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Activity Number: 299 - SPEED: Recent Advances in Statistical Genomics and Genetics
Type: Contributed
Date/Time: Tuesday, July 31, 2018 : 8:30 AM to 10:20 AM
Sponsor: Section on Statistics in Genomics and Genetics
Abstract #327166 Presentation
Title: SAVER: Gene Expression Recovery for UMI-Based Single Cell RNA Sequencing
Author(s): Mo Huang* and Jingshu Wang and Mingyao Li and Nancy Zhang
Companies: University of Pennsylvania and University of Pennsylvania and University of Pennsylvania and University of Pennsylvania
Keywords: Single cell; RNA sequencing; Statistical Genomics; Empirical Bayes; Lasso

Rapid advances in massively parallel single cell RNA sequencing (scRNA-seq) is paving the way for high-resolution single cell profiling of biological samples. In most scRNA-seq studies, only a small fraction of the transcripts present in each cell are sequenced. The efficiency, that is, the proportion of transcripts in the cell that are sequenced, can be especially low in highly parallelized experiments where the number of reads allocated for each cell is small. This leads to unreliable quantification of lowly expressed genes, hindering downstream analysis. To address this challenge, we introduce SAVER (Single-cell Analysis Via Expression Recovery), an expression recovery method for scRNA-seq that borrows information across genes and cells to improve the expression estimates for all genes. We show, by comparison to RNA fluorescence in situ hybridization (FISH) and by data down-sampling experiments, that SAVER reliably recovers cell-specific gene expression concentrations, cross-cell gene expression distributions, and gene-to-gene and cell-to-cell correlations. This improves the power and accuracy of any downstream analysis involving genes with low to moderate expression.

Authors who are presenting talks have a * after their name.

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