Skip to main content
NCBI home page
The American Journal of Pathology logoLink to The American Journal of Pathology
. 1995 Jun;146(6):1332–1340.

Correlation of microscopic phenotype with genotype in a formalin-fixed, paraffin-embedded testicular germ cell tumor with universal DNA amplification, comparative genomic hybridization, and interphase cytogenetics.

M R Speicher 1, A Jauch 1, H Walt 1, S du Manoir 1, T Ried 1, W Jochum 1, T Sulser 1, T Cremer 1
PMCID: PMC1870909  PMID: 7778673

Abstract

We present a strategy for the evaluation of numerical copy number changes of DNA segments within a solid tumor genome that allows the correlation of microscopic phenotype with genotype in formalin-fixed, paraffin-embedded tumor material. Cells from a human testicular germ cell tumor and adjacent tissue areas with normal seminiferous tubules were selected separately from microscopically analyzed histological tissue sections, and DNA was extracted from the selected areas. After universal DNA amplification, the amplification products were subjected to comparative genomic hybridization. The results confirmed balanced chromosome copy numbers for the normal tissue area, although the analysis of the tumor tissue area revealed numerous gains and losses of chromosome segments. The comparative genomic hybridization results were used to select DNA probes for interphase cytogenetics on serial sections. We conclude that this technique allows the screening of selected tissue areas for numerical DNA alterations, thus enabling a direct phenotype-genotype comparison.

