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Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.

González-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, da Silva AL, Teles e Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR, Middleton D - Nucleic Acids Res. (2014)

Bottom Line: AFND now contains >1400 populations from more than 10 million healthy individuals.Here, we report how the main features of AFND have been updated to include a new section on 'HLA epitope' frequencies in populations, a new section capturing the results of studies identifying HLA associations with adverse drug reactions (ADRs) and one for the examination of infectious and autoimmune diseases associated with KIR polymorphisms-thus extending AFND to serve a new user base in these growing areas of research.New criteria on data quality have also been included.

View Article: PubMed Central - PubMed

Affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico.

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(A) A world map in AFND showing the global allele frequencies of HLA B*57:01, which, for example, has been associated with adverse reactions to abacavir; (B) a query of KDDB for populations/studies in which associations between KIR genotypes have been made with Type 1 diabetes; (C) a heat map view of several populations in the HLA epitope database (filtered by epitopes from ‘locus A+B’); (D) a drug report in AFND showing all association data for carbamazepine.
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Figure 1: (A) A world map in AFND showing the global allele frequencies of HLA B*57:01, which, for example, has been associated with adverse reactions to abacavir; (B) a query of KDDB for populations/studies in which associations between KIR genotypes have been made with Type 1 diabetes; (C) a heat map view of several populations in the HLA epitope database (filtered by epitopes from ‘locus A+B’); (D) a drug report in AFND showing all association data for carbamazepine.

Mentions: As of September 2014, we have collected information on >1400 healthy populations from more than 10 million people. The HLA section contains the majority of the submissions with 1022 populations, followed by populations analyzed for polymorphisms in KIR (229), cytokine genes (114) and MIC (60) (Table 1, figures correct in September 2014). Currently, data sets from 138 countries are included within AFND—with highest coverage (by population number) the United States (121 populations), followed by China (110 populations)—summarized under the ‘Populations-Pops By Region’ menu in the database. In terms of the number of individuals, United States, Brazil and Italy have the largest amount of data, due to the inclusion of large data sets from bone marrow donor registries in the database. As described previously (1), the most popular tools in AFND include queries for particular allele/haplotype frequencies (viewed as a table or world map—Figure 1A), or analysis of all allele/haplotype frequencies within a given population or geographic region of the world.


Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.

González-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, da Silva AL, Teles e Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR, Middleton D - Nucleic Acids Res. (2014)

(A) A world map in AFND showing the global allele frequencies of HLA B*57:01, which, for example, has been associated with adverse reactions to abacavir; (B) a query of KDDB for populations/studies in which associations between KIR genotypes have been made with Type 1 diabetes; (C) a heat map view of several populations in the HLA epitope database (filtered by epitopes from ‘locus A+B’); (D) a drug report in AFND showing all association data for carbamazepine.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383964&req=5

Figure 1: (A) A world map in AFND showing the global allele frequencies of HLA B*57:01, which, for example, has been associated with adverse reactions to abacavir; (B) a query of KDDB for populations/studies in which associations between KIR genotypes have been made with Type 1 diabetes; (C) a heat map view of several populations in the HLA epitope database (filtered by epitopes from ‘locus A+B’); (D) a drug report in AFND showing all association data for carbamazepine.
Mentions: As of September 2014, we have collected information on >1400 healthy populations from more than 10 million people. The HLA section contains the majority of the submissions with 1022 populations, followed by populations analyzed for polymorphisms in KIR (229), cytokine genes (114) and MIC (60) (Table 1, figures correct in September 2014). Currently, data sets from 138 countries are included within AFND—with highest coverage (by population number) the United States (121 populations), followed by China (110 populations)—summarized under the ‘Populations-Pops By Region’ menu in the database. In terms of the number of individuals, United States, Brazil and Italy have the largest amount of data, due to the inclusion of large data sets from bone marrow donor registries in the database. As described previously (1), the most popular tools in AFND include queries for particular allele/haplotype frequencies (viewed as a table or world map—Figure 1A), or analysis of all allele/haplotype frequencies within a given population or geographic region of the world.

Bottom Line: AFND now contains >1400 populations from more than 10 million healthy individuals.Here, we report how the main features of AFND have been updated to include a new section on 'HLA epitope' frequencies in populations, a new section capturing the results of studies identifying HLA associations with adverse drug reactions (ADRs) and one for the examination of infectious and autoimmune diseases associated with KIR polymorphisms-thus extending AFND to serve a new user base in these growing areas of research.New criteria on data quality have also been included.

View Article: PubMed Central - PubMed

Affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico.

Show MeSH
Related in: MedlinePlus