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. 2016 Feb;13(2):109-10.

doi: 10.1038/nmeth.3739.

The mutation significance cutoff: gene-level thresholds for variant predictions

Yuval Itan¹, Lei Shang¹, Bertrand Boisson^{1

2

3}, Michael J Ciancanelli¹, Janet G Markle¹, Ruben Martinez-Barricarte¹, Eric Scott⁴, Ishaan Shah¹, Peter D Stenson⁵, Joseph Gleeson^{4

6}, David N Cooper⁵, Lluis Quintana-Murci^{7

8}, Shen-Ying Zhang^{1

2

3}, Laurent Abel^{1

2

3}, Jean-Laurent Casanova^{1

2

3

6

9}

Affiliations

Affiliations

¹ St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.
² Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
³ Paris Descartes University, Imagine Institute, Paris, France.
⁴ Neurogenetics Laboratory, Department of Neurosciences, University of California, San Diego, San Diego, California, USA.
⁵ Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK.
⁶ Howard Hughes Medical Institute, New York, New York, USA.
⁷ Human Evolutionary Genetics Unit, Institut Pasteur, Paris, France.
⁸ Centre National de la Recherche Scientifique, URA 3012, Paris, France.
⁹ Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France.

PMID: 26820543
PMCID: PMC4980758
DOI: 10.1038/nmeth.3739

The mutation significance cutoff: gene-level thresholds for variant predictions

Yuval Itan et al. Nat Methods. 2016 Feb.

. 2016 Feb;13(2):109-10.

doi: 10.1038/nmeth.3739.

Authors

Yuval Itan¹, Lei Shang¹, Bertrand Boisson^{1

2

3}, Michael J Ciancanelli¹, Janet G Markle¹, Ruben Martinez-Barricarte¹, Eric Scott⁴, Ishaan Shah¹, Peter D Stenson⁵, Joseph Gleeson^{4

6}, David N Cooper⁵, Lluis Quintana-Murci^{7

8}, Shen-Ying Zhang^{1

2

3}, Laurent Abel^{1

2

3}, Jean-Laurent Casanova^{1

2

3

6

9}

Affiliations

¹ St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.
² Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
³ Paris Descartes University, Imagine Institute, Paris, France.
⁴ Neurogenetics Laboratory, Department of Neurosciences, University of California, San Diego, San Diego, California, USA.
⁵ Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK.
⁶ Howard Hughes Medical Institute, New York, New York, USA.
⁷ Human Evolutionary Genetics Unit, Institut Pasteur, Paris, France.
⁸ Centre National de la Recherche Scientifique, URA 3012, Paris, France.
⁹ Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France.

PMID: 26820543
PMCID: PMC4980758
DOI: 10.1038/nmeth.3739

No abstract available

PubMed Disclaimer

Figures

Figure 1. Disease-associated mutation features
(A) Violin plots of the CADD scores across the various HGMD molecular categories of 174,183 disease-associated deleterious mutations. (B) A density plot of the proportion of 95% CIs for HGMD disease-associated deleterious mutations overlap between a given disease-causing human gene and all other 2,946 disease-causing human genes. (C) The 95% CIs MSC scores of HGMD 2,947 disease-associated genes. Blue color (CADD score below the MSC) suggests a low impact for the gene, orange color (CADD score above or equal to the MSC) suggests high impact, and the horizontal purple dashed lines indicate current predictions based on fixed CADD scores.

See this image and copyright information in PMC

References

1. Adzhubei IA, et al. Nat Methods. 2010;7:248–249. - PMC - PubMed
1. Kumar P, et al. Nat Protoc. 2009;4:1073–1081. - PubMed
1. Kircher M, et al. Nat Genet. 2014;46:310–315. - PMC - PubMed
1. Petrovski S, et al. PLoS Genet. 2013;9:e1003709. - PMC - PubMed
1. Samocha KE, et al. Nat Genet. 2014;46:944–950. - PMC - PubMed

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