Abstract
The sources of DNA discussed in this chapter are not nearly as old as those covered elsewhere in this book and, indeed, can hardly be considered “ancient” at all. Yet within the realm of diagnostic clinical medicine, for whose purposes these specimens are most often prepared, they are about as old—with the possible exception of certain extraordinary forensic or archaeological investigations—as any human tissues examined.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alanen KA, Klemi PJ, Joensuu H, Kujari H, Pekkala E (1989) Comparison of fresh, ethanol-preserved, and paraffin-embedded samples in DNA flow cytometry. Cytometry 10:81–85
Ben-Ezra J, Johnson DA, Rossi J, Cook N, Wu A (1991) Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J Histochem Cytochem 39:351–354
Bianchi AB, Navone NM, Conti CJ (1981) Detection of loss of heterozygosity in formalin-fixed paraffin-embedded tumor specimens by the polymerase chain reaction. Am J Pathol 138:279–284
Bramwell NH, Burns BF (1988) The effects of fixative type and fixation time on the quantity and quality of extractable DNA for hybridization studies. Exp Hematol 16:730–732
Bugawan TL, Saiki RK, Levenson CH, Watson RM, Erlich HA (1988) The use of non-radioactive oligonucleotide probes to analyze enzymatically amplified DNA for prenatal diagnosis and forensic HLA typing. Biotechnol 6:943–947
Calabrese LH, Proffitt MR, Yen-Lieberman B, Hobbs RE, Ratliff NB (1987) Congestive cardiomyopathy and illness related to the acquired immunodeficiency syndrome (AIDS) associated with isolation of retrovirus from myocardium. Ann Intern Med 107:691–692
Coates PJ, d’Ardenne AJ, Khan G, Kangro HO, Slavin G (1991) Simplified procedures for applying the polymerase chain reaction to routinely fixed paraffin wax sections. J Clin Pathol 44:115–118
Cohen PS, Seeger RC, Triche TJ, Israel MA (1988) Detection of N-myc gene expression in neuroblastoma tumors by in situ hybridization. Am J Pathol 131:391–397
Cohen C, Santoianni RA, Tickman RJ, Kennedy JC, DeRose PB (1991) Semiautomation of preparation of fixed paraffin-embedded tissue for DNA analysis. Anal Quant Cytol Histol 13:177–181
Conner BJ, Reyes AA, Morin C, Itakura K, Teplitz RL, Wallace RB (1983) Detection of sickle cell β-globin allele by hybridizaton with synthetic oligonucleotides. Proc Natl Acad Sci USA 80:278–282
Crisan D, Cadoff EM, Mattson JC, Hartle KA (1990) Polymerase chain reaction: amplification of DNA from fixed tissue. Clin Biochem 23:489–495
analysis of DNA extracted from formalin-fixed pathology specimens. Cancer Res 46:2964–2969
Esteban JM, Sheibani K, Owens M, Joyce J, Bailey A, Battifora H (1991) Effects of various fixatives and fixation conditions on DNA ploidy analysis: a need for strict internal DNA standards. Am J Clin Pathol 95:460–466
Fain JS, Bryan RN, Cheng L, Lewin KJ, Porter DD, Grody WW (1991) Rapid diagnosis of Legionella infection by a nonisotopic in situ hybridization method. Am J Clin Pathol 95:719–724
Feldman MY (1973) Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog Nucl Acid Res Mol Biol 13:1–49
Flomenbaum M, Soeiro R, Udem SA, Kress Y, Factor SM (1989) Proliferative membranopathy and human immunodeficiency virus in AIDS hearts. J AIDS 2:129–135
Fraenkel-Conrat H (1954) Reactions of nucleic acid with formaldehyde. Biochim Biophys Acta 15:307–309
Goelz SE, Hamilton SR, Vogelstein B (1985) Purification of DNA from formaldehyde fixed and paraffin embedded human tissue. Biochem Biophys Res Commun 130:118–126
Goudie RB (1989) A strategy for demonstrating the clonal origin of small numbers of T lymphocytes in histopathological specimens. J Pathol 158:261–265
Greer CE, Peterson SL, Kiviat NB, Manos MM (1991) PCR amplification from paraffin-embedded tissues: effects of fixative and fixation time. Am J Clim Pathol 95:117–124
