CADD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CADD
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Tool usage distribution map

This map represents all the scientific publications referring to CADD per scientific context
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Associated diseases

This word cloud represents CADD usage per disease context
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Popular tool citations

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Protocols

CADD specifications

Information


Unique identifier OMICS_02627
Name CADD
Alternative name Combined Annotation Dependent Depletion
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Some nucleotide variants.
Input format VCF
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 1.4
Stability Stable
Requirements
SAMtools, tabix, bx-Python, PySam, perl, Ensembl VEP
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


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Versioning


No version available

Maintainers


  • person_outline CADD
  • person_outline Martin Kircher

Information


Unique identifier OMICS_02627
Name CADD
Alternative name Combined Annotation Dependent Depletion
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Some nucleotide variants.
Input format VCF
Programming languages Python
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline CADD
  • person_outline Martin Kircher

Publications for Combined Annotation Dependent Depletion

CADD citations

 (464)
call_split

Systematic pan cancer analysis of somatic allele frequency

2018
Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0
call_split See protocol

[…] onal annotations and conservation scores were extracted using the SeattleSeq annotation 147 (http://snp.gs.washington.edu/SeattleSeqAnnotation147/index.jsp). Pathogenicity was modeled using PolyPhen, CADD and FATHMM methods, and conservation was assessed based on GERP scores–. Transcription factor binding sites were analyzed using TRANSFAC 7.0. […]

call_split

Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

2018
PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] further analysis. Missense variants were evaluated for functional impact using a variety of in-silico prediction tools including SIFT [], Polyphen2 [], MelaLR [], MetaSVN [], fathmm-MKL [], DANN [], CADD [], MutationTaster [], Mutation Assesser [] and LRT []. […]

call_split

Genomic characterization of chronic lymphocytic leukemia (CLL) in radiation exposed Chornobyl cleanup workers

2018
PMCID: 5930419
PMID: 29720177
DOI: 10.1186/s12940-018-0387-9
call_split See protocol

[…] Database. Coding variants predicted to affect protein sequence (e.g., nonsynonymous, stop gain, splicing) were analyzed further. To predict deleterious effects of variants, we used Polyphen, SIFT and Combined Annotation Dependent Depletion (CADD) tool version 1.3 (http://cadd.gs.washington.edu/score), which integrates information from multiple functional annotation tools into a single score. Final […]

library_books

Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank

2018
Sci Rep
PMCID: 5915424
PMID: 29691431
DOI: 10.1038/s41598-018-24735-y

[…] ted lead SNPs from our discovery analysis and annotated them with the closest gene with ANNOVAR. We used OMIM database to search for known genetic disorders for mapped genes. In addition, we obtained CADD scores, the score of deleteriousness of SNPs predicted by 63 functional annotations, and RegulomeDB scores, representing regulatory functionality of SNPs based on eQTLs and chromatin marks. SNPs […]

library_books

Identification of missing variants by combining multiple analytic pipelines

2018
BMC Bioinformatics
PMCID: 5902939
PMID: 29661148
DOI: 10.1186/s12859-018-2151-0

[…] ggesting that at least this proportion of these variants are likely true positives (Fig. , Additional file : Table S6). Also, 15.36% of single-unique variants identified are novel variants that had a CADD score (PHRED-like) of at least 20, indicating that these variants were amongst the top 1% of deleterious variants in the human genome. Again, this strongly indicates biological relevance of a sub […]

library_books

Identification of rare sequence variation underlying heritable pulmonary arterial hypertension

2018
Nat Commun
PMCID: 5897357
PMID: 29650961
DOI: 10.1038/s41467-018-03672-4

[…] ANNOVAR, respectively. Annotations included minor allele frequencies from other control data sets (i.e. ExAC, 1000 Genomes Project and UK10K) as well as deleteriousness and conservation scores (i.e., CADD, SIFT, PolyPhen-2 and Gerp) enabling further filtering and assessment of the likely pathogenicity of variants. To take forward only high quality calls, the pass frequency (proportion of samples c […]


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CADD institution(s)
Berlin Institute of Health (BIH), Berlin, Germany; Charite - Universitatsmedizin Berlin, Berlin, Germany; Department of Statistics and Biostatistics, University of Washington, Seattle, WA, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
CADD funding source(s)
Supported by National Cancer Institute (NCI) [1R01CA197139]; NHGRI [1U54HG006493]; Brotman Baty Institute for Precision Medicine; Berlin Institute of Health; Howard Hughes Medical Institute.

CADD review

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Combined Annotation Dependent Depletion (CADD) is a new tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. Most of pathogenicity prediction algorithms tend to exploit a single information such as conservation to create a score. CADD give a broadly applicable metric that weights and integrated diverse information using a SVM approach. It integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations.

Precomputed CADD scores can be downloaded on CADD website (http://cadd.gs.washington.edu/download). Scores have been included too in dbNSFP databases.

We have demonstrated that CADD is the most sensitive and specific prediction algorithms by comparison with the ClinVar, a database which aggregates information about genomic variation and its relationship to human health.