yao, Gasparini, Alessandra, Jones, David T., Kramer, Andreas, Kundu, Kunal, Lam, Hugo Y. K., Leonardi, Emanuela, Moult, John, Pal, Lipika R., Searls, David B., Shah, Sohela, Sunyaev, Shamil, Tosatto, Silvio C. E., Yin, Yizhou, & Buckley, Bethany A. Lessons from the CAGI-4 Hopkins clinical panel challenge. United States. doi:10.1002/humu.23225.
Chandonia, John-Marc, Adhikari, Aashish, Carraro, Marco, Chhibber, Aparna, Cutting, Garry R., Fu, Yao, Gasparini, Alessandra, Jones, David T., Kramer, Andreas, Kundu, Kunal, Lam, Hugo Y. K., Leonardi, Emanuela, Moult, John, Pal, Lipika R., Searls, David B., Shah, Sohela, Sunyaev, Shamil, Tosatto, Silvio C. E., Yin, Yizhou, and Buckley, Bethany A. Tue . "Lessons from the CAGI-4 Hopkins clinical panel challenge". United States. doi:10.1002/humu.23225.
@article{osti_1375505,
title = {Lessons from the CAGI-4 Hopkins clinical panel challenge},
author = {Chandonia, John-Marc and Adhikari, Aashish and Carraro, Marco and Chhibber, Aparna and Cutting, Garry R. and Fu, Yao and Gasparini, Alessandra and Jones, David T. and Kramer, Andreas and Kundu, Kunal and Lam, Hugo Y. K. and Leonardi, Emanuela and Moult, John and Pal, Lipika R. and Searls, David B. and Shah, Sohela and Sunyaev, Shamil and Tosatto, Silvio C. E. and Yin, Yizhou and Buckley, Bethany A.},
abstractNote = {},
doi = {10.1002/humu.23225},
journal = {Human Mutation},
number = 9,
volume = 38,
place = {United States},
year = {2017},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/humu.23225

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Cited by: 1 work
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Works referenced in this record:

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
journal, July 2010

  • Wang, K.; Li, M.; Hakonarson, H.
  • Nucleic Acids Research, Vol. 38, Issue 16
  • DOI: 10.1093/nar/gkq603

A general framework for estimating the relative pathogenicity of human genetic variants
journal, February 2014

  • Kircher, Martin; Witten, Daniela M.; Jain, Preti
  • Nature Genetics, Vol. 46, Issue 3
  • DOI: 10.1038/ng.2892

Analysis of protein-coding genetic variation in 60,706 humans
journal, August 2016

  • Lek, Monkol; Karczewski, Konrad J.; Minikel, Eric V.
  • Nature, Vol. 536, Issue 7616
  • DOI: 10.1038/nature19057

Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2
journal, January 2013

  • Adzhubei, Ivan; Jordan, Daniel M.; Sunyaev, Shamil R.
  • Current Protocols in Human Genetics, Vol. 76, Issue 1
  • DOI: 10.1002/0471142905.hg0720s76

Genetic Misdiagnoses and the Potential for Health Disparities
journal, August 2016

  • Manrai, Arjun K.; Funke, Birgit H.; Rehm, Heidi L.
  • New England Journal of Medicine, Vol. 375, Issue 7
  • DOI: 10.1056/NEJMsa1507092

Applying Cystic Fibrosis Transmembrane Conductance Regulator Genetics and CFTR2 Data to Facilitate Diagnoses
journal, February 2017


Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
journal, June 2009

  • Kumar, Prateek; Henikoff, Steven; Ng, Pauline C.
  • Nature Protocols, Vol. 4, Issue 7
  • DOI: 10.1038/nprot.2009.86

Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium
journal, June 2016

  • Amendola, Laura M.; Jarvik, Gail P.; Leo, Michael C.
  • The American Journal of Human Genetics, Vol. 98, Issue 6
  • DOI: 10.1016/j.ajhg.2016.03.024

Assessment of the InSiGHT Interpretation Criteria for the Clinical Classification of 24 MLH1 and MSH2 Gene Variants
journal, October 2016

  • Tricarico, Rossella; Kasela, Mariann; Mareni, Cristina
  • Human Mutation, Vol. 38, Issue 1
  • DOI: 10.1002/humu.23117

ClinVar: public archive of interpretations of clinically relevant variants
journal, November 2015

  • Landrum, Melissa J.; Lee, Jennifer M.; Benson, Mark
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1222

Estimating the Support of a High-Dimensional Distribution
journal, July 2001


Molecular diagnostic experience of whole-exome sequencing in adult patients
journal, December 2015

  • Posey, Jennifer E.; Rosenfeld, Jill A.; James, Regis A.
  • Genetics in Medicine, Vol. 18, Issue 7
  • DOI: 10.1038/gim.2015.142

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
journal, June 2010


Crowdsourcing biomedical research: leveraging communities as innovation engines
journal, July 2016

  • Saez-Rodriguez, Julio; Costello, James C.; Friend, Stephen H.
  • Nature Reviews Genetics, Vol. 17, Issue 8
  • DOI: 10.1038/nrg.2016.69

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples
journal, August 2016

  • Walsh, Roddy; Thomson, Kate L.; Ware, James S.
  • Genetics in Medicine, Vol. 19, Issue 2
  • DOI: 10.1038/gim.2016.90

Molecular genetic testing and the future of clinical genomics
journal, May 2013

  • Katsanis, Sara Huston; Katsanis, Nicholas
  • Nature Reviews Genetics, Vol. 14, Issue 6
  • DOI: 10.1038/nrg3493

Human Gene Mutation Database (HGMD ® ): 2003 update : HGMD 2003 UPDATE
journal, April 2003

  • Stenson, Peter D.; Ball, Edward V.; Mort, Matthew
  • Human Mutation, Vol. 21, Issue 6
  • DOI: 10.1002/humu.10212

Reassessment of Genomic Sequence Variation to Harmonize Interpretation for Personalized Medicine
journal, November 2016

  • Garber, Kathryn B.; Vincent, Lisa M.; Alexander, John J.
  • The American Journal of Human Genetics, Vol. 99, Issue 5
  • DOI: 10.1016/j.ajhg.2016.09.015

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders
journal, November 2014


The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine
journal, January 2014

  • Vassy, Jason L.; Lautenbach, Denise M.; McLaughlin, Heather M.
  • Trials, Vol. 15, Issue 1
  • DOI: 10.1186/1745-6215-15-85

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
journal, December 2004

  • Hamosh, A.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki033

SIFT: predicting amino acid changes that affect protein function
journal, July 2003


Computational Approach to Annotating Variants of Unknown Significance in Clinical Next Generation Sequencing
journal, November 2015

  • Schulz, Wade L.; Tormey, Christopher A.; Torres, Richard
  • Laboratory Medicine, Vol. 46, Issue 4
  • DOI: 10.1309/LMWZH57BRWOPR5RQ