PMID- 38293199
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240214
DP  - 2024 Jan 16
TI  - A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq 
      data.
LID - 2023.05.22.541750 [pii]
LID - 10.1101/2023.05.22.541750 [doi]
AB  - Accurate identification of human leukocyte antigen (HLA) alleles is essential for 
      various clinical and research applications, such as transplant matching and drug 
      sensitivities. Recent advances in RNA-seq technology have made it possible to 
      impute HLA types from sequencing data, spurring the development of a large number 
      of computational HLA typing tools. However, the relative performance of these 
      tools is unknown, limiting the ability for clinical and biomedical research to 
      make informed choices regarding which tools to use. Here we report the study 
      design of a comprehensive benchmarking of the performance of 12 HLA callers 
      across 682 RNA-seq samples from 8 datasets with molecularly defined gold standard 
      at 5 loci, HLA-A, -B, -C, -DRB1, and -DQB1. For each HLA typing tool, we will 
      comprehensively assess their accuracy, compare default with optimized parameters, 
      and examine for discrepancies in accuracy at the allele and loci levels. We will 
      also evaluate the computational expense of each HLA caller measured in terms of 
      CPU time and RAM. We also plan to evaluate the influence of read length over the 
      HLA region on accuracy for each tool. Most notably, we will examine the 
      performance of HLA callers across European and African groups, to determine 
      discrepancies in accuracy associated with ancestry. We hypothesize that RNA-Seq 
      HLA callers are capable of returning high-quality results, but the tools that 
      offer a good balance between accuracy and computational expensiveness for all 
      ancestry groups are yet to be developed. We believe that our study will provide 
      clinicians and researchers with clear guidance to inform their selection of an 
      appropriate HLA caller.
FAU - Yu, Dottie
AU  - Yu D
AUID- ORCID: 0009-0004-5682-7362
AD  - Department of Quantitative and Computational Biology, Dornsife College of 
      Letters, Arts and Sciences, University of Southern California, 1975 Zonal Ave, 
      Los Angeles, CA 90033, USA.
FAU - Ayyala, Ram
AU  - Ayyala R
AUID- ORCID: 0000-0001-7275-271X
AD  - Department of Quantitative and Computational Biology, Dornsife College of 
      Letters, Arts and Sciences, University of Southern California, 1975 Zonal Ave, 
      Los Angeles, CA 90033, USA.
FAU - Sadek, Sarah Hany
AU  - Sadek SH
AD  - Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and 
      Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
AD  - Department of Biology, and Department of Computer Science, California State 
      University, Fullerton, Fullerton, CA 92831.
FAU - Chittampalli, Likhitha
AU  - Chittampalli L
AUID- ORCID: 0000-0002-3976-1750
AD  - Department of Computer Science, Viterbi School of Engineering University of 
      Southern California, Los Angeles, CA, USA.
FAU - Farooq, Hafsa
AU  - Farooq H
AUID- ORCID: 0009-0002-6260-5016
AD  - Department of Computer Science, Georgia State University Atlanta, GA 30303 USA.
FAU - Jung, Junghyun
AU  - Jung J
AUID- ORCID: 0000-0001-6832-4368
AD  - Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and 
      Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
AD  - Center for Genetic Epidemiology, Keck School of Medicine, University of Southern 
      California, Los Angeles, CA, USA.
FAU - Nahid, Abdullah Al
AU  - Nahid AA
AUID- ORCID: 0000-0002-4390-0768
AD  - Department of Biochemistry and Molecular Biology, Shahjalal University of Science 
      and Technology, Sylhet 3114, Bangladesh.
FAU - Boldirev, Grigore
AU  - Boldirev G
AD  - Department of Computer Science, College of Arts and Sciences, Georgia State 
      University, Atlanta, GA, 30303, USA.
FAU - Jung, Mina
AU  - Jung M
AD  - Department of Quantitative and Computational Biology, Dornsife College of 
      Letters, Arts and Sciences, University of Southern California, 1975 Zonal Ave, 
      Los Angeles, CA 90033, US.
FAU - Park, Sungmin
AU  - Park S
AD  - Department of Computer Science and Engineering, Dongguk University-Seoul, Seoul, 
      04620, South Korea.
FAU - Nguyen, Austin
AU  - Nguyen A
AUID- ORCID: 0000-0001-7940-4830
AD  - Computational Biologist, Immune Monitoring & Cancer Omics Oregon Health & Science 
      University, Biomedical Engineering, 3181 S.W. Sam Jackson Park Road Portland, OR 
      97239-3098.
FAU - Zelikovsky, Alex
AU  - Zelikovsky A
AD  - Department of Computer Science, College of Arts and Sciences, Georgia State 
      University, Atlanta, GA, 30303, USA.
FAU - Mancuso, Nicholas
AU  - Mancuso N
AUID- ORCID: 0000-0002-9352-5927
AD  - Assistant Professor of Population and Public Health Sciences, Keck School of 
      Medicina, University of Southern California, 1845 N. Soto Street, USA.
FAU - Joo, Jong Wha J
AU  - Joo JWJ
AUID- ORCID: 0000-0002-1863-4664
AD  - Department of Computer Science and Engineering, Dongguk University-Seoul, Seoul, 
      04620, South Korea.
AD  - Division of AI Software Convergence, Dongguk University-Seoul, Seoul, 04620, 
      South Korea.
FAU - Thompson, Reid F
AU  - Thompson RF
AUID- ORCID: 0000-0003-3661-5296
AD  - Assistant Professor of Radiation Medicine, School of Medicine, OHSU, Portland, OR 
      97239.
AD  - Assistant Professor of Biomedical Engineering, School of Medicine, OHSU, 
      Portland, OR 97239.
AD  - Staff Physician, VA Portland Healthcare System, Portland OR 97239.
FAU - Alachkar, Houda
AU  - Alachkar H
AUID- ORCID: 0000-0001-5567-5521
AD  - Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and 
      Pharmaceutical Sciences, University of Southern California, CA, USA.
FAU - Mangul, Serghei
AU  - Mangul S
AUID- ORCID: 0000-0003-4770-3443
AD  - Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and 
      Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, 
      Los Angeles, CA 90033, USA.
AD  - Department of Quantitative and Computational Biology, University of Southern 
      California, Los Angeles.
LA  - eng
GR  - R01 AI173172/AI/NIAID NIH HHS/United States
PT  - Preprint
DEP - 20240116
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
PMC - PMC10827116
COIS- Competing interests The authors declare that the research was conducted in the 
      absence of any commercial or financial relationships that could be construed as a 
      potential conflict of interest.
EDAT- 2024/01/31 06:42
MHDA- 2024/01/31 06:43
PMCR- 2024/01/30
CRDT- 2024/01/31 04:21
PHST- 2024/01/31 06:42 [pubmed]
PHST- 2024/01/31 06:43 [medline]
PHST- 2024/01/31 04:21 [entrez]
PHST- 2024/01/30 00:00 [pmc-release]
AID - 2023.05.22.541750 [pii]
AID - 10.1101/2023.05.22.541750 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2024 Jan 16:2023.05.22.541750. doi: 
      10.1101/2023.05.22.541750.