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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

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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 in pipelines

 (31)
2018
PMCID: 5792481
PMID: 29386531
DOI: 10.1038/s41598-018-20114-9

[…] database, exome aggregation consortium browser, human genetic variation database (hgvd, http://www.genome.med.kyoto-u.ac.jp/snpdb), and tommo database. all variants were predicted in silico using cadd scores and were excluded if cadd scores were less than 10. after variant filtering, variants were checked for known pathogenic relationships with cardiovascular diseases in the human genome […]

2018
PMCID: 5798313
PMID: 29417091
DOI: 10.1212/NXG.0000000000000212

[…] the effect on the resulting protein. variants of interest were further annotated with functional domain information from the refseq database and with in silico pathogenicity predictions using cadd. variants were then evaluated according to american college of medical genetics and genomics guidelines., we received full approval from the unc institutional review board to perform this study. […]

2018
PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] annotations dataset: ftp://ftp.ebi.ac.uk/pub/databases/go/goa/human/, gene ontology tool: http://wego.genomics.org.cn/cgi-bin/wego/index.pl, bcftools-1.2.1 http://www.htslib.org/download/, online cadd annotation tool: http://cadd.gs.washington.edu/score, online vep tool: http://asia.ensembl.org/tools/vep, we are thankful to dr. qasim ayub, from the wellcome trust sanger institute, wellcome […]

2018
PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] the genome/exome sequencing data of pakistani individuals publically available in 1000 genomes project (pjl), and exome aggregation consortium (exac) south asia. by applying a set of tools such as combined annotation dependent depletion (cadd), annovar, and variant effect predictor (vep), we highlighted 561 potentially detrimental variants from pjl data, and 7374 variants from exac south asian […]

2018
PMCID: 5830370
PMID: 29217778
DOI: 10.3324/haematol.2017.180778

[…] confirmation, dna was extracted from skin fibroblasts and/or hair follicles, and targets were amplified and sequenced as previously described. the degree of deleteriousness was calculated using the combined annotation-dependent depletion scoring system (cadd-score). the variants with cadd-scores higher than 20 were further evaluated for their role in hematologic disease or cancer, thereby […]


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CADD in publications

 (331)
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0

[…] of the harboring gene (supplementary tables  and )., we then tested vr:d in correlation with mutation pathogenicity as modeled through several popular functionality predictive tools: polyphen (pph), combined annotation dependent depletion (cadd), genomic evolutionary rate profiling (gerp)–, and functional analysis through hidden markov models (fathmm),. we did not observe a strong correlation […]

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

[…] databases, suggesting that the majority of aligner-specific variants are likely true positives. in addition, 8.85% of bwa-unique, and 9.4% of novo-unique variants were novel variants that had a combined annotation dependent depletion (cadd) score (phred-like) of at least 20 [], indicating that these variants are amongst the top 1% of deleterious variants in the human genome and likely […]

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

[…] 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 […]

PMCID: 5896995
PMID: 29649263
DOI: 10.1371/journal.pone.0195761

[…] (exac, 1000genome or clinvar) [–]. predictive values from selected prediction algorithms (for example sift [], mutation analyzer [], mutationtaster [], lrt [], polyphen-2 [], phylop [], gerp [], cadd [] or spidex (https://www.deepgenomics.com/spidex) were added to the annotated alternative variants., for a comparison with czecanca sequencing, the data from routine analyses using the trusight […]

PMCID: 5902712
PMID: 29692703
DOI: 10.3389/fnins.2018.00230

[…] 0.3.1) (lek et al., ) and the ensembl genome browser (aken et al., ). predictions of variant pathogenicity were based on the genomic evolutionary rate profiling (gerp) (davydov et al., ) and the combined annotation dependent depletion (cadd) algorithm (v1.3, http://cadd.gs.washington.edu) (kircher et al., ). all putative damaging variants (scores gerp ≥ 2.95 and cadd ≥ 12.37) (amendola et […]


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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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Anonymous user #89

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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.