Detection of chromosome changes by CGH, array-CGH and SNP array techniques in tumours
Authors:
Tatiana Vosecká 1; Zdeněk Musil 1,2; Aleš Vícha 1
Authors‘ workplace:
Klinika dětské hematologie a onkologie 2. LF UK a FN Motol
1; Ústav biologie a lékařské a genetiky, 1. LF UK a VFN V Praze
2
Published in:
Čes.-slov. Patol., 50, 2014, No. 1, p. 25-29
Category:
Reviews Article
Overview
New molecular biology methods have specified the evidence of chromosomal changes in the tumor tissue. These alterations can be proven to exist in the majority of malignant tumors. The fast progress of whole genome molecular biological methods has helped to improve the knowledge of tumor genetics. The evidence of genetic changes is a component of currently used diagnostic and prognostic schemes in particular cancer diseases. Karyotyping was the first method used in the clinical practice but its importance has decreased with the arrival of new molecular biological methods. The most common methods used for the detection of chromosomal deletions or amplifications are CGH, array-CGH and SNP array. The first two methods are based on the principle of comparison between tumor DNA and control DNA. The principle of SNP array uses the presence of single nucleotide polymorphisms that are located in the whole genome in each individual. SNP array can prove not only deletions or amplifications of the chromosomes but unlike CGH techniques it can also detect a loss of heterozygosity or uniparental disomy. The screening of chromosomal changes has nowadays become routine. These techniques are used for diagnosis, prognosis and treatment of cancer disease in certain cases.
Keywords:
cytogenetic – CGH – array-CGH – SNP array – genetic aberration
Sources
1. Delattre O, Zucman J, Melot T, et al. The Ewing family of tumors--a subgroup of small-round-cell tumors defined by specific chimeric transcripts. N Engl J Med 1994; 331: 294-249.
2. Zoubek A, Pfleiderer C, Salzer-Kuntschik M, et al. Variability of EWS chimaeric transcripts in Ewing tumours: a comparison of clinical and molecular data. Br J Cancer 1994; 70: 908-913.
3. Domingo-Fernandez R, Watters K, Piskareva O, et al. The role of genetic and epigenetic alterations in neuroblastoma disease pathogenesis. Pediatr Surg Int 2013; 29: 101-119.
4. Imataka G, Arisaka O. Chromosome analysis using spectral karyotyping (SKY). Cell Biochem Biophys 2012; 62: 13-17.
5. Kearney L. Multiplex-FISH (M-FISH): technique, developments and applications. Cytogenet Genome Res 2006; 114: 189-198.
6. Mackinnon RN, Chudoba I. The use of M-FISH and M-BAND to define chromosome abnormalities. Methods Mol Biol 2011; 730: 203-218.
7. Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992; 258: 818-821.
8. Weiss MM, Hermsen MA, Meijer GA, et al. Comparative genomic hybridisation. Mol Pathol 1999; 52: 243-251.
9. Solinas-Toldo S, Lampel S, Stilgenbauer S, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997; 20: 399-407.
10. Ylstra B, van den Ijssel P, Carvalho B, et al. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 2006; 34: 445-450.
11. Kirchhoff M, Gerdes T, Rose H, et al. Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry 1998; 31: 163-173.
12. Lichter P, Joos S, Bentz M, et al. Comparative genomic hybridization: uses and limitations Semin Hematol 2000; 37: 348-357.
13. Costa JL, Meijer G, Ylstra B, et al. Array comparative genomic hybridization copy number profiling: a new tool for translational research in solid malignancies. Semin Radiat Oncol 2008; 18: 98-104.
14. Fiegler H, Gribble SM, Burford DC, et al. Array painting: a method for the rapid analysis of aberrant chromosomes using DNA microarrays. J Med Genet 2003; 40: 664-670.
15. Nowak D, Hofmann WK, Koeffler HP. Genome-wide Mapping of Copy Number Variations Using SNP Arrays. Transfus Med Hemother 2009; 36: 246-251.
16. Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 2003; 33 Suppl: 228-237.
17. Bacolod MD, Schemmann GS, Giardina SF, et al. Emerging paradigms in cancer genetics: some important findings from high-density single nucleotide polymorphism array studies. Cancer Res 2009; 69: 723-727.
18. Taylor MD, Northcott PA, Korshunov A, et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol 2012; 123: 465-472.
19. Van Mater D, Knelson EH, Kaiser-Rogers KA, et al. Neuroblastoma in a pediatric patient with a microduplication of 2p involving the MYCN locus. Am J Med Genet A 2013 161A(3): 605-610.
20. Brodeur GM, Maris JM, Yamashiro DJ, et al. Biology and genetics of human neuroblastomas. J Pediatr Hematol Oncol 1997; 19: 93-101.
21. Schleiermacher G, Janoueix-Lerosey I, Ribeiro A, et al. Accumulation of segmental alterations determines progression in neuroblastoma. J Clin Oncol 2010; 28: 3122-3130.
22. Schleiermacher G, Michon J, Ribeiro A, et al. Segmental chromosomal alterations lead to a higher risk of relapse in infants with MYCN-non-amplified localised unresectable/disseminated neuroblastoma (a SIOPEN collaborative study). Br J Cancer 2011; 105: 1940-1948.
23. Matthay KK, Reynolds CP, Seeger RC, et al. Long-term results for children with high-risk neuroblastoma treated on a randomized trial of myeloablative therapy followed by 13-cis-retinoic acid: a children‘s oncology group study. J Clin Oncol 2009; 27: 1007-1013.
24. Matthay KK, Villablanca JG, Seeger RC, et al. Treatment of high-risk neuroblastoma with intensive chemotherapy, radiotherapy, autologous bone marrow transplantation, and 13-cis-retinoic acid. Children‘s Cancer Group. N Engl J Med 1999; 341: 1165-1173.
25. Parsons K, Bernhardt B, Strickland B Targeted immunotherapy for high-risk neuroblastoma--the role of monoclonal antibodies. Ann Pharmacother 2013; 47: 210-218.
26. Gunn S, Reveles X, Weldon K, et al. Molecular cytogenetics as a clinical test for prognostic and predictive biomarkers in newly diagnosed ovarian cancer. J Ovarian Res 2013; 6: 2.
27. Sapkota Y, Ghosh S, Lai R, et al. Germline DNA copy number aberrations identified as potential prognostic factors for breast cancer recurrence. PLoS One 2013; 8: e53850.
28. Shi ZZ, Zhang YM, Shang L, et al. Genomic profiling of rectal adenoma and carcinoma by array-based comparative genomic hybridization. BMC Med Genomics 2012; 5: 52.
29. Vainio P, Wolf M, Edgren H, et al. Integrative genomic, transcriptomic, and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer. Prostate 2012; 72: 789-802.
30. Swarts DR, Claessen SM, Jonkers YM, et al. Deletions of 11q22.3-q25 are associated with atypical lung carcinoids and poor clinical outcome. Am J Pathol 2011; 179: 1129-1137.
Labels
Anatomical pathology Forensic medical examiner ToxicologyArticle was published in
Czecho-Slovak Pathology
2014 Issue 1
Most read in this issue
- Cell cultures
- Lynch syndrome in the hands of pathologists
- Detection of chromosome changes by CGH, array-CGH and SNP array techniques in tumours
- Uterine tumors resembling ovarian sex cord tumors (UTROSCT). Report of a case with lymph node metastasis