Human Cell

, Volume 24, Issue 4, pp 135–145 | Cite as

Construction of Japanese BAC library Yamato-2 (JY2): a set of 330K clone resources of damage-minimized DNA taken from a genetically established Japanese individual

  • Yasunobu Terabayashi
  • Keiko Morita
  • Joon Young Park
  • Soichiro Saito
  • Takashi Shiina
  • Hidetoshi Inoko
  • Isamu Ishiwata
  • Kazuhiro E. Fujimori
  • Takashi HiranoEmail author
Research Article


A bacterial artificial chromosome (BAC) library referred to as Yamato-2 (JY2), was constructed from a Japanese individual and contained 330,000 clones. Library construction was based on 2 concepts: Japanese pedigree and non-immortalization. Genomic DNA was extracted from white blood cells from umbilical cord blood of a Japanese male individual. Four traits of the sample, (1) amelogenin DNA, (2) short tandem repeat (STR), (3) mitochondrial DNA (mtDNA), and (4) HLA-allele typing, were investigated to verify attribution of the donor. One of the samples with quite good Japanese characteristics was named JY2 and used as a resource for construction of a BAC library. Amelogenin DNA indicated male. STR indicated Mongoloid. MtDNA suggested haplogroup B, which is different from any other diploid whose sequence has been reported. The HLA gene was classified into east-Asian specific haplotype. These results revealed that JY2 was obtained from a Japanese male. We sequenced both ends of 185,012 BAC clones. By using the BLAST search, BAC end sequences (BESs) were mapped on the human reference sequence provided by NCBI. Inserts of individual BAC clones were mapped with both ends properly placed. As a result, 103,647 BAC clones were successfully mapped. The average insert size of BAC calculated from the mapping information was 130 kb. Coverage and redundancy of the reference sequence by successfully mapped BAC clones were 96.4% and 3.9-fold, respectively. This library will be especially suitable as a Japanese standard genome resource. The availability of an accurate library is indispensable for diagnostics or drug-design based on genome information, and JY2 will provide an accurate sequence of the Japanese genome as an important addition to the human genome.


Human BAC library Japanese standard genome resource Umbilical cord blood Non-immortalization Comparative mapping 



The authors thank Dr Tadao Ohno for the encouragement of this work. This study was partially supported by a grant-in-aid from the New Energy and Industrial Technology Development Organization (NEDO), and by Okinawa Prefectural Government, Japan. All experiments were performed in accordance with both public and domestic guidelines. Japanese public guidelines, “Ethics Guidelines for Human Genome/Gene Analysis Research (” was approved by 3 ministries: the Ministry of Education, Culture, Sports, Science and Technology (MEXT); the Ministry of Health, Labor, and Welfare (MHLW); and the Ministry of Economy, Trade, and Industry (METI), and was implemented in 2001 (updated in 2008). Laboratory domestic guidelines, “handling guidelines for experiments using samples from humans” were approved by AIST Institutional Review Board (IRB).


