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Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8059-8064. doi: 10.1073/pnas.1707945114. Epub 2017 Jul 3.
2
Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms.
Front Immunol. 2021 Mar 31;12:652258. doi: 10.3389/fimmu.2021.652258. eCollection 2021.
3
HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data.
Hum Mutat. 2017 Jul;38(7):788-797. doi: 10.1002/humu.23230. Epub 2017 May 12.
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Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.
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Hla-mapper: An application to optimize the mapping of HLA sequences produced by massively parallel sequencing procedures.
Hum Immunol. 2018 Sep;79(9):678-684. doi: 10.1016/j.humimm.2018.06.010. Epub 2018 Jul 3.
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Benchmarking NGS-Based HLA Typing Algorithms.
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State-of-the-art genome inference in the human MHC.
Int J Biochem Cell Biol. 2021 Feb;131:105882. doi: 10.1016/j.biocel.2020.105882. Epub 2020 Nov 12.
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HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data.
BMC Genomics. 2015;16 Suppl 2(Suppl 2):S7. doi: 10.1186/1471-2164-16-S2-S7. Epub 2015 Jan 21.
10
Next-generation sequencing for HLA typing of class I loci.
BMC Genomics. 2011 Jan 18;12:42. doi: 10.1186/1471-2164-12-42.

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consHLA: a next generation sequencing consensus-based HLA typing workflow.
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Computational methods and data resources for predicting tumor neoantigens.
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Advances in neoantigen-based immunotherapy for head and neck squamous cell carcinoma: a comprehensive review.
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Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (Review).
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A computational HLA allele-typing protocol to de-noise and leverage nanopore amplicon data.
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Circulating HBsAg-specific B cells are partially rescued in chronically HBV-infected patients with functional cure.
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Host genetic and immune factors drive evasion of HIV-1 pathogenesis in viremic non-progressors.
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本文引用的文献

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High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.
PLoS Comput Biol. 2016 Oct 28;12(10):e1005151. doi: 10.1371/journal.pcbi.1005151. eCollection 2016 Oct.
2
Deep sequencing of 10,000 human genomes.
Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11901-11906. doi: 10.1073/pnas.1613365113. Epub 2016 Oct 4.
3
The IPD-IMGT/HLA Database - New developments in reporting HLA variation.
Hum Immunol. 2016 Mar;77(3):233-237. doi: 10.1016/j.humimm.2016.01.020. Epub 2016 Jan 27.
4
Improved genome inference in the MHC using a population reference graph.
Nat Genet. 2015 Jun;47(6):682-8. doi: 10.1038/ng.3257. Epub 2015 Apr 27.
5
HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data.
BMC Genomics. 2015;16 Suppl 2(Suppl 2):S7. doi: 10.1186/1471-2164-16-S2-S7. Epub 2015 Jan 21.
6
Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.
Nucleic Acids Res. 2015 Jan;43(Database issue):D784-8. doi: 10.1093/nar/gku1166. Epub 2014 Nov 20.
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Fast and sensitive protein alignment using DIAMOND.
Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17.
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OptiType: precision HLA typing from next-generation sequencing data.
Bioinformatics. 2014 Dec 1;30(23):3310-6. doi: 10.1093/bioinformatics/btu548. Epub 2014 Aug 20.
9
HLA diversity in the 1000 genomes dataset.
PLoS One. 2014 Jul 2;9(7):e97282. doi: 10.1371/journal.pone.0097282. eCollection 2014.
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CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.

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