본문 바로가기
HOME> 논문 > 논문 검색상세

논문 상세정보

Comparison of Methods for Detecting and Quantifying Variation in Copy Numbers of Duplicated Genes

Jeon, Jin-Tae    (Division of Animal Life Science, Gyeongsang National University   ); Ahn, Sung-Jin    (Department of Information Statistics, RICIC and RINS, Gyeongsang National University  );
  • 초록

    Copy number variations(CNVs) are known as one of the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing real-time polymerase chain reaction(PCR), invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed. PCR followed by a quantitative oligonucleotide ligation assay(qOLA) was developed for quantifying CNVs. The aim of this study was to compare the two methods for detecting and quantifying the CNVs of duplicated gene: the published pyrosequencing assay(pyro_CNV) and the newly developed qOLA_CNV. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares(RMSs) of bias and standard deviation of qOLA_CNV were 2.09 and 0.45, respectively. These values are less than half of those of pyro CNV.


  • 주제어

    Copy number variation .   quantitative oligonucleotide ligation assay .   pyrosequencing assay .   root mean square.  

  • 참고문헌 (16)

    1. Ahn, S. J. (2007). Statistical Quality Control using Minitab 14, Free Academy, Seoul, 260?262 
    2. Aldred, P. M., Hollox, E. J. and Armour, J. A. (2005). Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3, Human Molecular Genetics, 14, 2045?2052 
    3. Everitt, B. (1974). Cluster Analysis, Heinemann Educational Books, London 
    4. Giuffra, E., Evans, G., T$\ddot{o}$rnsten, A., Wales, R., Day, A., Looft, H., Plastow, G. and Andersson, L. (1999). The Belt mutation in pigs is an allele at the Dominant White (I/KIT) locus, Mammalian Genome, 10, 1132?1136 
    5. Hirooka, H., de Koning, D. J., van Arendonk, J. A. M., Harlizius, B., de Groot, P. N. and Bovenhuis, H. (2002). Genome scan reveals new coat color loci in exotic pig cross, Journal of Heredity, 93, 1?8 
    6. Johansson, M., Chaudhary R., Hellm´en, E., H¨oyheim, B., Chowdhary, B. and Andersson, L. (1996). Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor, Mammalian Genome, 7, 822?830 
    7. Johansson, M., Moller, M., Ellegren, H., Marklund, L., Gustavsson, U., Ringmar-Cederberg, E., Andersson, K., Edfors-Lilja, I. and Andersson, L. (1992). The gene for dominant white color in the pig is closely linked to ALB and PDGRFRA on chromosome 8, Genomics, 14, 965?969 
    8. Kehrer-Sawatzki, H. (2007). What a difference copy number variation makes, BioEssays, 29, 311?313 
    9. Marklund, S., Kijas, J., Rodriguez-Martinez, H., R$\ddot{o}$nnstrand, L., Funa, K., Moller, M., Lange, D., Edfors-Lilja, I. and, Andersson, L. (1998). Molecular basis for the dominant white phenotype in the domestic pig, Genome Research, 8, 826?833 
    10. Nevilie, M., Selzer, R., Aizenstein, B., Maguire, M., Hogan, K., Walton, R., Welsh, K., Neri, B. and de Arruda, M. (2002). Characterization of cytochrome P450 2D6 alleles using the Invader system, Biotechniques, Suppl 34?38, 40?43 
    11. Pielberg, G., Day, A. E., Plastow, G. S. and Andersson, L. (2003). A sensitive method for detecting variation in copy numbers of duplicated genes, Genome Research, 13, 2171?2177 
    12. Pielberg, G., Olsson, C., Syv¨anen, A. C. and Andersson, L. (2002). Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig, Genetics, 160, 305?311 
    13. Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Cho, E. K., Dallaire, S., Freeman, J. L., Gonz´alez, J. R., Gratac`os, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J. R., Marshall, C. R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A.,Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, L., Conrad, D. F., Estivill, X., Tyler-Smith, C., Carter, N. P., Aburatani, H., Lee, C., Jones, K.W., Scherer, S.W. and Hurles, M. E. (2006). Global variation in copy number in the human genome, Nature, 444, 444?454 
    14. SAS Institute Inc. (2004). SAS/STAT 9.1 user's guide Volume 6. SAS Institute, Cary, N.C., 1377?1427 
    15. Stranger, B. E., Forrest, M. S., Dunning, M., Ingle, C. E., Beazley, C., Thorne, N., Redon, R., Bird, C. P., de Grassi A, Lee, C., Tyler-Smith, C., Carter, N., Scherer, S. W., Tavar´e, S., Deloukas, P., Hurles, M. E. and Dermitzakis, E. T. (2007). Relative impact of nucleotide and copy number variation on gene expression phenotypes, Science, 315, 848?853 
    16. Westgard, J. O. and Hunt, M. R. (1973). Use and interpretation of common statistical tests in method comparison studies, Clinical Chemistry, 19, 49?57 

