Title: "Thousands of cells; thousands of genomes: Deriving single-cell genomic profiles from highly multiplexed NextGen DNA sequencing"
Speaker: James Hicks; Professor of Genomics, Cold Spring Harbor Laboratory, NY

Place: Lilly (LILY) Hall G126
Date: October 7, 2014; Tuesday
Time: 4:30pm


Single-cell sequencing has become an important tool for probing cancer, neurobiology, and developmental biology. Studying genomic variation at the single-cell level allows investigators to unravel the genetic heterogeneity within a sample and enables the phylogenetic reconstruction of subpopulations beyond what is possible with analysis of bulk populations.

As a rule, whole-genome amplification (WGA) techniques are needed to prepare the DNA within a single cell for high-throughput sequencing. Despite dramatic improvements since their introduction, WGA protocols inevitably have variable amplification efficiency across the genome and even total loss of coverage in certain regions. These issues necessitate the development of specialized statistical, bioinformatic and technical methods for detecting and validating genomic variants, from single nucleotide mutations to large-scale copy number variations (CNV).

We will discuss the application of these techniques to further our understanding of cancer initiation, progression and diagnosis, through the use of CNV and mutational profiling and the application of "GINKGO" a novel web-based tool for integrated bioinformatics processing of single-cell sequencing data which can be accessed at: qb.cshl.edu/ginkgo.
Associated reading:
No reading.

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