Grody WW, Hilborne LH (1992) Diagnostic applications of recombinant nucleic acid technology: genetic diseases. Lab Med 23:166–171
Grody WW, Cheng L, Lewin KJ (1987) In situ viral DNA hybridization in diagnostic surgical pathology. Hum Pathol 18:535–543
Grody WW, Lewin KJ, Naeim F (1988) Detection of cytomegalovirus DNA in classic and epidemic Kaposi’s sarcoma by in situ hybridization. Hum Pathol 19:524–528
Grody WW, Gatti RA, Naeim F (1989a) Diagnostic molecular pathology. Mod Pathol 2:553–568
Grody WW, Hilborne LH, Spector EB (1989b) Clinical applications of molecular techniques in the diagnosis of inherited disease: the case of Duchenne muscular dystrophy. ASCP Clin Chem Check Sample 29(2):1–7
Grody WW, Cheng L, Lewis W (1990) Infection of the heart by the human immunodeficiency virus. Am J Cardiol 66:203–206
Hanson CA, Holbrook EA, Sheldon S, Schnitzer B, Roth MS (1990) Detection of Philadelphia chromosome-positive cells from glass slide smears using the polymerase chain reaction. Am J Pathol 137:1–6
Haselkorn R, Doty P (1960) The reaction of formaldehyde with polynucleotides. J Biol Chem 236:2738–2745
Hayashi Y, Watanabe J-I, Nakata K, Fukayama M, Ikeda H (1990) A novel diagnostic method of Pneumocystis carinii: in situ hybridization of ribosomal ribonucleic acid with biotinylated oligonucleotide probes. Lab Invest 63:576–580
Hedley DW, Friedlander ML, Taylor IW, Rugg CA, Musgrove EA (1983) Method for analysis of cellular DNA content of paraffin-embedded pathological material using flow cytometry. J Histochem Cytochem 31:1333–1335
Heller MJ, Burgart LJ, TenEyck CJ, Anderson MEk, Greiner TC, Robinson RA (1991) An efficient method for the extraction of DNA from formalin-fixed, paraffin-embedded tissue by sonication. BioTechniques 11:372–377
Herbert DJ, Nishiyama RH, Bagwell CB, Munson ME, Hitchcox SA, Lovett EJ (1989) Effects of several commonly used fixatives on DNA and total nuclear protein analysis by flow cytometry. Am J Clin Pathol 91:535–541
Hilborne LH, Grody WW (1992) Diagnostic applications of recombinant nucleic acid technology: infectious diseases. Lab Med 23:89–94
Hilborne LH, Nieberg RK, Cheng L, Lewin KJ (1987) Direct in situ hybridization for rapid detection of cytomegalovirus in bronchoalveolar lavage. Am J Clin Pathol 87:766–769
Hsu H-C, Pen S-Y, Shun C-T (1991) High quality of DNA retrieved for Southern blot hybridization from microwave-fixed, paraffin-embedded liver tissues. J Virol Meth 31:251–262
Impraim CC, Saiki RK, Erlich HA, Teplitz RL (1987) Analysis of DNA extracted from formalin-fixed, paraffin-embedded tissues by enzymatic amplification and hybridization with sequence-specific oligonucleotides. Biochem Biophys Res Commun 142:710–716
Jackson DP, Bell S, Payne J, Lewis FA, Sutton J, Taylor GR, Quirke P (1989) Extraction and amplification of DNA from archival haematoxylin and eosin sections and cervical cytology Papanicalaou smears. Nucl Acids Res 17:10134
Jackson V (1978) Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell 15:945–954
Jackson V, Chalkey R (1974) Separation of newly synthesized nucleohistone by equilibrium centrifugation in cesium chloride. Biochemistry 13:3952–3956
Jeffreys AG, Wilson V, Neumann R, Keyte J (1988) Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucl Acids Res 16:10953–10971
Jonveaux P (1991) PCR amplification of specific DNA sequences from routinely fixed chromosomal spreads. Nucl Acids Res 19: 1946
Junqueira LC, Carneiro J (1971) Basic Histology, 3rd ed. Los Altos, Cal.: Lange Medical Publications, pp. 2–3
Lai-Goldman M, Lai E, Grody WW (1988) Detection of human immunodeficiency virus infection in formalin-fixed, paraffin-embedded tissues by DNA amplification. Nucl Acids Res 16:8191
Langer PR, Waldrop AA, Ward DC (1981) Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc Natl Acad Sci USA 78:6633–6637
Lee JH, Lee DH, Park SS, Seok SE, Lee JD (1988) Oncogene expression detected by in situ hybridization in human primary lung cancer. Chest 94:1046–1049