  1. 1.
    Kim UJ, Birren BW, Slepak T, et al. Construction and characterization of a human bacterial artificial chromosome library. Genomics. 1996;34:213–8.PubMedCrossRefGoogle Scholar
  2. 2.
    Osoegawa K, Mammoser AG, Wu C, et al. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 2001;11:483–96.PubMedCrossRefGoogle Scholar
  3. 3.
    Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA. 1992;89:8794–7.PubMedCrossRefGoogle Scholar
  4. 4.
    Myers EW, Sutton GG, Delcher AL, et al. A whole-genome assembly of Drosophila. Science. 2000;287:2196–204.PubMedCrossRefGoogle Scholar
  5. 5.
    Green P. Against a whole-genome shotgun. Genome Res. 1997;7:410–7.PubMedGoogle Scholar
  6. 6.
    International Human Genome Mapping Consortium. A physical map of the human genome. Nature. 2001;409:934–41.CrossRefGoogle Scholar
  7. 7.
    Levy S, Sutton G, Ng PC, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5:e254.PubMedCrossRefGoogle Scholar
  8. 8.
    Wheeler DA, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008;452:872–6.PubMedCrossRefGoogle Scholar
  9. 9.
    International HapMap Consortium. A haplotype map of the human genome. Nature. 2005;437:1299–320.CrossRefGoogle Scholar
  10. 10.
    Hehir-Kwa JY, Egmont-Petersen M, Janssen IM, Smeets D, van Kessel AG, Veltman JA. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res. 2007;14:1–11.PubMedCrossRefGoogle Scholar
  11. 11.
    McCarroll SA. Extending genome-wide association studies to copy-number variation. Hum Mol Genet. 2008;17:R135–42.PubMedCrossRefGoogle Scholar
  12. 12.
    The HUGO Pan-Asian SNP Consortium. Mapping human genetic diversity in Asia. Science. 2009;326:1541–5.CrossRefGoogle Scholar
  13. 13.
    Manolio TA, Brooks LD, Collins FS. A HapMap harvest of insights into the genetics of common disease. J Clin Invest. 2008;118:1590–605.PubMedCrossRefGoogle Scholar
  14. 14.
    Ma F, Sun T, Shi Y, et al. Polymorphisms of EGFR predict clinical outcome in advanced non-small-cell lung cancer patients treated with Gefitinib. Lung Cancer. 2009;66:114–9.PubMedCrossRefGoogle Scholar
  15. 15.
    Dagan T, Sorek R, Sharon E, Ast G, Graur D. AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res. 2004;32:D489–92.PubMedCrossRefGoogle Scholar
  16. 16.
    Kreahling J, Graveley BR. The origins and implications of Aluternative splicing. Trends Genet. 2004;20:1–4.PubMedCrossRefGoogle Scholar
  17. 17.
    Asakawa S, Abe I, Kudoh Y, et al. Human BAC library: construction and rapid screening. Gene. 1997;191:69–79.PubMedCrossRefGoogle Scholar
  18. 18.
    Katamine S, Otsu M, Tada K, et al. Epstein–Barr virus transforms precursor B cells even before immunoglobulin gene rearrangements. Nature. 1984;309:369–72.PubMedCrossRefGoogle Scholar
  19. 19.
    Otsu M, Katamine S, Uno M, et al. Molecular characterization of novel reciprocal translocation t(6;14) in an Epstein–Barr virus-transformed B cell precursor. Mol Cell Biol. 1987;7:708–17.PubMedGoogle Scholar
  20. 20.
    Altiok E, Klein G, Zech L, et al. Epstein–Barr virus-transformed pro-B cells are prone to illegitimate recombination between the switch region of the mu chain gene and other chromosomes. Proc Natl Acad Sci USA. 1989;86:6333–7.PubMedCrossRefGoogle Scholar
  21. 21.
    Khanna R, Burrows SR, Moss DJ. Immune regulation in Epstein–Barr virus-associated diseases. Microbiol Rev. 1995;59:387–405.PubMedGoogle Scholar
  22. 22.
    Acute Leukemia Working Party of European Blood and Marrow Transplant Group. Transplants of umbilical-cord blood or bone marrow from unrelated donors in adults with acute leukemia. N Engl J Med. 2004;351:2276–85.Google Scholar
  23. 23.
    Istrail S, Sutton GG, Florea L, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci USA. 2004;101:1916–21.PubMedCrossRefGoogle Scholar
  24. 24.
    Khaja R, Zhang J, MacDonald JR, et al. Genome assembly comparison identifies structural variants in the human genome. Nat Genet. 2006;38:1413–8.PubMedCrossRefGoogle Scholar
  25. 25.
    Bentley DR. Whole-genome re-sequencing. Curr Opin Genet Dev. 2006;16:545–52.PubMedCrossRefGoogle Scholar
  26. 26.
    Nakahori Y, Takenaka O, Nakagome Y. A human X-Y homologous region encodes “Amelogenin”. Genomics. 1991;9:264–9.PubMedCrossRefGoogle Scholar
  27. 27.
    Ruitberg CM, Reeder DJ, Butler JM. STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res. 2001;29:320–2.PubMedCrossRefGoogle Scholar
  28. 28.
