Advertisement

Array-CGH in Childhood MDS

  • Marcel Tauscher
  • Inka Praulich
  • Doris Steinemann
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 973)

Abstract

To study genomic imbalances potentially involved in disease development and/or progression of childhood MDS, array-based comparative genomic hybridization (aCGH) is a helpful tool. Copy number alterations (CNA) of subtle chromosomal regions containing potential candidate genes, e.g., TP53 or RUNX1 can be detected. However, characterizing small and/or heterogeneous tumor subpopulations by high-resolution aCGH within a majority of normal cells is a challenge in MDS and requires validation by independent methods like FISH or quantitative PCR. For the identification of tumor-relevant CNA, the analysis of DNA isolated from purified granulocytes or myeloid populations instead of DNA from whole bone marrow (BM) cells is helpful to overcome some of these limitations.

Key words

Copy number alterations Copy number variation Childhood MDS Array-CGH Monosomy 7 TP53 

Notes

Acknowledgments

The authors are grateful to Prof. Brigitte Schlegelberger and Gillian Teicke for critically reading the manuscript and to Dr. Gudrun Göhring for providing the karyogram.

References

  1. 1.
    Niemeyer CM, Arico M, Basso G, Biondi A, Cantu RA, Creutzig U, Haas O, Harbott J, Hasle H, Kerndrup G, Locatelli F, Mann G, Stollmann-Gibbels B, Veer-Korthof ET, van Wering E, Zimmermann M (1997) Chronic myelomonocytic leukemia in childhood: a retrospective analysis of 110 cases. European Working Group on Myelodysplastic Syndromes in Childhood (EWOG-MDS). Blood 89(10):3534–3543PubMedGoogle Scholar
  2. 2.
    Hasle H (2007) Myelodysplastic and myeloproliferative disorders in children. Curr Opin Pediatr 19(1):1–8PubMedCrossRefGoogle Scholar
  3. 3.
    Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP (2003) DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 36(4):361–374PubMedCrossRefGoogle Scholar
  4. 4.
    Albertson DG, Pinkel D (2003) Genomic microarrays in human genetic disease and cancer. Hum Mol Genet 12(Spec No 2):R145–R152PubMedCrossRefGoogle Scholar
  5. 5.
    Wessendorf S, Fritz B, Wrobel G, Nessling M, Lampel S, Goettel D, Kuepper M, Joos S, Hopman T, Kokocinski F, Dohner H, Bentz M, Schwaenen C, Lichter P (2002) Automated screening for genomic imbalances using matrix-based comparative genomic hybridization. Lab Invest 82(1):47–60PubMedCrossRefGoogle Scholar
  6. 6.
    Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407PubMedCrossRefGoogle Scholar
  7. 7.
    Niemeyer C, Stollmann-Gibbels B, Ebell W, Gaedicke G, Creutzig U (1992) Myelodysplastic diseases in childhood. Klin Padiatr 204(4):190–197PubMedCrossRefGoogle Scholar
  8. 8.
    Clark DM, Lampert IA (1990) Apoptosis is a common histopathological finding in myelodysplasia: the correlate of ineffective haematopoiesis. Leuk Lymphoma 2(6):415–418CrossRefGoogle Scholar
  9. 9.
    Kerbauy DB, Deeg HJ (2007) Apoptosis and antiapoptotic mechanisms in the progression of myelodysplastic syndrome. Exp Hematol 35(11):1739–1746PubMedCrossRefGoogle Scholar
  10. 10.
    Gondek LP, Tiu R, O’Keefe CL, Sekeres MA, Theil KS, Maciejewski JP (2008) Chromosomal lesions and uniparental disomy detected by SNP arrays in MDS, MDS/MPD, and MDS-derived AML. Blood 111(3):1534–1542PubMedCrossRefGoogle Scholar
  11. 11.
    Evers C, Beier M, Poelitz A, Hildebrandt B, Servan K, Drechsler M, Germing U, Royer HD, Royer-Pokora B (2007) Molecular definition of chromosome arm 5q deletion end points and detection of hidden aberrations in patients with myelodysplastic syndromes and isolated del(5q) using oligonucleotide array CGH. Genes Chromosomes Cancer 46(12):1119–1128PubMedCrossRefGoogle Scholar
  12. 12.
    Praulich I, Tauscher M, Gohring G, Glaser S, Hofmann W, Feurstein S, Flotho C, Lichter P, Niemeyer CM, Schlegelberger B, Steinemann D (2010) Clonal heterogeneity in childhood myelodysplastic syndromes–challenge for the detection of chromosomal imbalances by array-CGH. Genes Chromosomes Cancer 49(10):885–900PubMedCrossRefGoogle Scholar
  13. 13.
    Griesshammer M, Klippel S, Strunck E, Temerinac S, Mohr U, Heimpel H, Pahl HL (2004) PRV-1 mRNA expression discriminates two types of essential thrombocythemia. Ann Hematol 83(6):364–370PubMedCrossRefGoogle Scholar
  14. 14.
    Porta G, Maserati E, Mattarucchi E, Minelli A, Pressato B, Valli R, Zecca M, Bernardo ME, Lo CF, Locatelli F, Danesino C, Pasquali F (2007) Monosomy 7 in myeloid malignancies: parental origin and monitoring by real-time quantitative PCR. Leukemia 21(8):1833–1835PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Marcel Tauscher
    • 1
  • Inka Praulich
    • 1
  • Doris Steinemann
    • 1
  1. 1.Institute of Cell and Molecular Pathology, Hannover Medical SchoolHannoverGermany

Personalised recommendations