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Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami

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HLA Typing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1802))

Abstract

Accurate typing of human leukocyte antigen (HLA) is essential for successful organ transplantation and HLA genes are heavily associated with various diseases. Widely used typing assays often involve a set of specially designed primers or probes requiring additional experiments. With the maturing of high-throughput sequencing (HTS) technologies, whole genome sequencing (WGS) as well as other HTS assays are becoming more accessible even in the clinical settings. We describe various computational methods capable of directly typing HLA genes using HTS data including Kourami, our HLA assembler. Kourami is the first HLA assembler capable of discovering novel alleles. Kourami assembles full-length sequences across the peptide-binding regions of HLA genes. Here, we focus on how a user would use Kourami on a new sample. We demonstrate the application by typing HLA alleles from a recently published WGS data with validated HLA types using Kourami.

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References

  1. Boegel S, Löwer M, Schäfer M et al (2012) HLA typing from RNA-Seq sequence reads. Genome Med 4(12):102

    Article  PubMed  PubMed Central  Google Scholar 

  2. Robinson J, Halliwell JA, Hayhurst JD et al (2015) The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res 43(Database issue):D423–D431. https://doi.org/10.1093/nar/gku1161

    Article  PubMed  CAS  Google Scholar 

  3. Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189):872–876

    Article  CAS  PubMed  Google Scholar 

  4. Telenti A, Pierce LCT, Biggs WH et al (2016) Deep sequencing of 10,000 human genomes. Proc Natl Acad Sci U S A 113(42):11901–11906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Nagasaki M, Yasuda J, Katsuoka F et al (2015) Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat Commun 6:8018

    Article  CAS  PubMed  Google Scholar 

  6. Gudbjartsson DF, Helgason H, Gudjonsson SA et al (2015) Large-scale whole-genome sequencing of the Icelandic population. Nat Genet 47(5):435–444

    Article  CAS  PubMed  Google Scholar 

  7. National Heart, Lung and Blood Institute (2017) Trans-Omics for Precision Medicine (TOPMed) Program. https://www.nhlbi.nih.gov/research/resources/nhlbi-precision-medicine-initiative/topmed/. Accessed 29 Nov 2017

  8. Lee H, Kingsford C (2018) Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery. Genome Biology 19:16

    Google Scholar 

  9. Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25(14):1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Consortium T1GP (2015) A global reference for human genetic variation. Nature 526(7571):68–74

    Article  CAS  Google Scholar 

  13. Seo J-S, Rhie A, Kim J et al (2016) De novo assembly and phasing of a Korean human genome. Nature 538(7624):243–247

    Article  CAS  PubMed  Google Scholar 

  14. Zheng-Bradley X, Streeter I, Fairley S et al (2017) Alignment of 1000 genomes project reads to reference assembly GRCh38. GigaScience 6(7):1–8

    Article  PubMed  PubMed Central  Google Scholar 

  15. Meienberg J, Bruggmann R, Oexle K et al (2016) Clinical sequencing: is WGS the better WES? Hum Genet 135(3):359–362

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Asan, Xu Y, Jiang H et al (2011) Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol 12(9):R95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 1000 Genomes This README explains the alignment pipeline used to remap all the 1000 Genomes Project Phase 3 reads to GRCh38DH. ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/README.1000genomes.GRCh38DH.alignment. Accessed 29

  18. Warren RL, Choe G, Freeman DJ et al (2012) Derivation of HLA types from shotgun sequence datasets. Genome Med 4(12):95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kim HJ, Pourmand N (2013) HLA haplotyping from RNA-seq data using hierarchical read weighting. PLoS One 8(6):e67885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bai Y, Ni M, Cooper B et al (2014) Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. BMC Genomics 15:325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Huang Y, Yang J, Ying D et al (2015) HLAreporter: a tool for HLA typing from next generation sequencing data. Genome Med 7(1):25

    Article  PubMed  PubMed Central  Google Scholar 

  22. Nariai N, Kojima K, Saito S et al (2015) HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. BMC Genomics 16(Suppl 2):S7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Dilthey AT, Gourraud P-A, Mentzer AJ et al (2016) High-accuracy HLA type inference from whole-genome sequencing data using population reference graphs. PLoS Comput Biol 12(10):e1005151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding

This research was funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554 to C.K., by the US National Science Foundation (CCF-1256087, CCF-1319998) and by the US National Institute of Health (R01HG007104, R01GM122935).

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Correspondence to Heewook Lee .

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Lee, H., Kingsford, C. (2018). Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami. In: Boegel, S. (eds) HLA Typing. Methods in Molecular Biology, vol 1802. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8546-3_17

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  • DOI: https://doi.org/10.1007/978-1-4939-8546-3_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8545-6

  • Online ISBN: 978-1-4939-8546-3

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