RNA2HLA: HLA-based quality control of RNA-seq datasets
RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participa...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2021
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| _version_ | 1826289132749455360 |
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| author | Chelysheva, I Pollard, AJ O’Connor, D |
| author_facet | Chelysheva, I Pollard, AJ O’Connor, D |
| author_sort | Chelysheva, I |
| collection | OXFORD |
| description | RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, we propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. We introduce RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, our tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC. |
| first_indexed | 2024-03-07T02:24:15Z |
| format | Journal article |
| id | oxford-uuid:a50b92b9-d712-4ea3-aad8-4dd9a236c584 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:24:15Z |
| publishDate | 2021 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:a50b92b9-d712-4ea3-aad8-4dd9a236c5842022-03-27T02:37:44ZRNA2HLA: HLA-based quality control of RNA-seq datasetsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:a50b92b9-d712-4ea3-aad8-4dd9a236c584EnglishSymplectic ElementsOxford University Press2021Chelysheva, IPollard, AJO’Connor, DRNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, we propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. We introduce RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, our tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC. |
| spellingShingle | Chelysheva, I Pollard, AJ O’Connor, D RNA2HLA: HLA-based quality control of RNA-seq datasets |
| title | RNA2HLA: HLA-based quality control of RNA-seq datasets |
| title_full | RNA2HLA: HLA-based quality control of RNA-seq datasets |
| title_fullStr | RNA2HLA: HLA-based quality control of RNA-seq datasets |
| title_full_unstemmed | RNA2HLA: HLA-based quality control of RNA-seq datasets |
| title_short | RNA2HLA: HLA-based quality control of RNA-seq datasets |
| title_sort | rna2hla hla based quality control of rna seq datasets |
| work_keys_str_mv | AT chelyshevai rna2hlahlabasedqualitycontrolofrnaseqdatasets AT pollardaj rna2hlahlabasedqualitycontrolofrnaseqdatasets AT oconnord rna2hlahlabasedqualitycontrolofrnaseqdatasets |