Multi-omics data layers

As part of the Human Functional Genomics Project, the 2000HIV project utilizes the combination of extensive clinical data in combination with state-of-the-art techniques to generate a wide array of data layers, which together are aimed to increase our understanding of the factors and pathways involved in the body’s response to infection and inflammation in people living with HIV.

For more in detail methodologies, please see the links below, or view the open access publication describing the 2000HIV cohort:

The 2000HIV study: Design, multi-omics methods and participant characteristics, W.A.J.W. Vos, A.L. Groenendijk, et al. Frontiers in Immunology, section Viral Immunology, Volume 13 -2022 (Go to article)

Genomics The identify a wide array of single nucleotide polymorphisms (SNPs), DNA was genotyped using the Illumina Infinium Global Screening Array. Raw data from the array was imputed referenced to the human reference consortium (HRC). We will study the influence of common genetic polymorphisms on immunological functioning (ex vivo cytokine production, immune cell phenotyping, and immunoglobin subclasses) by using quantitative trait loci (QTL) mapping. Furthermore, in a subset of 200 individuals, whole genome sequencing was performed.

Epigenomics An Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) will be performed in a subset of the cohort, among which are spontaneous HIV controllers. In this subset, ATAC-seq was employed on bulk peripheral blood mononuclear cells as well as 5 different cell subtypes (CD4+, CD8+, CD56+, CD19+ and CD14+) isolated by means of magnetic bead selection.

Transcriptomics Using currently available Illumina technology (>30 million reads per sample) bulk RNA will be sequenced from peripheral blood mononuclear cells. Gene expressions patterns resulting from sequencing can identify molecular phenotypes and will be investigated in relation to other -omics data layers and clinical data. Pathway enrichment analysis may identify regulatory pathways enriched in stratified subgroups. Furthermore, single-cell RNA sequencing will be performed in a subset of the cohort (n=200).