GuavaH: a compendium of host genomic data in HIV biology and disease

Retrovirology

Amalio Telenti²  Jacques Fellay¹  Angela Ciuffi²  Paul J McLaren¹  István Bartha¹ 

[1] Swiss Institute of Bioinformatics, Lausanne, Switzerland;Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland

关键词: HIV latency;    Transcriptome analysis;    Exome analysis;    Genome-wide association studies;   

Others  :  804162
DOI  :  10.1186/1742-4690-11-6

 received in 2013-12-03, accepted in 2014-01-07,  发布年份 2014

【 摘 要 】

Background

There is an ever-increasing volume of data on host genes that are modulated during HIV infection, influence disease susceptibility or carry genetic variants that impact HIV infection. We created GuavaH (Genomic Utility for Association and Viral Analyses in HIV, http://www.GuavaH.org webcite), a public resource that supports multipurpose analysis of genome-wide genetic variation and gene expression profile across multiple phenotypes relevant to HIV biology.

Findings

We included original data from 8 genome and transcriptome studies addressing viral and host responses in and ex vivo. These studies cover phenotypes such as HIV acquisition, plasma viral load, disease progression, viral replication cycle, latency and viral-host genome interaction. This represents genome-wide association data from more than 4,000 individuals, exome sequencing data from 392 individuals, in vivo transcriptome microarray data from 127 patients/conditions, and 60 sets of RNA-seq data. Additionally, GuavaH allows visualization of protein variation in ~8,000 individuals from the general population. The publicly available GuavaH framework supports queries on (i) unique single nucleotide polymorphism across different HIV related phenotypes, (ii) gene structure and variation, (iii) in vivo gene expression in the setting of human infection (CD4+ T cells), and (iv) in vitro gene expression data in models of permissive infection, latency and reactivation.

Conclusions

The complexity of the analysis of host genetic influences on HIV biology and pathogenesis calls for comprehensive motors of research on curated data. The tool developed here allows queries and supports validation of the rapidly growing body of host genomic information pertinent to HIV research.

【 授权许可】

   
2014 Bartha et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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