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POD-FISH: A New Technique for Parental Origin Determination Based on Copy Number Variation Polymorphism

  • Anja WeiseEmail author
  • Madeleine Gross
  • Sophie Hinreiner
  • Vera Witthuhn
  • Hasmik Mkrtchyan
  • Thomas Liehr
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 659)

Abstract

With the progress of array technologies and the enabled screening of individual human genomes, a new kind of polymorphism has been described – the so-called copy number variation (CNV) polymorphism. Copy number variants can be found in around 12% of the human genome sequence and have a size of up to several hundred kilobase pairs. These variants can not only differ between individuals, but also between corresponding alleles on homologous chromosomes. We recently developed a cytological assay for parental origin determination that relies on the design of CNV-based sets of probes for fluorescence in situ hybridization (POD-FISH). Here we describe an improved POD-FISH protocol that exploits “high frequency” variants for better discrimination of homologous chromosomes.

Key words

Parental origin determination fluorescence in situ hybridization Copy number variation Homologues Chromosomes Bacterial artificial chromosome 

Notes

Acknowledgments

Supported in parts by the DFG (436 RUS 17/109/04, 436 RUS 17/22/06, WE 3617/2-1, 436 ARM 17/5/06, LI820/11-1, LI820/17-1), Boehringer Ingelheim Fonds, Evangelische Studienwerk e.V. Villigst, IZKF Jena (Start-up S16), IZKF together with the TMWFK (TP 3.7 and B307-04004), University Jena, Stiftung Leukämie, and Stefan-Morsch-Stiftung.

References

  1. 1.
    Lee, C. (2005) Vive la difference! Nat Genet 37, 660–661.PubMedCrossRefGoogle Scholar
  2. 2.
    Schlötterer, C. (2004) The evolution of molecular markers-just a matter of fashion? Nat Rev Genet 5, 63–69.PubMedCrossRefGoogle Scholar
  3. 3.
    Liehr, T., Ziegler, M., Starke, H., Heller, A., Kuechler, A., Kittner, G., Beensen, V., Seidel, J., Hassler, H., Musebeck, J., Claussen, U. (2003) Conspicuous GTG-banding results of the centromere-near region can be caused by alphoid DNA heteromorphism. Clin Genet 64, 166–167.PubMedCrossRefGoogle Scholar
  4. 4.
    Müller, H., Klinger, H.P., Glasser, M. (1975) Chromosome polymorphism in a human newborn population II Potentials of polymorphic chromosome variants for characterizing the idiogram of an individual. Cytogenet Cell Genet 15, 239–255.PubMedCrossRefGoogle Scholar
  5. 5.
    Gardner, R.G.M., Sutherland, G.R. (2004) Oxford Monographs on Medical Genetics No 46: Chromosome abnormalities and genetic counselling. 3rd edition Oxford University Press, Oxford, New York.Google Scholar
  6. 6.
    Shaffer, L.G., Tommerup, N. (eds) (2005) ISCN: An international System for Human Cytogenetic Nomenclature. S. Karger, Basel, Switzerland.Google Scholar
  7. 7.
    Liehr, T., Nietzel, A., Starke, H., Heller, A., Weise, A., Kuechler, A., Senger, G., Ebner, S., Martin, T., Stumm, M., Wegner, R., Tonnies, H., Hoppe, C., Claussen, U., von Eggeling, F. (2003) Characterization of small marker chromosomes (smc) by recently developed molecular cytogenetic approaches. J Assoc Genet Technol 29, 5–10.PubMedGoogle Scholar
  8. 8.
    Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W., Lee, C. (2004) Detection of large-scale variation in the human genome. Nat Genet 36, 949–951.PubMedCrossRefGoogle Scholar
  9. 9.
    Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., Navin, N., Lucito, R., Healy, J., Hicks, J., Ye, K., Reiner, A., Gilliam, T.C., Trask, B., Patterson, N., Zetterberg, A., Wigler, M. (2004) Large-scale copy number polymorphism in the human genome. Science 23, 525–528.CrossRefGoogle Scholar
  10. 10.
    Feuk, L., Marshall, C.R., Wintle, R.F., Scherer, S.W. (2006) Structural variants: changing the landscape of chromosomes and design of disease studies. Hum Mol Genet 15, 57–66.CrossRefGoogle Scholar
  11. 11.
    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., González, J.R., Gratacòs, 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., Hurles, M.E. (2006) Global variation in copy number in the human genome. Nature 444, 444–454.PubMedCrossRefGoogle Scholar
  12. 12.
    Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F., Hakonarson, H., Bucan, M. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17, 1665–1674.PubMedCrossRefGoogle Scholar
  13. 13.
    Perry, G.H., Ben-Dor, A., Tsalenko, A., Sampas, N., Rodriguez-Revenga, L., Tran, C.W., Scheffer, A., Steinfeld, I., Tsang, P., Yamada, N.A., Park, H.S., Kim, J.I., Seo, J.S., Yakhini, Z., Laderman, S., Bruhn, L., Lee, C. (2008) The fine-scale and complex architecture of human copy-number variation. Am J Hum Genet 82, 685–695.PubMedCrossRefGoogle Scholar
  14. 14.
    Weise, A., Gross, M., Mrasek, K., Mkrtchyan, H., Horsthemke, B., Jonsrud, C., Von Eggeling, F., Hinreiner, S., Witthuhn, V., Claussen, U., Liehr, T. (2008) Parental-origin-determination fluorescence in situ hybridization distinguishes homologous human chromosomes on a single-cell level. Int J Mol Med 21, 189–200.PubMedGoogle Scholar
  15. 15.
    Telenius, H., Carter, N.P., Bebb, C.E., Nordenskjöld, M., Ponder, B.A., Tunnacliffe, A. (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13, 718–725.PubMedCrossRefGoogle Scholar
  16. 16.
    Liehr, T., Claussen, U. (2002) FISH on chromosome preparations of peripheral blood, in: FISH-Technology (Rautenstrauss, B., Liehr, T., eds) Springer, Berlin, 73–81.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Anja Weise
    • 1
    Email author
  • Madeleine Gross
    • 2
  • Sophie Hinreiner
    • 1
  • Vera Witthuhn
    • 1
  • Hasmik Mkrtchyan
    • 2
  • Thomas Liehr
    • 1
  1. 1.Institut für Humangenetik und AnthropologieUniversity of JenaJenaGermany
  2. 2.Institut für HumangenetikUniversity of JenaJenaGermany

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