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Computational and analytical challenges in single-cell transcriptomics

Key Points

  • Until recently, RNA profiling was limited to ensemble-based approaches, which average over bulk populations of cells. Technological advances in single-cell RNA sequencing (scRNA-seq) now enable the transcriptomes of large numbers of individual cells to be assayed in an unbiased manner.

  • To ensure that scRNA-seq data are fully exploited and interpreted correctly, it is important to apply appropriate computational and statistical approaches. Methods and principles previously developed for bulk RNA sequencing can be reused for this purpose; however, scRNA-seq data analysis poses several unique challenges that require new analytical strategies.

  • At the experimental design stage, unique molecular identifiers and quantitative standards such as spike-ins need to be considered to allow accurate normalization and quality control of the raw data.

  • Prior to using scRNA-seq data for biological discovery, it is important to consider both technical variability and confounding factors such as batch effects, the cell cycle or apoptosis. Computational methods that account for technical variation and remove confounding factors are beginning to emerge.

  • The processed and normalized scRNA-seq data provide unique analysis opportunities that allow novel biological discoveries to be made. These include identification and characterization of cell types and the study of their organization in space and/or time; inference of gene regulatory networks and their robustness across individual cells; and characterization of the stochastic component of transcription.

Abstract

The development of high-throughput RNA sequencing (RNA-seq) at the single-cell level has already led to profound new discoveries in biology, ranging from the identification of novel cell types to the study of global patterns of stochastic gene expression. Alongside the technological breakthroughs that have facilitated the large-scale generation of single-cell transcriptomic data, it is important to consider the specific computational and analytical challenges that still have to be overcome. Although some tools for analysing RNA-seq data from bulk cell populations can be readily applied to single-cell RNA-seq data, many new computational strategies are required to fully exploit this data type and to enable a comprehensive yet detailed study of gene expression at the single-cell level.

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Figure 1: Comparison of bulk and scRNA-seq analytical strategies.
Figure 2: Quality control and normalization.
Figure 3: Confounding variables and how to account for them.
Figure 4: Finding new cell types and allocating cells along a differentiation cascade.
Figure 5: The kinetics of transcription.

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Acknowledgements

The authors acknowledge members of the Marioni, Stegle and Teichmann groups for comments on the manuscript. They also acknowledge S. Linnarsson for advice on how to present computational challenges relating to scRNA-seq data generated using UMI-based protocols.

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Correspondence to John C. Marioni.

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PowerPoint slides

Glossary

Spike-in

A few types of RNA with known sequence and quantity (generated either artificially or from a pool of RNA from a distantly related species) that are added as internal controls in RNA sequencing experiments.

Unique molecular identifiers

(UMIs). Tens of thousands of short DNA sequences (6–10 nucleotides in length), which are incorporated in molecules of interest before amplification, thus allowing biases to be accounted for.

Technical variability

Variability in gene expression levels between cells that arises through technical effects.

Read alignment

The alignment of short reads generated from a next-generation sequencing experiment to a reference genome or transcriptome.

Gene expression counts

The number of sequencing reads or unique molecular identifiers that map to a particular gene. These raw data form the basis of gene expression level quantification approaches.

Duplicated reads

Identical copies of a sequencing read generated by the PCR amplification process.

Principal component analysis

(PCA). A statistical method to simplify a complex data set by transforming a series of correlated variables into a smaller number of uncorrelated variables called principal components.

Fragments per kilobase of exon per million fragments mapped

(FPKM). A method for quantifying gene expression levels from RNA sequencing data that normalizes for sequencing depth and transcript length.

Size factors

Quantities used to normalize gene expression levels between independently generated RNA sequencing libraries; they account for differences in sequencing depth.

Allele-specific expression

Gene expression levels measured separately for each of the two parental alleles. RNA derived from each allele can be quantified and assessed separately when RNA sequencing reads overlap with heterozygous sites in the genome.

Capture efficiency

The percentage of mRNA molecules in the cell lysate that are captured, amplified and sequenced. This is normally quantified using spike-in molecules.

Confounding factors

Unobserved covariates that affect gene expression levels and that can obscure the interpretation if not accounted for.

Batch effects

Systematic differences in gene expression levels between independent cells from the same population, which arise as a result of sample preparation.

Biological replicates

Independent replicates from the same population.

Markov random field

(MRF). A particular class of statistical model that can exploit smoothness of measurements in a spatial grid, thereby improving the accuracy of parameter estimates.

Dropout

The false quantification of a gene as 'unexpressed' due to the corresponding transcript being 'missed' during the reverse-transcription step. This leads to a lack of detection during sequencing.

Monoallelic expression

The expression of only one of the two parental alleles.

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Stegle, O., Teichmann, S. & Marioni, J. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet 16, 133–145 (2015). https://doi.org/10.1038/nrg3833

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