    Malyarchuk BA, Rogozin IB, Berikov VB, Derenko MV. Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region. Hum Genet. 2002;111:46–53.PubMedCrossRefGoogle Scholar
  29. 29.
    Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet. 2002;70:635–51.PubMedCrossRefGoogle Scholar
  30. 30.
    Shiina T, Hosomichi K, Inoko H, Kulski JK. The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet. 2009;54:15–39.PubMedCrossRefGoogle Scholar
  31. 31.
    Riley E, Olerup O. HLA polymorphisms and evolution. Immunol Today. 1992;13:333–5.PubMedCrossRefGoogle Scholar
  32. 32.
    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. 2005;57:1–13.CrossRefGoogle Scholar
  33. 33.
    Osoegawa K, Woon PY, Zhao B, Frengen E, Tateno M, Catanese JJ, de Jong PJ. An improved approach for construction of bacterial artificial chromosome libraries. Genomics. 1998;52:1–8.PubMedCrossRefGoogle Scholar
  34. 34.
    Frengen E, Weichenhan D, Zhao B, Osoegawa K, van Geel M, de Jong PJ. A modular, positive selection bacterial artificial chromosome vector with multiple cloning sites. Genomics. 1999;58:250–3.PubMedCrossRefGoogle Scholar
  35. 35.
    Ewing B, Hillier L, Wendl M, Green P. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8:175–85.PubMedGoogle Scholar
  36. 36.
    Ewing B, Green P. Basecalling of automated sequencer traces using phred II. Error probabilities. Genome Res. 1998;8:186–94.PubMedGoogle Scholar
  37. 37.
    Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.PubMedCrossRefGoogle Scholar
  38. 38.
    Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7.PubMedCrossRefGoogle Scholar
  39. 39.
    Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–9.PubMedCrossRefGoogle Scholar
  40. 40.
    Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature. 2008;456:60–5.PubMedCrossRefGoogle Scholar
  41. 41.
    Kim JI, Ju YS, Park H, et al. A highly annotated whole-genome sequence of a Korean individual. Nature. 2009;460:1011–5.PubMedGoogle Scholar
  42. 42.
    Nakajima F, Nakamura J, Yokota T. Analysis of HLA haplotypes in Japanese, using high resolution allele typing. MHC. 2001;8:1–32.Google Scholar
  43. 43.
    Park MH, Lee HJ, Bok J, et al. Korean BAC library construction and characterization of HLA-DRA, HLA-DRB3. J Biochem Mol Biol. 2006;39:418–25.PubMedCrossRefGoogle Scholar
  44. 44.
    Fujimoto A, Nakagawa H, Hosono N, et al. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet. 2010;42:931–6.PubMedCrossRefGoogle Scholar
  45. 45.
    Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2010;38:D234–6.PubMedCrossRefGoogle Scholar
  46. 46.
    Clarke L, Carbon JA. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell. 1976;9:91–9.PubMedCrossRefGoogle Scholar
  47. 47.
    Cavalli IJ, Mattevi MS, Erdtmann B, Sbalqueiro IJ, Maia NA. Equivalence of the total constitutive heterochromatin content by an interchromosomal compensation in the C band sizes of chromosomes 1, 9, 16, and Y in Caucasian and Japanese individuals. Hum Hered. 1985;35:379–87.PubMedCrossRefGoogle Scholar
  48. 48.
    Hsu LY, Benn PA, Tannenbaum HL, Perlis TE, Carlson AD. Chromosomal polymorphisms of 1, 9, 16, and Y in 4 major ethnic groups: a large prenatal study. Am J Med Genet. 1987;26:95–101.PubMedCrossRefGoogle Scholar
  49. 49.
    Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet. 2004;36:949–51.PubMedCrossRefGoogle Scholar
  50. 50.
    Sarov M, Stewart AF. The best control for the specificity of RNAi. Trends Biotechnol. 2005;23:446–8.PubMedCrossRefGoogle Scholar

Copyright information

© Japan Human Cell Society and Springer 2011

Authors and Affiliations

  • Yasunobu Terabayashi
    • 1
  • Keiko Morita
    • 1
  • Joon Young Park
    • 1
  • Soichiro Saito
    • 1
  • Takashi Shiina
    • 2
  • Hidetoshi Inoko
    • 2
  • Isamu Ishiwata
    • 3
  • Kazuhiro E. Fujimori
    • 4
  • Takashi Hirano
    • 5
    • 6
    Email author
  1. 1.Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
  2. 2.Division of Molecular Medical Science and Molecular Medicine, Department of Molecular Life ScienceTokai University School of MedicineIseharaJapan
  3. 3.Ishiwata Obstetrics and Gynecology HospitalMitoJapan
  4. 4.Ministry of Economy, Trade, and Industry (METI)TokyoJapan
  5. 5.Research and Innovation Promotion Headquarters, AISTTsukubaJapan
  6. 6.Okinawa Science and Technology Promotion CenterUrumaJapan

Personalised recommendations