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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

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 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.

Keywords

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

Notes

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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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

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