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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

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Abstract

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 ty**, 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 map** 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.

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References

  1. Kim UJ, Birren BW, Slepak T, et al. Construction and characterization of a human bacterial artificial chromosome library. Genomics. 1996;34:213–8.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  4. Myers EW, Sutton GG, Delcher AL, et al. A whole-genome assembly of Drosophila. Science. 2000;287:2196–204.

    Article  PubMed  CAS  Google Scholar 

  5. Green P. Against a whole-genome shotgun. Genome Res. 1997;7:410–7.

    PubMed  CAS  Google Scholar 

  6. International Human Genome Map** Consortium. A physical map of the human genome. Nature. 2001;409:934–41.

    Article  Google Scholar 

  7. Levy S, Sutton G, Ng PC, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5:e254.

    Article  PubMed  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  9. International HapMap Consortium. A haplotype map of the human genome. Nature. 2005;437:1299–320.

    Article  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  11. McCarroll SA. Extending genome-wide association studies to copy-number variation. Hum Mol Genet. 2008;17:R135–42.

    Article  PubMed  CAS  Google Scholar 

  12. The HUGO Pan-Asian SNP Consortium. Map** human genetic diversity in Asia. Science. 2009;326:1541–5.

    Article  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  16. Kreahling J, Graveley BR. The origins and implications of Aluternative splicing. Trends Genet. 2004;20:1–4.

    Article  PubMed  CAS  Google Scholar 

  17. Asakawa S, Abe I, Kudoh Y, et al. Human BAC library: construction and rapid screening. Gene. 1997;191:69–79.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  21. Khanna R, Burrows SR, Moss DJ. Immune regulation in Epstein–Barr virus-associated diseases. Microbiol Rev. 1995;59:387–405.

    PubMed  CAS  Google Scholar 

  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. 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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  25. Bentley DR. Whole-genome re-sequencing. Curr Opin Genet Dev. 2006;16:545–52.

    Article  PubMed  CAS  Google Scholar 

  26. Nakahori Y, Takenaka O, Nakagome Y. A human X-Y homologous region encodes “Amelogenin”. Genomics. 1991;9:264–9.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  31. Riley E, Olerup O. HLA polymorphisms and evolution. Immunol Today. 1992;13:333–5.

    Article  PubMed  CAS  Google Scholar 

  32. Itoh Y, Mizuki N, Shimada T, et al. High-throughput DNA ty** of HLA-A, -B, -C, and -DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population. Immunogenetics. 2005;57:1–13.

    Article  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    PubMed  CAS  Google Scholar 

  36. Ewing B, Green P. Basecalling of automated sequencer traces using phred II. Error probabilities. Genome Res. 1998;8:186–94.

    PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  39. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–9.

    Article  PubMed  CAS  Google Scholar 

  40. Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature. 2008;456:60–5.

    Article  PubMed  CAS  Google Scholar 

  41. Kim JI, Ju YS, Park H, et al. A highly annotated whole-genome sequence of a Korean individual. Nature. 2009;460:1011–5.

    PubMed  CAS  Google Scholar 

  42. Nakajima F, Nakamura J, Yokota T. Analysis of HLA haplotypes in Japanese, using high resolution allele ty**. MHC. 2001;8:1–32.

    CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  49. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet. 2004;36:949–51.

    Article  PubMed  CAS  Google Scholar 

  50. Sarov M, Stewart AF. The best control for the specificity of RNAi. Trends Biotechnol. 2005;23:446–8.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

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 (http://www.lifescience.mext.go.jp/files/pdf/)” 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).

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Authors and Affiliations

  1. Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan

    Yasunobu Terabayashi, Keiko Morita, Joon Young Park & Soichiro Saito

  2. Division of Molecular Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan

    Takashi Shiina & Hidetoshi Inoko

  3. Ishiwata Obstetrics and Gynecology Hospital, Mito, Japan

    Isamu Ishiwata

  4. Ministry of Economy, Trade, and Industry (METI), Tokyo, Japan

    Kazuhiro E. Fujimori

  5. Research and Innovation Promotion Headquarters, AIST, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan

    Takashi Hirano

  6. Okinawa Science and Technology Promotion Center, Uruma, Japan

    Takashi Hirano

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  1. Yasunobu Terabayashi
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Correspondence to Takashi Hirano.

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Terabayashi, Y., Morita, K., Park, J.Y. et al. 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. Human Cell 24, 135–145 (2011). https://doi.org/10.1007/s13577-011-0019-y

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