Liang X-M, Wieczorek RL, Koss LG (1991) In situ hybridization with human papillomavirus using biotinylated DNA probes on archival cervical smears. J Histochem Cytochem 39:771–775
Lloyd RV (1987) Use of molecular probes in the study of endocrine diseases. Hum Pathol 18:1199–1211
MacDonald MR, Cohen BB (1990) Southern blot analysis of DNA extracted from paraffin wax-embedded tissue. Dis Markers 8:341–345
Mark A, Trowell H, Dyall-Smith ML, Dyall-Smith DJ (1987) Extraction of DNA from formalin-fixed paraffin-embedded pathology specimens and its use in hybridization (histoblot) assays. Application to the detection of human papillomavirus DNA. Nucl Acids Res 15:8565
McFadden GI, Bonig I, Cornish EC, Clarke AE (1988) A simple fixation and embedding method for use in hybridization histochemistry on plant tissues. Histochem J 20:575–586
McGhee JD, Von Hippel PH (1977) Formaldehyde as a probe of DNA structure. 4. Mechanism of the initial reaction of formaldehyde with DNA. Biochemistry 16: 3276–3293
Mies C, Houldsworth J, Chaganti RSK (1991) Extraction of DNA from paraffin blocks for Southern analysis. Am J Surg Pathol 15:169–174
Moerkerk PT, Kessels HJ, ten Kate J, de Goeij FPM, Bosman FT (1990) Southern and dot blot analysis of DNA from formalin-fixed, paraffin-embedded tissue samples from colonic carcinomas. Virch Arch B Cell Pathol 58:351–355
Myerson D, Hackman RC, Nelson JA, Ward DC, McDougall JK (1984) Widespread presence of histologically occult cytomegalovirus. Hum Pathol 87:766–769
Nicoll JAR, Maitland NJ, Love S (1991) Use of the polymerase chain reaction to detect herpes simplex virus DNA in paraffin sections of human brain at necropsy. J Neurol Neurosurg Psychiat 54:167–168
Nuovo GJ, Richart RM (1989) Buffered formalin is the superior fixative for the detection of HPV DNA by in situ hybridization analysis. Am J Pathol 134:837–842
Nuovo GJ, Silverstein SJ (1988) Comparison of formalin, buffered formalin, and Bouin’s fixation on the detection of human papillomavirus deoxyribonucleic acid from genital lesions. Lab Invest 59:720–728
Ohyashiki JH, Ohyashiki K, Toyama K (1988) Analysis of DNA from cells fixed in Carnoy’s solution for cytogenetic study. Cancer Genet Cytogenet 34:159–163
Onadim Z, Cowell JK (1991) Application of PCR amplification of DNA from paraffin embedded tissue sections to linkage analysis in familial retinoblastoma. J Med Genet 28:312–316
Peiper SC, Myers JL, Broussard EE, Sixbey JW (1990) Detection of Epstein-Barr virus genomes in archival tissues by polymerase chain reaction. Arch Pathol Lab Med 114:711–714
Radosevich JA, Maminta LD, Rosen ST, Gould VE (1991) The amount of paraffin-embedded tissue needed for DNA molecular analysis: a rapid extraction procedure. Lab Med 22:543–546
Redline RW, Genest DR, Tycko B (1991) Detection of enteroviral infection in paraffin-embedded tissue by the RNA polymerase chain reaction technique. Am J Clin Pathol 96:568–571
Rijntjes PJM, Van Ditzhuijes TJM, Van Loon AM, Van Haelst UJGM, Bronkhorst FB, Yap SH (1985) Hepatitis B virus DNA detected in formalin-fixed liver specimens and its relation to serologic markers and histopathologic features in chronic liver disease. Am J Pathol 120:411–418
Rogers BB, Alpert LC, Hine EAS, Buffone GJ (1990) Analysis of DNA in fresh and fixed tissue by the polymerase chain reaction. Am J Pathol 136:541–548
Scholefield JH, McIntyre P, Palmer JG, Coates PJ, Shepherd NA, Northover JMA (1990) DNA hybridisation of routinely processed tissue for detecting HPV DNA in anal squamous cell carcinomas over 40 years. J Clin Pathol 43:133–136
Seckinger D, Sugarbaker E, Frankfurt O (1989) DNA content in human cancer: Application in pathology and clinical medicine. Arch Pathol Lab Med 113:619–626
Seto E, Yen TSB (1987) Detection of cytomegalovirus infection by means of DNA isolated from paraffin-embedded tissues and dot hybridization. Am J Pathol 127:409–413
