Omics

HFGP uses sophisticated, cutting-edge techniques to generate and analyze omics data. Our work spans genomics, transcriptomics, proteomics, metabolomics, and microbiome research.

DNA is isolated from EDTA blood, and multiple platforms are used for genomic analysis: Illumina SNP arrays, and whole exome sequencing is performed for some volunteers. DNA is available for extending genetic studies.

The transcriptome is evaluated in various settings: whole blood profiles (collected in PAXgene tubes), and in vitro after stimulation of peripheral blood mononuclear cells (PBMC) with different pattern recognition receptor ligands, bacterial, viral, or fungal stimuli.

The concentrations of various proteins in the circulation are measured using the Olink® technology using different panels depending on the research question.

Bacterial composition is determined using 16S sequencing and metagenomics using platforms developed by the Broad Institute/MIT within the Human Microbiome Project. Microbiome in fecal, oral, vaginal, and skin niches are evaluated.

The metabolome is usually measured in plasma and urine using NMR metabolomics or mass spectrometry based techniques.