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 me...
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| Published in | Bioinformatics Vol. 36; no. 12; pp. 3905 - 3906 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.06.2020
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/btaa264 |
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| Abstract | 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. |
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| AbstractList | 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.SUMMARYBulk 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.scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount.AVAILABILITY AND IMPLEMENTATIONscHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. 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. 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. scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount. Supplementary data are available at Bioinformatics online. |
| Author | Marks, Patrick J Martínez Barrio, Álvaro Fiddes, Ian T Darby, Charlotte A Stubbington, Michael J T |
| AuthorAffiliation | b2 10x Genomics , Pleasanton, CA 94588, USA b1 Department of Computer Science , Johns Hopkins University, Baltimore, MD 21218, USA |
| AuthorAffiliation_xml | – name: b2 10x Genomics , Pleasanton, CA 94588, USA – name: b1 Department of Computer Science , Johns Hopkins University, Baltimore, MD 21218, USA |
| Author_xml | – sequence: 1 givenname: Charlotte A orcidid: 0000-0003-2195-5300 surname: Darby fullname: Darby, Charlotte A organization: Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA – sequence: 2 givenname: Michael J T orcidid: 0000-0001-5924-3566 surname: Stubbington fullname: Stubbington, Michael J T organization: 10x Genomics, Pleasanton, CA 94588, USA – sequence: 3 givenname: Patrick J surname: Marks fullname: Marks, Patrick J organization: 10x Genomics, Pleasanton, CA 94588, USA – sequence: 4 givenname: Álvaro surname: Martínez Barrio fullname: Martínez Barrio, Álvaro email: martinezbarrio.alvaro@gmail.com organization: 10x Genomics, Pleasanton, CA 94588, USA – sequence: 5 givenname: Ian T surname: Fiddes fullname: Fiddes, Ian T email: martinezbarrio.alvaro@gmail.com organization: 10x Genomics, Pleasanton, CA 94588, USA |
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| Cites_doi | 10.1186/s12920-018-0354-x 10.1093/nar/gku1161 10.1126/science.aao4572 10.1111/j.1399-0039.2012.01881.x 10.1038/s41467-019-11591-1 10.1371/journal.pgen.1008091 10.1038/ncomms10582 10.1093/bioinformatics/bty125 10.1038/nbt.3519 10.1038/s41467-018-06300-3 |
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Summary
Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and... Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion.... |
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| SubjectTerms | Alleles Applications Notes Gene Expression Humans Sequence Analysis, RNA Single-Cell Analysis Software Workflow |
| Title | scHLAcount: allele-specific HLA expression from single-cell gene expression data |
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