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This article shows you how to understand the CADD database, the content is concise and easy to understand, can definitely brighten your eyes, through the detailed introduction of this article, I hope you can gain something.

When measuring the impact of a variation site, it is usually given a type of variation, such as synonymous SNV, to indicate its effect. CADD created an original scoring algorithm to measure the harm of mutation sites.

For a group of variation sites, CADD combines the polymorphism of alleles, the pathogenicity of variation and other factors, constructs a model, evaluates each variation site, and gives a specific score, referred to as C-Scores. The score directly given by the statistical model is called RawScore, and the higher this value, the higher the probability that the mutation site is a harmful mutation.

For the variation sites of different groups, such as 1000G and ESP, due to the differences of various factors, the models are different, and RawScore can not be directly compared between different models. Therefore, the concept of scaled C-scores is put forward. The RawScores is sorted from large to small, and the scaled C-scores is calculated by using the formula of-10*log10 (rank/total). Because this formula is similar to the way phread is defined, scaled C-scores is also called PHREAD.

PHREAD is usually filtered when analyzing potential pathogenic variants. The official recommendation threshold is 10, 15, 15 and 20, but it is more recommended to combine C-Scores and other experimental evidence to evaluate the pathogenicity of the mutation site, rather than a simple numerical filter.

The CADD official website provides the following three services

1. Download service

Links are as follows:

Http://cadd.gs.washington.edu/download

Corresponding to different data sets, such as 1000G, ESP, Exac, etc., the corresponding CADD score is given.

The contents of the downloaded file are as follows:

# Chrom Pos Ref Alt RawScore PHRED1 861349 C T 6.591020 311 865545 G A 5.989520 27.81 865584 G A 3.632951 23.21 865625 G A 5.624605 26.61 865628 G A 2.938829 22.01 865662 G A 1.597527 13.842. Online annotation service

Through the online service, the variation sites can be scored by CADD. Links are as follows:

Http://cadd.gs.washington.edu/score

Upload a file in VCF format, allowing up to 10000 variation sites at a time, and then click Upload variants to start the analysis. The results are as follows

# # CADD v1.3 (c) University of Washington and Hudson-Alpha Institute for Biotechnology 2013-2015. All rights reserved.#CHROM POS REF ALT RawScore PHRED16 50745926 CT 4.355927 24.120 1110696 A G 0.142763 4.06820 1110696 A T 0.005222 2.63620 1234567 TTCT T-0.369022 0.45920 1234569 C AC-0.290183 0.6993. Online search

Links are as follows:

Http://cadd.gs.washington.edu/snv

Enter the location of the SNV site on the page shown below, and then click the Lookup variant button to submit

The returned result is as follows

The above content is how to understand CADD database. Have you learned any knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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