Abstract
Super high resolution-single molecule-sequence-based typing (SS-SBT) is an HLA DNA typing method to the field 4 level of allelic resolution (formerly known as 8-digit typing) to efficiently detect novel and null alleles without phase ambiguity by combination of long ranged PCR amplification and next-generation sequencing (NGS) technologies. In this chapter, we describe three basic steps, long ranged PCR, NGS, and allele assignment.
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References
Santamaria P, Lindstrom AL, Boyce-Jacino MT, Myster SH, Barbosa JJ, Faras AJ, Rich SS (1993) HLA class I sequence-based typing. Hum Immunol 37(1):39–50
Saiki RK, Walsh PS, Levenson CH, Erlich HA (1989) Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A 86(16):6230–6234
Adams SD, Barracchini KC, Chen D, Robbins F, Wang L, Larsen P, Luhm R, Stroncek DF (2004) Ambiguous allele combinations in HLA Class I and Class II sequence-based typing: when precise nucleotide sequencing leads to imprecise allele identification. J Transl Med 2(1):30. https://doi.org/10.1186/1479-5876-2-30
Wiseman RW, Karl JA, Bimber BN, O’Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres E Jr, Wright C, Harkins T, O’Connor DH (2009) Major histocompatibility complex genotyping with massively parallel pyrosequencing. Nat Med 15(11):1322–1326. https://doi.org/10.1038/nm.2038
Lind C, Ferriola D, Monos D (2010) Next generation sequencing: entering a new era in HLA sequence-based typing. ASHI 34(3):8–14
Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D’Arcy M, Gai X, Goodridge D, Sayer D, Monos D (2010) Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol 71(10):1033–1042. https://doi.org/10.1016/j.humimm.2010.06.016
Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Proll J (2009) Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 70(11):960–964. https://doi.org/10.1016/j.humimm.2009.08.009
Lank SM, Wiseman RW, Dudley DM, O’Connor DH (2010) A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. Hum Immunol 71(10):1011–1017. https://doi.org/10.1016/j.humimm.2010.07.012
Holcomb CL, Hoglund B, Anderson MW, Blake LA, Bohme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, Ladner M, Lind C, Monos D, Pando MJ, Proll J, Sayer DC, Schmitz-Agheguian G, Simen BB, Thiele B, Trachtenberg EA, Tyan DB, Wassmuth R, White S, Erlich HA (2011) A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 77(3):206–217. https://doi.org/10.1111/j.1399-0039.2010.01606.x
Shiina T, Suzuki S, Ozaki Y, Taira H, Kikkawa E, Shigenari A, Oka A, Umemura T, Joshita S, Takahashi O, Hayashi Y, Paumen M, Katsuyama Y, Mitsunaga S, Ota M, Kulski JK, Inoko H (2012) Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. Tissue Antigens 80(4):305–316. https://doi.org/10.1111/j.1399-0039.2012.01941.x
Ozaki Y, Suzuki S, Shigenari A, Okudaira Y, Kikkawa E, Oka A, Ota M, Mitsunaga S, Kulski JK, Inoko H, Shiina T (2014) HLA-DRB1, -DRB3, -DRB4 and -DRB5 genotyping at a super-high resolution level by long range PCR and high-throughput sequencing. Tissue Antigens 83(1):10–16. https://doi.org/10.1111/tan.12258
Kulski JK, Suzuki S, Ozaki Y, Mitsunaga S, Inoko H, Shiina T (2014) In phase HLA genotyping by next generation sequencing – a comparison between two massively parallel sequencing bench-top systems, the Roche GS Junior and Ion Torrent PGM. HLA and associated important diseases. Intech, Croatia
University of California SCU (2017) Blat software. http://hgdownload.cse.ucsc.edu/admin/exe/
Knaus BJ (2014) fastq2fasta.pl file format conversion program
IPD-IMGT/HLA (2017) HLA allele sequences. ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/
QIAGEN (2016) Protocol of QIAamp DNA Blood Mini Kit. https://www.qiagen.com/us/resources/resourcedetail?id=62a200d6-faf4-469b-b50f-2b59cf738962&lang=en
Coulter B (2016) Protocol of Agencourt AMPure XP. https://beckman.jp/files/products/genomics/AMPureXP/IFU_AMPureXP.pdf
Scientific TF (2008) Protocol of Quant-iT PicoGreen dsDNA Assay Kit. https://www.thermofisher.com/order/catalog/product/P11496?SID=srch-srp-P11496
Scientific TF (2016) Protocol of Ion Plus Fragment Library kit. https://tools.thermofisher.com/content/sfs/manuals/MAN0009847_IonXpressPlus_gDNA_FragLibraryPrep_UG.pdf#search=%27Ion+Xpress%E2%84%A2+Plus+gDNA+Fragment+Library+Preparation%27
Agilent (2013) Protocol of Agilent High Sensitivity DNA Kit. http://www.agilent.com/cs/library/usermanuals/Public/G2938-90321_SensitivityDNA_KG_EN.pdf#search=%27Agilent+High+Sensitivity+DNA+Kit%27
Scientific TF (2017) Protocol of Ion PGM Hi-Q OT2 Kit
Scientific TF (2017) Protocol of Ion PGM Hi Q Sequencing Kit. https://tools.thermofisher.com/content/sfs/manuals/MAN0009816_Ion_PGM_HiQ_Sequencing_Kit_UG.pdf#search=%27HiQ+sequencing%27
Shiina T, Suzuki S, Kulski JK (2016) MHC genotyping in human and nonhuman species by PCR-based next-generation sequencing. Next generation sequencing. Intech, Croatia
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Shiina, T., Suzuki, S., Kulski, J.K., Inoko, H. (2018). Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA Loci Using Ion Torrent PGM. 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_8
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DOI: https://doi.org/10.1007/978-1-4939-8546-3_8
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