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Editor to share with you what is the use of Haplotype Reference Consortium database, I believe most people do not know much about it, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

When filling genotypes, the selection of reference panel has a great influence on the filling results. HapMap contains more than 3 million SNP sites, 420 haplotypes, and 1000G contains more than 80 million sites and 5008 haplotypes. In addition to these two commonly used reference panel, there are many large-scale human genome sequencing projects, such as UK10K and so on. The more haplotypes contained in reference panel, the higher the accuracy of filling, and the more SNP sites covered, the more sites can be used for GWAS analysis after filling, which can mine association signals more effectively.

Haplotype Reference Consortium, referred to as HRC, integrates the results from UK10K, 1000G and other projects to construct a reference panel containing more than 30 million SNP loci and 64976 haplotypes. The corresponding article is published on nature genetics, and the link is as follows

Https://www.nature.com/articles/ng.3643

In this paper, the effects of different reference panel on filling accuracy are compared. The results are as follows.

Abscissa is the proportion of SNP sites not in reference panel in study samples, and ordinate is the accuracy of filling. It can be seen that the filling accuracy of HRC is significantly higher than that of UK10K and 1000G. In addition, the effects of reference panel on GWAS results are also compared, and the results are as follows.

Showing the Manhattan map on chromosome 14, rs28929474 is positive, from left to right, corresponding to hapmap, 1000G and HRC, respectively. Using HapMap filling, the positive site was not recognized, and the positive site was recognized by 1000G and HRC.

The link to the official website of HRC is as follows

Http://www.haplotype-reference-consortium.org/

The genome sequencing projects included are as follows

Most of them are the results of low-depth whole genome sequencing, containing a total of 32611 samples. unfortunately, the information of the database is not fully public. at present, only through two online websites, the database can be used to fill genotypes. the URL is as follows

Https://imputation.sanger.ac.uk/

Https://imputationserver.sph.umich.edu/

In EBI, a subset of the database is included for download at the following URL

Https://www.ebi.ac.uk/ega/studies/EGAS00001001710

For genotype filling, the construction of a larger haplotype database is an effective way to improve the accuracy, and the use of HRC database can effectively provide filling accuracy.

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