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Intro
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Cell pathology revealed by single cell genotype- phenotype mapping
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The genetic cause of most cancers is known
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Tumor heterogeneity masks mutation co-occurrence
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Droplet microfluidics provides scalability and cost efficiency
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Single cell sequencing resolves tissue heterogeneity
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DNA is the gold standard for genotyping
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Single cell DNA sequencing requires harsh cell lysis
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Proteinase K digestion of chromatin releases DNA and can be heat inactivated
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Multiplexed PCR in droplets selects for the regions of interest
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Uniform target amplification ensures low allele dropout
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Single cell genotyping allows deconvoluting clonal heterogeneity
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To link the genotype to the phenotype we need both
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Single cell immunophenotyping is well established
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Attaching DNA barcodes to antibodies allows for a sequencing readout
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A genotype vector and an antibody count vector is measured for each cell
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To visualize high dimensional data 2D projections are used
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A synthetic cell mixture proves that the method works
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How does a lengthy disease history affect clonal diversity?
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The phenotype maps into a tight compartment
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A patient with atypical blasts, what drives it?
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Divergent differentiation response hints at unchartered variability
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Partnering with Mission Bio helps adopting of method by other labs
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New questions
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HIV remains an incurable disease due to the latent reservoir
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What is special about cells with latent HIV?
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Can we make an assay that exploits this marker?
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The HIV provirus is a perfect biomarker - can DAb-seq exploit it?
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Integrated HIV genomes can reliably be detected in complex samples
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Distinct T cell subcompartments are resolved
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Strong tropism for distinct CD4+ T cell compartments
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Concluding remarks
Description:
Explore a 33-minute webinar on cell pathology revealed through single-cell genotype-phenotype mapping. Delve into the complexities of cancer genetics, focusing on how somatic mutations drive disease progression and serve as prognostic markers. Learn about the challenges of linking genotypes to phenotypes in polyclonal tissues and discover how single-cell resolution methods address these issues. Examine the application of droplet microfluidics and single-cell sequencing techniques in resolving tumor heterogeneity. Investigate the process of single-cell genotyping and immunophenotyping, including DNA barcoding of antibodies for sequencing readouts. Analyze high-dimensional data visualization techniques and their application in understanding clonal diversity and disease progression. Explore case studies demonstrating the method's effectiveness in complex patient samples. Finally, consider the potential applications of this technology in studying HIV latency and identifying distinct T cell subcompartments affected by the virus. Read more

Cell Pathology Revealed by Single-Cell Genotype-Phenotype Mapping

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#Science #Biology #Cell Biology #Genomics #DNA Sequencing #Data Science #Bioinformatics #Single-Cell Analysis #Cancer Biology #Tumor Heterogeneity
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Intro