次世代シークエンス用アリル判定プログラム（SeaBass）の開発とその検証
膨大な次世代シークエンスデータを用いるアリル判定法の開発は，HLA DNAタイピングの簡略化や迅速化のために必要である。筆者らは，次世代シークエンス用アリル判定プログラム（SeaBass）を開発し，極めて高い精度でアリル判定が可能であることを確認した。したがって，SeaBassは新規アリルやnullアリルの検出のための優れたアリル判定ツールの一つであると考えられる。...
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| Published in | 日本組織適合性学会誌 Vol. 22; no. 2; pp. 102 - 107 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | Japanese |
| Published |
日本組織適合性学会
2015
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| Subjects | |
| Online Access | Get full text |
| ISSN | 2186-9995 2187-4239 |
| DOI | 10.12667/mhc.22.102 |
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| Abstract | 膨大な次世代シークエンスデータを用いるアリル判定法の開発は，HLA DNAタイピングの簡略化や迅速化のために必要である。筆者らは，次世代シークエンス用アリル判定プログラム（SeaBass）を開発し，極めて高い精度でアリル判定が可能であることを確認した。したがって，SeaBassは新規アリルやnullアリルの検出のための優れたアリル判定ツールの一つであると考えられる。 |
|---|---|
| AbstractList | 膨大な次世代シークエンスデータを用いるアリル判定法の開発は，HLA DNAタイピングの簡略化や迅速化のために必要である。筆者らは，次世代シークエンス用アリル判定プログラム（SeaBass）を開発し，極めて高い精度でアリル判定が可能であることを確認した。したがって，SeaBassは新規アリルやnullアリルの検出のための優れたアリル判定ツールの一つであると考えられる。 |
| Author | 鈴木, 進悟 猪子, 英俊 桝屋, 安里 重成, 敦子 光永, 滋樹 椎名, 隆 尾崎, 有紀 |
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| References | 14)Holcomb CL, Höglund B, Anderson MW, et al.: A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens (77): 206–217, 2011. 11)Chang CJ, Chen PL, Chao KM, et al.: A fault-tolerant method for HLA typing with PacBio data. BMC Bioinformatics 15296, 2014. 19)Lind C, Ferriola D, Mackiewicz K, et al.: Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol (71): 1033–1042, 2010. 9)Ozaki, Y, Suzuki, S, Shiina, T. et al.: Cost-efficient multiplex PCR for routine genotyping of up to nine classical HLA loci in a single analytical run of multiple samples by next generation sequencing. BMC Genomics (16): 318, 2015. 4)Rozemuller E: Collection and analysis of SBT results data. 13th IHWS Technology Joint Report. Immunobiology of Human MHC Vol. 1 (ed. Hansen JA), p. 413–416, 2006. 18)Smith AG, Pyo CW, Nelson W, et al.: Next generation sequencing to determine HLA class II genotypes in a cohort of hematopoietic cell transplant patients and donors. Hum Immunol (75): 1040–1046, 2014. 15)Erlich RL, Jia X, Anderson S, et al.: Next-generation sequencing for HLA typing of class I loci. BMC Genomics (12): 42, 2011. 13)Gabriel C, Danzer M, Hackl C, et al.: Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol (70): 960–964, 2009. 21)Hosomichi K, Jinam TA, Mitsunaga S, et al.: Phase-defined complete sequencing of the HLA genes by next-generation sequencing. BMC Genomics (14): 355, 2013. 8)Ozaki Y, Suzuki S, Shiina T, et al.: HLA-DRB1, -DRB3, -DRB4 and -DRB5 genotyping at a super-high resolution level by long range PCR and high-throughput sequencing. Tissue Antigens (83): 10–16, 2014. 16)Moonsamy PV, Williams T, Bonella P, et al.: High throughput HLA genotyping using 454 sequencing and the Fluidigm Access ArrayTM System for simplified amplicon library preparation. Tissue Antigens (81): 141–149, 2013. 2)Santamaria P, Boyce-Jacino MT, Lindstrom AL, et al.: HLA class II ”typing”: direct sequencing of DRB, DQB, and DQA genes. Hum Immunol 1992: 33: 69–81. 5)Shiina T, Suzuki S, Ozaki Y, et al.: 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): 305–316, 2012. 20)Wang C, Krishnakumar S, Wilhelmy J, et al.: High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci U S A (109): 8676–8681, 2012. 17)Lange V, Böhme I, Hofmann J, et al.: Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics (15): 63, 2014. 3)Itoh Y, Mizuki N, Shimada T, et al.: High-throughput DNA typing of HLA-A, -B, -C, and -DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population. Immunogenetics (57): 717–729, 2005. 1)Robinson J, Halliwell JA, McWilliam H, et al.: The IMGT/HLA Database. Nucleic Acids Research (41): D1222–1227, 2013. 6)鈴木進悟，尾崎有紀，椎名 隆，他：次世代シークエンサーを用いたHLAクラスI遺伝子の超高解像度DNAタイピング（Super high resolution Single molecule-Sequence Based Typing; SS-SBT）法の開発．MHC学会誌 (20)1: 43–53, 2012. 12)Bentley G, Higuchi R, Hoglund B, et al.: High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens (74): 393–403, 2010. 7)尾崎有紀，鈴木進悟，椎名 隆，他：次世代シークエンサーを用いたHLA-DRB1遺伝子の超高解像度DNAタイピング（Super high resolution Single molecule-Sequence Based Typing; SS-SBT）法の開発．MHC学会誌 19(2): 211–222, 2012. 10)Major E, Rigó K, Juhos S, et al.: HLA typing from 1000 genomes whole genome and whole exome illumina data. PLoS One (8): e78410, 2014. 22)Wada A, Shiina, T, Michino J, et al.: A novel HLA-B allele, HLA-B*44:184, identified by super high-resolution single-molecule sequence-based typing in a Japanese individual. Tissue Antigens 83: 198–199, 2014. |