Full text

PDF
1332

Images in this article

1333Figure 1
on p.1333
1335Figure 2
on p.1335
1338Figure 4
on p.1338

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Atkin N. B., Baker M. C. i(12p): specific chromosomal marker in seminoma and malignant teratoma of the testis? Cancer Genet Cytogenet. 1983 Oct;10(2):199–204. doi: 10.1016/0165-4608(83)90125-5. [DOI] [PubMed] [Google Scholar]
  2. Ben-Ezra J., Johnson D. A., Rossi J., Cook N., Wu A. Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J Histochem Cytochem. 1991 Mar;39(3):351–354. doi: 10.1177/39.3.1704393. [DOI] [PubMed] [Google Scholar]
  3. Emmerich P., Jauch A., Hofmann M. C., Cremer T., Walt H. Interphase cytogenetics in paraffin embedded sections from human testicular germ cell tumor xenografts and in corresponding cultured cells. Lab Invest. 1989 Aug;61(2):235–242. [PubMed] [Google Scholar]
  4. Goelz S. E., Hamilton S. R., Vogelstein B. Purification of DNA from formaldehyde fixed and paraffin embedded human tissue. Biochem Biophys Res Commun. 1985 Jul 16;130(1):118–126. doi: 10.1016/0006-291x(85)90390-0. [DOI] [PubMed] [Google Scholar]
  5. Hedley D. W., Friedlander M. L., Taylor I. W., Rugg C. A., Musgrove E. A. Method for analysis of cellular DNA content of paraffin-embedded pathological material using flow cytometry. J Histochem Cytochem. 1983 Nov;31(11):1333–1335. doi: 10.1177/31.11.6619538. [DOI] [PubMed] [Google Scholar]
  6. Hopman A. H., van Hooren E., van de Kaa C. A., Vooijs P. G., Ramaekers F. C. Detection of numerical chromosome aberrations using in situ hybridization in paraffin sections of routinely processed bladder cancers. Mod Pathol. 1991 Jul;4(4):503–513. [PubMed] [Google Scholar]
  7. Houldsworth J., Chaganti R. S. Comparative genomic hybridization: an overview. Am J Pathol. 1994 Dec;145(6):1253–1260. [PMC free article] [PubMed] [Google Scholar]
  8. Kallioniemi A., Kallioniemi O. P., Piper J., Tanner M., Stokke T., Chen L., Smith H. S., Pinkel D., Gray J. W., Waldman F. M. Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2156–2160. doi: 10.1073/pnas.91.6.2156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kallioniemi A., Kallioniemi O. P., Sudar D., Rutovitz D., Gray J. W., Waldman F., Pinkel D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992 Oct 30;258(5083):818–821. doi: 10.1126/science.1359641. [DOI] [PubMed] [Google Scholar]
  10. Kallioniemi O. P., Kallioniemi A., Sudar D., Rutovitz D., Gray J. W., Waldman F., Pinkel D. Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol. 1993 Feb;4(1):41–46. [PubMed] [Google Scholar]
  11. Lengauer C., Riethman H. C., Speicher M. R., Taniwaki M., Konecki D., Green E. D., Becher R., Olson M. V., Cremer T. Metaphase and interphase cytogenetics with Alu-PCR-amplified yeast artificial chromosome clones containing the BCR gene and the protooncogenes c-raf-1, c-fms, and c-erbB-2. Cancer Res. 1992 May 1;52(9):2590–2596. [PubMed] [Google Scholar]
  12. Poddighe P. J., Ramaekers F. C., Hopman A. H. Interphase cytogenetics of tumours. J Pathol. 1992 Mar;166(3):215–224. doi: 10.1002/path.1711660303. [DOI] [PubMed] [Google Scholar]
  13. Ried T., Petersen I., Holtgreve-Grez H., Speicher M. R., Schröck E., du Manoir S., Cremer T. Mapping of multiple DNA gains and losses in primary small cell lung carcinomas by comparative genomic hybridization. Cancer Res. 1994 Apr 1;54(7):1801–1806. [PubMed] [Google Scholar]
  14. Schröck E., Thiel G., Lozanova T., du Manoir S., Meffert M. C., Jauch A., Speicher M. R., Nürnberg P., Vogel S., Jänisch W. Comparative genomic hybridization of human malignant gliomas reveals multiple amplification sites and nonrandom chromosomal gains and losses. Am J Pathol. 1994 Jun;144(6):1203–1218. [PMC free article] [PubMed] [Google Scholar]
  15. Shibata D. K., Arnheim N., Martin W. J. Detection of human papilloma virus in paraffin-embedded tissue using the polymerase chain reaction. J Exp Med. 1988 Jan 1;167(1):225–230. doi: 10.1084/jem.167.1.225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Shibata D., Hawes D., Li Z. H., Hernandez A. M., Spruck C. H., Nichols P. W. Specific genetic analysis of microscopic tissue after selective ultraviolet radiation fractionation and the polymerase chain reaction. Am J Pathol. 1992 Sep;141(3):539–543. [PMC free article] [PubMed] [Google Scholar]
  17. Shibata D., Martin W. J., Arnheim N. Analysis of DNA sequences in forty-year-old paraffin-embedded thin-tissue sections: a bridge between molecular biology and classical histology. Cancer Res. 1988 Aug 15;48(16):4564–4566. [PubMed] [Google Scholar]
  18. Speicher M. R., Howe C., Crotty P., du Manoir S., Costa J., Ward D. C. Comparative genomic hybridization detects novel deletions and amplifications in head and neck squamous cell carcinomas. Cancer Res. 1995 Mar 1;55(5):1010–1013. [PubMed] [Google Scholar]
  19. Speicher M. R., Prescher G., du Manoir S., Jauch A., Horsthemke B., Bornfeld N., Becher R., Cremer T. Chromosomal gains and losses in uveal melanomas detected by comparative genomic hybridization. Cancer Res. 1994 Jul 15;54(14):3817–3823. [PubMed] [Google Scholar]
  20. Speicher M. R., Schoell B., du Manoir S., Schröck E., Ried T., Cremer T., Störkel S., Kovacs A., Kovacs G. Specific loss of chromosomes 1, 2, 6, 10, 13, 17, and 21 in chromophobe renal cell carcinomas revealed by comparative genomic hybridization. Am J Pathol. 1994 Aug;145(2):356–364. [PMC free article] [PubMed] [Google Scholar]
  21. Speicher M. R., du Manoir S., Schröck E., Holtgreve-Grez H., Schoell B., Lengauer C., Cremer T., Ried T. Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification. Hum Mol Genet. 1993 Nov;2(11):1907–1914. doi: 10.1093/hmg/2.11.1907. [DOI] [PubMed] [Google Scholar]
  22. Stein A., Raoult D. A simple method for amplification of DNA from paraffin-embedded tissues. Nucleic Acids Res. 1992 Oct 11;20(19):5237–5238. doi: 10.1093/nar/20.19.5237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Telenius H., Pelmear A. H., Tunnacliffe A., Carter N. P., Behmel A., Ferguson-Smith M. A., Nordenskjöld M., Pfragner R., Ponder B. A. Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Genes Chromosomes Cancer. 1992 Apr;4(3):257–263. doi: 10.1002/gcc.2870040311. [DOI] [PubMed] [Google Scholar]
  24. Walt H., Emmerich P., Cremer T., Hofmann M. C., Bannwart F. Supernumerary chromosome 1 in interphase nuclei of atypical germ cells in paraffin-embedded human seminiferous tubules. Lab Invest. 1989 Nov;61(5):527–531. [PubMed] [Google Scholar]
  25. Waye J. S., England S. B., Willard H. F. Genomic organization of alpha satellite DNA on human chromosome 7: evidence for two distinct alphoid domains on a single chromosome. Mol Cell Biol. 1987 Jan;7(1):349–356. doi: 10.1128/mcb.7.1.349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Willard H. F., Waye J. S. Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J Mol Evol. 1987;25(3):207–214. doi: 10.1007/BF02100014. [DOI] [PubMed] [Google Scholar]
  27. de Jong B., Oosterhuis J. W., Castedo S. M., Vos A., te Meerman G. J. Pathogenesis of adult testicular germ cell tumors. A cytogenetic model. Cancer Genet Cytogenet. 1990 Sep;48(2):143–167. doi: 10.1016/0165-4608(90)90115-q. [DOI] [PubMed] [Google Scholar]
  28. du Manoir S., Schröck E., Bentz M., Speicher M. R., Joos S., Ried T., Lichter P., Cremer T. Quantitative analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):27–41. doi: 10.1002/cyto.990190105. [DOI] [PubMed] [Google Scholar]
  29. du Manoir S., Speicher M. R., Joos S., Schröck E., Popp S., Döhner H., Kovacs G., Robert-Nicoud M., Lichter P., Cremer T. Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet. 1993 Feb;90(6):590–610. doi: 10.1007/BF00202476. [DOI] [PubMed] [Google Scholar]

Articles from The American Journal of Pathology are provided here courtesy of American Society for Investigative Pathology

RESOURCES