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ScHLAcount: allele-specific HLA expression from single-cell gene expression data.

ABSTRACT:

Summary

Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion. Single-cell gene expression assays have the potential to further resolve these expression patterns, but currently available methods do not perform allele-specific quantification at the molecule level. Here, we present scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes allele-specific molecule counts of the HLA genes based on a personalized reference constructed from the sample's HLA genotypes.

Availability and implementation

scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Darby CA

PROVIDER: S-EPMC7320622 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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scHLAcount: allele-specific HLA expression from single-cell gene expression data.

Darby Charlotte A CA Stubbington Michael J T MJT Marks Patrick J PJ Martínez Barrio Álvaro Á Fiddes Ian T IT

Bioinformatics (Oxford, England) 20200601 12

<h4>Summary</h4>Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion. Single-cell gene expression assays have the potential to further resolve these expression patterns, but currently available methods do not perform allele-specific quantification at the molecule level. Here, we present scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes allele-specific molecule co ...[more]

PMID: 32330223

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