| References_xml | – reference: 1)Robinson J, Halliwell JA, McWilliam H, et al.: The IMGT/HLA Database. Nucleic Acids Research (41): D1222–1227, 2013. – reference: 4)Rozemuller E: Collection and analysis of SBT results data. 13th IHWS Technology Joint Report. Immunobiology of Human MHC Vol. 1 (ed. Hansen JA), p. 413–416, 2006. – reference: 19)Lind C, Ferriola D, Mackiewicz K, et al.: Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol (71): 1033–1042, 2010. – reference: 11)Chang CJ, Chen PL, Chao KM, et al.: A fault-tolerant method for HLA typing with PacBio data. BMC Bioinformatics 15296, 2014. – reference: 21)Hosomichi K, Jinam TA, Mitsunaga S, et al.: Phase-defined complete sequencing of the HLA genes by next-generation sequencing. BMC Genomics (14): 355, 2013. – reference: 12)Bentley G, Higuchi R, Hoglund B, et al.: High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens (74): 393–403, 2010. – reference: 17)Lange V, Böhme I, Hofmann J, et al.: Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics (15): 63, 2014. – reference: 18)Smith AG, Pyo CW, Nelson W, et al.: Next generation sequencing to determine HLA class II genotypes in a cohort of hematopoietic cell transplant patients and donors. Hum Immunol (75): 1040–1046, 2014. – reference: 6)鈴木進悟，尾崎有紀，椎名 隆，他：次世代シークエンサーを用いたHLAクラスI遺伝子の超高解像度DNAタイピング（Super high resolution Single molecule-Sequence Based Typing; SS-SBT）法の開発．MHC学会誌 (20)1: 43–53, 2012. – reference: 16)Moonsamy PV, Williams T, Bonella P, et al.: High throughput HLA genotyping using 454 sequencing and the Fluidigm Access ArrayTM System for simplified amplicon library preparation. Tissue Antigens (81): 141–149, 2013. – reference: 2)Santamaria P, Boyce-Jacino MT, Lindstrom AL, et al.: HLA class II ”typing”: direct sequencing of DRB, DQB, and DQA genes. Hum Immunol 1992: 33: 69–81. – reference: 8)Ozaki Y, Suzuki S, Shiina T, et al.: HLA-DRB1, -DRB3, -DRB4 and -DRB5 genotyping at a super-high resolution level by long range PCR and high-throughput sequencing. Tissue Antigens (83): 10–16, 2014. – reference: 5)Shiina T, Suzuki S, Ozaki Y, et al.: 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): 305–316, 2012. – reference: 14)Holcomb CL, Höglund B, Anderson MW, et al.: A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens (77): 206–217, 2011. – reference: 15)Erlich RL, Jia X, Anderson S, et al.: Next-generation sequencing for HLA typing of class I loci. BMC Genomics (12): 42, 2011. – reference: 22)Wada A, Shiina, T, Michino J, et al.: A novel HLA-B allele, HLA-B*44:184, identified by super high-resolution single-molecule sequence-based typing in a Japanese individual. Tissue Antigens 83: 198–199, 2014. – reference: 3)Itoh Y, Mizuki N, Shimada T, et al.: High-throughput DNA typing of HLA-A, -B, -C, and -DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population. Immunogenetics (57): 717–729, 2005. – reference: 10)Major E, Rigó K, Juhos S, et al.: HLA typing from 1000 genomes whole genome and whole exome illumina data. PLoS One (8): e78410, 2014. – reference: 9)Ozaki, Y, Suzuki, S, Shiina, T. et al.: Cost-efficient multiplex PCR for routine genotyping of up to nine classical HLA loci in a single analytical run of multiple samples by next generation sequencing. BMC Genomics (16): 318, 2015. – reference: 13)Gabriel C, Danzer M, Hackl C, et al.: Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol (70): 960–964, 2009. – reference: 20)Wang C, Krishnakumar S, Wilhelmy J, et al.: High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci U S A (109): 8676–8681, 2012. – reference: 7)尾崎有紀，鈴木進悟，椎名 隆，他：次世代シークエンサーを用いたHLA-DRB1遺伝子の超高解像度DNAタイピング（Super high resolution Single molecule-Sequence Based Typing; SS-SBT）法の開発．MHC学会誌 19(2): 211–222, 2012. |
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| Snippet | 膨大な次世代シークエンスデータを用いるアリル判定法の開発は，HLA DNAタイピングの簡略化や迅速化のために必要である。筆者らは，次世代シークエンス用アリル判... |
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| SubjectTerms | DNAタイピング アリル ヒト白血球抗原 次世代シークエンサー |
| Title | 次世代シークエンス用アリル判定プログラム（SeaBass）の開発とその検証 |
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