Shibata D, Arnheim N, Martin WJ (1988a) Detection of human papillomavirus in paraffin-embedded tissue using the polymerase chain reaction. J Exp Med 167:225–230
Shibata D, Martin WJ, Arnheim N (1988b) Analysis of DNA sequences in forty-year-old paraffin-embedded thin-tissue sections: a bridge between molecular biology and classical histology. Cancer Res 48:4564–4566
Shibata D, Brynes RK, Nathwani B, Kwok S, Sninsky J, Arnheim N (1989) Human immunodeficiency viral DNA is readily found in lymph node biopsies from seropositive individuals: analysis of fixed tissue using the polymerase chain reaction. Am J Pathol 135:697–702
Shibata D, Hu E, Weiss LM, Brynes RK, Nathwani BN (1990a) Detection of specific t(14; 18) chromosomal translocations in fixed tissues. Hum Pathol 21:199–203
Shibata D, Namiki T, Higuchi R (1990b) Identification of a mislabeled fixed specimen by DNA analysis. Am J Surg Pathol 14:1076–1078
Shibata D, Tokunaga M, Sasaki N, Nanba K (1991) Detection of human T-cell leukemia virus type I proviral sequences from fixed tissues of seropositive patients. Am J Clin Pathol 95:536–539
Smith LJ, Braylan RC, Nutkis JE, Edmundson KB, Downing JR, Wakeland EK (1987) Extraction of cellular DNA from human cells and tissues fixed in ethanol. Anal Biochem 160:135–138
Stanta G, Schneider C (1991) RNA extracted from paraffin-embedded human tissues is amenable to analysis by PCR amplification. BioTechniques 11:304–308
Tecott LH, Barchas JD, Eberwine JH (1988) In situ transcription: specific synthesis of complementary DNA in fixed tissue sections. Science 240:1661–1664
Tokuda Y, Nakamura T, Satonaka K, Maeda S, Doi K, Baba S, Sugiyama T (1990) Fundamental study on the mechanism of DNA degradation in tissues fixed in formaldehyde. J Clin Pathol 43:748–751
Van den Berg FM, Zijlmans H, Langenberg W, Rauws E, Schipper M (1989) Detection of Campylobacter pylori in stomach tissue by DNA in situ hybridization. J Clin Pathol 42:995–1000
Vindelov LL, Christensen IJ, Nissen NI (1983) A detergent-trypsin method for the preparation of nuclei for flow cytometric DNA analysis. Cytometry 3:323–327
Volkenandt M, McNutt NS, Albino AP (1991) Sequence analysis of DNA from formalin-fixed, paraffin-embedded human malignant melanoma. J Cutan Pathol 18:210–214
Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10:506–513
Wan JH, Trainor KJ, Brisco MJ, Morley AA (1990) Monoclonality in B cell lymphoma detected in paraffin wax embedded sections using the polymerase chain reaction. J Clin Pathol 43:888–890
Warford A, Pringle JH, Hay J, Henderson SD, Lauder I (1988) Southern blot analysis of DNA extracted from formol-saline fixed and paraffin wax embedded tissue. J Pathol 154:313–320
Weizsacker FV, Labeit S, Koch HK, Oehlert W, Gerok W, Blum He (1991) A simple and rapid method for the detection of RNA in formalin-fixed, paraffin-embedded tissues by PCR amplification. Biochem Biophys Res Commun 174:176–180
Wolber RA, Beals TG, Lloyd RV, Maasab HF (1988) Ultrastructural localization of viral nucleic acid by in situ hybridization. Lab Invest 59:144–151
Wu AM, Ben-Ezra J, Winberg C, Colombero AM, Rappaport H (1990) Analysis of antigen receptor gene rearrangements in ethanol and formaldehyde-fixed, paraffin-embedded specimens. Lab Invest 63:107–114
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Springer-Verlag New York Inc.
About this chapter
Cite this chapter
Grody, W.W. (1994). Screening for Pathogenic DNA Sequences in Clinically Collected Human Tissues. In: Herrmann, B., Hummel, S. (eds) Ancient DNA. Springer, New York, NY. https://doi.org/10.1007/978-1-4612-4318-2_5
Download citation
DOI: https://doi.org/10.1007/978-1-4612-4318-2_5
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-94308-4
Online ISBN: 978-1-4612-4318-2
eBook Packages: Springer Book Archive