Skip to main content
SpringerLink
Log in

Diagnostic Methodology and Technology

  • Chapter
Molecular Genetic Pathology

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Suggested Reading

Additional Methodologies for Nucleic Acid Detection

  • Alwine JC, Kemp DJ, Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 1977;74(12):5350–5354.

    Article  CAS  PubMed  Google Scholar 

  • Buongiorno-Nardelli M, Amaldi F. Autoradiographic detection of molecular hybrids between RNA and DNA in tissue sections. Nature 1970;225(5236):946–948.

    Article  CAS  PubMed  Google Scholar 

  • Conner BJ, Reyes, AA, Morin C, et al. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci USA 1983;80:278–282.

    Article  CAS  PubMed  Google Scholar 

  • Darby IA, Bisucci T, Desmouliere A, et al. In situ hybridization using cRNA probes: isotopic and nonisotopic detection methods. Methods Mol Biol. 2006;326:17–31.

    CAS  PubMed  Google Scholar 

  • Gall JG, Pardue ML. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 1969;63(2):378–383.

    Article  CAS  PubMed  Google Scholar 

  • Hicks DG, Longoria G, Pettay J, et al. In situ hybridization in the pathology laboratory: general principles, automation, and emerging research applications for tissue-based studies of gene expression. J Mol Histol. 2004;35:595–601.

    Article  CAS  PubMed  Google Scholar 

  • Hubbard RA. Human papillomavirus testing methods. Arch Pathol Lab Med. 2003;127:940–945.

    CAS  PubMed  Google Scholar 

  • Iftner T, Villa LL. Human papillomavirus technologies. J Natl Cancer Inst Monogr. 2003;31:80–88.

    PubMed  Google Scholar 

  • John HA, Birnstiel ML, Jones KW. RNA-DNA hybrids at the cytological level. Nature 1969;223:582–587.

    Article  CAS  PubMed  Google Scholar 

  • Porchet N, Aubert JP. Northern blot analysis of large mRNAs. Methods Mol Biol. 2000;125:305–312.

    CAS  PubMed  Google Scholar 

  • Princivalle AP, Parker RM, Dover TJ, et al. mRNA: detection by in situ and northern hybridization. Methods Mol Biol. 2005;306:51–91.

    CAS  PubMed  Google Scholar 

  • Ragoussis J, Elvidge G. Affymetrix GeneChip system: moving from research to the clinic. Expert Rev Mol Diagn. 2006;6:145–152.

    Article  CAS  PubMed  Google Scholar 

  • Southern EM. Blotting at 25. Trends Biochem Sci. 2000;25:585–588.

    Article  CAS  PubMed  Google Scholar 

  • Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975;98(3):503–517.

    Article  CAS  PubMed  Google Scholar 

  • Stoneking M, Hedgecock D, Higuchi RG, et al. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet. 1991;48:370–382.

    CAS  PubMed  Google Scholar 

Amplification Methods

  • Andras SC, Power JB, Cocking EC, et al. Strategies for signal amplification in nucleic acid detection. Mol Biotechnol. 2001;19:29–44.

    Article  CAS  PubMed  Google Scholar 

  • Barany F. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad of Sci USA 1991;88(1):189–193.

    Article  CAS  Google Scholar 

  • Heid CA, Stevens J, Livak KJ, et al. Real time quantitative PCR. Genome Res. 1996;6(10):986–994.

    Article  CAS  PubMed  Google Scholar 

  • Hellyer TJ, Nadeau JG. Strand displacement amplification: a versatile tool for molecular diagnostics. Expert Rev Mal Diagn. 2004;4(2):251–261.

    Article  CAS  Google Scholar 

  • Mickey SU, 1994.

    Google Scholar 

  • Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a polymerasecatalyzed chain reaction. Methods Enzymol. 1987;155:335–350.

    Article  CAS  PubMed  Google Scholar 

  • Schneeberger C, Speiser P, Kury F, et al. Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain. PCR Methods Appl. 1995;4(4):234–238.

    CAS  PubMed  Google Scholar 

  • Urdea MS. Branched DNA signal amplification. Nature Biotechnol. 1994;12:926–928.

    Article  CAS  Google Scholar 

  • Zhang D, Feng T, Ye F, et al. Recent advances in probe amplification technologies, In: Tang YW, Stratton CW, eds. Advanced Techniques in Diagnostic Microbiology. New York, NY: Springer; 2006;210–227.

    Chapter  Google Scholar 

DNA Separation Methods

  • Arshad MF, Dunn FJ, Vega R, et al. Progress in developing improved programs for pulsed field agarose gel electrophoresis of DNA. Electrophoresis 1993;14:344–348.