 저자의 다른 논문

  • 전진태 (30)

    1. 2003 "Single Stranded Conformation Polymorphism 분석에 의한 돼지 Duroc 품종의 미토콘드리아 DNA 유전적 변이" 한국동물자원과학회지 = Journal of animal science and technology 45 (6): 911~916    
    2. 2003 "검정소 검정돈의 품종 및 환경요인의 효과 추정" 한국동물자원과학회지 = Journal of animal science and technology 45 (6): 923~932    
    3. 2003 "돼지 leptin receptor내 초위성체 다형성과 경제형질과의 연관성 구명" 한국동물자원과학회지 = Journal of animal science and technology 45 (5): 679~688    
    4. 2003 "전산관리 양돈농가의 번식성적에 미치는 요인에 관한 연구" 한국동물자원과학회지 = Journal of animal science and technology 45 (6): 917~922    
    5. 2004 "Identification of Quantitative Trait Loci (QTL) Affecting Teat Number in Pigs" Asian-Australasian journal of animal sciences 17 (9): 1210~1213    
    6. 2004 "대한민국내 주요 돼지 품종의 순종 식별을 위한 품종특이 DNA marker의 활용" 한국동물자원과학회지 = Journal of animal science and technology 46 (5): 735~742    
    7. 2004 "돼지 5품종에 있어서 mtDNA ND2 유전자의 선택적 개시코돈의 특성과 빈도" 한국동물자원과학회지 = Journal of animal science and technology 46 (6): 903~908    
    8. 2004 "돼지 Duroc 품종에서 미토콘드리아 유전체 서열의 특성과 집단의 유전적 다양성" 한국동물자원과학회지 = Journal of animal science and technology 46 (6): 937~946    
    9. 2004 "돼지 Melanocortin Receptor 1(MC1R) 대립유전자 3의 신규 유전변이 탐색" 한국동물자원과학회지 = Journal of animal science and technology 46 (1): 1~6    
    10. 2004 "한우의 도체형질 유전모수 추정을 위한 REML과 Bayesian via Gibbs Sampling 방법의 비교 연구" 한국동물자원과학회지 = Journal of animal science and technology 46 (5): 719~728    
  • Ahn, Sung-Jin (4)

 활용도 분석

  • 상세보기

    amChart 영역
  • 원문보기

    amChart 영역

원문보기

무료다운로드
  • NDSL :
  • 한국통계학회 : 저널
유료다운로드

유료 다운로드의 경우 해당 사이트의 정책에 따라 신규 회원가입, 로그인, 유료 구매 등이 필요할 수 있습니다. 해당 사이트에서 발생하는 귀하의 모든 정보활동은 NDSL의 서비스 정책과 무관합니다.

원문복사신청을 하시면, 일부 해외 인쇄학술지의 경우 외국학술지지원센터(FRIC)에서
무료 원문복사 서비스를 제공합니다.

NDSL에서는 해당 원문을 복사서비스하고 있습니다. 위의 원문복사신청 또는 장바구니 담기를 통하여 원문복사서비스 이용이 가능합니다.

이 논문과 함께 출판된 논문 + 더보기