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O'Hara, A.; Han, Y.; Fan, Y.; Corney, D.; Mozdzierz, C.; Latif, H.; Zhou, G.
Cytotherapy (Oxford, England), June 2024, 2024-06-00, Volume: 26, Issue: 6Journal Article
The omics era has greatly expanded the repertoire of approaches available for researchers and clinicians to unravel the complexity underpinning human health: Next Generation Sequencing (NGS) approaches can characterize genomes, epigenomes, transcriptomes and proteomes. The analyses are critical to assess in individuals both pre- and post-treatment during therapeutic development and early-stage clinical trials. Peripheral blood mononuclear cells (PBMCs) offer a non-invasive approach that, when combined with omics tools, can provide a near holistic view of immune processes across patient cohorts. Meanwhile, Formalin Fixed Paraffin Embedded (FFPE) tissues are a staple in clinical diagnostics and an ideal means to store archival tissue but can be difficult to work with in traditional NGS assays. Here we detail workflows using both fresh and fixed patient samples to rapidly produce a diverse set of multiomics results including genomics, epigenomics, transcriptomics and proteomics. For fresh blood draws, this starts with automated sample handling and processing to ensure high viability and yield of PBMCs, along with simultaneous plasma separation and collection. Samples are then aliquoted and simultaneously processed for whole exome sequencing, single cell RNA sequencing, epigenetic characterization and Olink biomarker analysis. For fixed tissues, FFPE blocks were serially sliced into various FFPE slides, with a single slide H&E stained. Individual slides were then utilized for genome, epigenome, single cell RNA-seq, and digital spatial profiling. Genome information was captured using hybrid capture based approaches followed by deep NGS on an Illumina platform and analyzed for a variety of variants and tumor mutational burden. DNA methylation was detailed using target capture probes targeting DNA methylation sites. Single cell approaches were applied to explore the transcriptome using 10X Genomics scRNAseq kit, and Digital Spatial Profiling (DSP) was done using the NanoString GeoMx® Whole Transcriptome Atlas and immunostaining. With these robust workflows, all these datatypes can be produced within days of fresh or fixed sample receipt using minimal sample amounts. High throughput integrative omics workflows, as described here, drive greater insights in human health, allowing for a rapid combined approach to address the biological questions at hand.
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