    Article  CAS  PubMed  Google Scholar 

  • Cariello NF, Skopek TR. Mutational analysis using denaturing gradient gel electrophoresis and PCR. Mutat Res. 1993;288:103–112.

    CAS  PubMed  Google Scholar 

  • Fischer SG, Lerman S. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci. USA 1983;80(6):1579–1583.

    Article  CAS  PubMed  Google Scholar 

  • Fodde R, Losekoot M. Mutation detection by denaturing gradient gel electrophoresis (DGGE). Hum Mutat. 1994;3:83–94.

    Article  CAS  PubMed  Google Scholar 

  • Godde R, Akkad DA, Arning L, et al. Electrophoresis of DNA in human genetic diagnostics — state-of-the-art, alternatives and future prospects. Electrophoresis 2006;27:939–946.

    Article  PubMed  Google Scholar 

  • Kemp G. Capillary electrophoresis: a versatile family of analytical techniques. Biotechnol Appl Biochem. 1998;27(1):9–17.

    CAS  PubMed  Google Scholar 

  • Maniatis T, Jeffrey A, van deSande H. Chain length determination of small double-and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry 1975;14:3787–3794.

    Article  CAS  PubMed  Google Scholar 

  • Nataraj AJ, Olivos-Glander I, Kusukawa N, et al. Single-strand conformation polymorphism and heteroduplex analysis for gel-based mutation detection. Electrophoresis 1999;20:1177–1185.

    Article  CAS  PubMed  Google Scholar 

  • Olson MV. Separation of large DNA molecules by pulsed-field gel electrophoresis. A review of the basic phenomenology. J Chromatogr. 1989;470:377–383.

    Article  CAS  PubMed  Google Scholar 

  • Pourzand C, Cerutti P. Genotypic mutation analysis by RFLP/PCR. Mutat Res. 1993;288:113–121.

    CAS  PubMed  Google Scholar 

  • Raymond S, Weintraub L. Acrylamide gel as a supporting medium for zone electrophoresis. Science 1959;130:711.

    Article  CAS  PubMed  Google Scholar 

  • Schwartz DC, Cantor CR. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 1984;37(1):67–75.

    Article  CAS  PubMed  Google Scholar 

  • Serwer P. Sieving of double-stranded DNA during agarose gel electrophoresis. Electrophoresis 1989;10:327–331.

    Article  CAS  PubMed  Google Scholar 

Protein Detection Methods

  • Dunbar B. Troubleshooting and artifacts in two-dimensional polyacrylamide gel electrophoresis, In: Dunbar BS, ed. Two-Dimensional Electrophoresis and Immunological Techniques. New York, NY: Plenum; 1987:173–195.

    Google Scholar 

  • Fenyo D, Qin J, Chait BT. Protein identification using mass spectrometric information. Electrophoresis 1998;19:998–1005.

    Article  CAS  PubMed  Google Scholar 

  • Gillespie PG, Hudspeth AJ. Chemiluminescence detection of proteins from single cells. Proc Natl Acad Sci USA 1991;88:2563–2567.

    Article  CAS  PubMed  Google Scholar 

  • Hames BD, Rickwood D, eds. Gel Electrophoresis of Proteins: A Practical Approach (2nd ed), New York, NY: Oxford University Press; 1990.

    Google Scholar 

  • Harlow E, Lane D. Immunoblotting in Antibodies: a Laboratory Manual. Cold Spring Harbor: New York, NY: Cold Spring Harbor Laboratory Press: 1988;471–510.

    Google Scholar 

  • Hochstrasser DF, Harrington MC, Hochstrasser AC, et al. Methods for increasing the resolution of two-dimensional protein electrophoresis. Anal Biochem. 1988;173:424–435.

    Article  CAS  PubMed  Google Scholar 

  • Patterson SD. Matrix-assisted laser-desorption/ionization mass spectrometric approaches for the identification of gel-separated proteins in the 5–50 pmol range. Electrophoresis 1995;16:1104–1114.

    Article  CAS  PubMed  Google Scholar 

  • Porstmann T, Kiessig ST. Enzyme immunoassay techniques, an overview. J Immunol Methods. 1992;150(1–2):5–21.

    Article  CAS  PubMed  Google Scholar 

  • Smith JA. Electroelution of proteins from stained gels, In: Ausubel FA, Brent R, Kingston RE, et al, eds. Current Protocols in Molecular Biology. New York, NY: John Wiley & Sons; 1993:10.15.1–10.15.5.

    Google Scholar 

  • Stults JT. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Curr Opin Struct Biol. 1995;5:691–698.

    Article  CAS  PubMed  Google Scholar 

Sample Collection and Processing Methods

  • O’Leary TJ, Brindza L, Kant JA, et al. Immunoglobulin and T-cell Receptor Gene Rearrangement Assays; approved guidline. Wayne, PA: NCCLS; publication MM2-A: 1995;15(18).

