PMID- 33758920
OWN - NLM
STAT- MEDLINE
DCOM- 20211122
LR  - 20220323
IS  - 1477-4054 (Electronic)
IS  - 1467-5463 (Print)
IS  - 1467-5463 (Linking)
VI  - 22
IP  - 5
DP  - 2021 Sep 2
TI  - RNA2HLA: HLA-based quality control of RNA-seq datasets.
LID - 10.1093/bib/bbab055 [doi]
LID - bbab055
AB  - 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.
CI  - (c) The Author(s) 2021. Published by Oxford University Press.
FAU - Chelysheva, Irina
AU  - Chelysheva I
AUID- ORCID: 0000-0001-7802-7025
AD  - Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the 
      NIHR Oxford Biomedical Research Centre, Oxford, UK.
FAU - Pollard, Andrew J
AU  - Pollard AJ
AUID- ORCID: 0000-0001-7361-719X
AD  - Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the 
      NIHR Oxford Biomedical Research Centre, Oxford, UK.
FAU - O'Connor, Daniel
AU  - O'Connor D
AUID- ORCID: 0000-0002-6902-9886
AD  - Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the 
      NIHR Oxford Biomedical Research Centre, Oxford, UK.
LA  - eng
GR  - MR/R005982/1/MRC_/Medical Research Council/United Kingdom
GR  - MR/R005982/1/HIC-Vac Network Medical Research Council/
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Brief Bioinform
JT  - Briefings in bioinformatics
JID - 100912837
RN  - 0 (HLA Antigens)
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - Algorithms
MH  - Alleles
MH  - Base Sequence/genetics
MH  - Benchmarking/methods
MH  - Computational Biology/*methods
MH  - Data Accuracy
MH  - Genotype
MH  - HLA Antigens/*genetics
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - *Quality Control
MH  - RNA/genetics/immunology
MH  - RNA-Seq/*methods
MH  - Software
MH  - Transcriptome
MH  - Workflow
PMC - PMC8425422
OTO - NOTNLM
OT  - HLA
OT  - RNA-sequencing
OT  - bioinformatics
OT  - quality control
OT  - system biology
OT  - transcriptomics
EDAT- 2021/03/25 06:00
MHDA- 2021/11/23 06:00
PMCR- 2021/03/24
CRDT- 2021/03/24 06:50
PHST- 2020/12/16 00:00 [received]
PHST- 2021/01/16 00:00 [revised]
PHST- 2021/02/02 00:00 [accepted]
PHST- 2021/03/25 06:00 [pubmed]
PHST- 2021/11/23 06:00 [medline]
PHST- 2021/03/24 06:50 [entrez]
PHST- 2021/03/24 00:00 [pmc-release]
AID - 6184409 [pii]
AID - bbab055 [pii]
AID - 10.1093/bib/bbab055 [doi]
PST - ppublish
SO  - Brief Bioinform. 2021 Sep 2;22(5):bbab055. doi: 10.1093/bib/bbab055.