    Google Scholar 

  • Rainen L, Arbique JC, Asthana, et al. Collection, Transport, Preparation, and Storage of Specimens for Molecular Methods; approved guideline. Wayne, PA: Clinical and Laboratory Standards Institute; publication MM13-A: 2006;25(31).

    Google Scholar 

Sequencing of Nucleic Acids

  • Brown PR, Robb CS, Geldart SE. Perspectives on analyses of nucleic acid constituents: the basis of genomics. J Chromatography A 2002; 965(1–2):163–173.

    Article  CAS  Google Scholar 

  • Dolnik V. DNA sequencing by capillary electrophoresis (review). J Biochem Biophys Methods 1999;41(2–3):103–119.

    Article  CAS  PubMed  Google Scholar 

  • Dovichi NJ. DNA sequencing by capillary electrophoresis. Electrophoresis 1997;18:2393–2399.

    Article  CAS  PubMed  Google Scholar 

  • Heller C. Principles of DNA separation with capillary electrophoresis. Electrophoresis 2001;22(4):629–643.

    Article  CAS  PubMed  Google Scholar 

  • Maxam AM, Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560.

    Article  CAS  PubMed  Google Scholar 

  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci USA 1977;74(12):5463–5467.

    Article  CAS  PubMed  Google Scholar 

Signal Detection Methods

  • Thelwell N, Millington S, Solinas A, et al. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. 2000;28(19):3752–3761.

    Article  CAS  PubMed  Google Scholar 

  • Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996;14(3):303–308.

    Article  CAS  PubMed  Google Scholar 

  • Wittwer CT, Ririe KM, Andrew RV, et al. The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. Biotechniques 1997;22(1):176–181.

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Pathology, Mount Sinai School of Medicine, New York, NY

    Josephine Wu DDS, CLSp(MB), CLDir (Assistant Professor), Tao Feng MS, MP (ASCP) (Research Assistant), Fei Ye PhD (Assistant Professor), Bruce E. Petersen MD (Molecular Genetic Pathology Fellow) & David Y. Zhang MD, PhD, MPH (Associate Professor of Pathology Director, Molecular Pathology Laboratory)

  2. Mount Sinai Medical Center, New York, NY

    Josephine Wu DDS, CLSp(MB), CLDir (Assistant Professor), Tao Feng MS, MP (ASCP) (Research Assistant), Fei Ye PhD (Assistant Professor), Bruce E. Petersen MD (Molecular Genetic Pathology Fellow) & David Y. Zhang MD, PhD, MPH (Associate Professor of Pathology Director, Molecular Pathology Laboratory)

  3. Department of Pathology, New York University School of Medicine, New York, NY

    Ruliang Xu MD, PhD (Associate Professor of Pathology)

  4. Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN

    Liang Cheng MD (Professor of Pathology and Urology, Director of Molecular Pathology Laboratory, Chief, Genitourinary Pathology Division)

  5. Clarian Pathology Laboratory, Indiana University School of Medicine, Indianapolis, IN

    Liang Cheng MD (Professor of Pathology and Urology, Director of Molecular Pathology Laboratory, Chief, Genitourinary Pathology Division)

Authors
  1. Josephine Wu DDS, CLSp(MB), CLDir
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tao Feng MS, MP (ASCP)
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ruliang Xu MD, PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fei Ye PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Bruce E. Petersen MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Liang Cheng MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. David Y. Zhang MD, PhD, MPH
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Pathology and Laboratory Medicine and Clarian Pathology Laboratory, Indiana University School of Medicine, Indianapolis, IN

    Liang Cheng MD (Professor of Pathology and Urology, Director of Molecular Pathology Laboratory, Chief of Genitourinary Pathology Division) (Professor of Pathology and Urology, Director of Molecular Pathology Laboratory, Chief of Genitourinary Pathology Division)

  2. Department of Pathology, Mount Sinai School of Medicine, New York, NY

    David Y. Zhang MD, PhD, MPH (Associate Professor of Pathology Director, Molecular Pathology Laboratory) (Associate Professor of Pathology Director, Molecular Pathology Laboratory)

  3. Mount Sinai Medical Center, New York, NY

    David Y. Zhang MD, PhD, MPH (Associate Professor of Pathology Director, Molecular Pathology Laboratory) (Associate Professor of Pathology Director, Molecular Pathology Laboratory)

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Wu, J. et al. (2008). Diagnostic Methodology and Technology. In: Cheng, L., Zhang, D.Y. (eds) Molecular Genetic Pathology. Humana Press. https://doi.org/10.1007/978-1-59745-405-6_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-405-6_3

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-974-1

  • Online ISBN: 978-1-59745-405-6

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation