Mutation detection by denaturing gradient gel electrophoresis (DGGE)

The molecular analysis of genetic diseases relies on several technical approaches which allow genetic and physical mapping, characterization of the gene structure, expression studies, and identification of disease‐causing mutations. Denaturing gradient gel electrophoresis (DGGE) allows the rapid screening for single base changes in enzymatically amplified DNA. The technique is based on the migration of double‐stranded DNA molecules through polyacrylamide gels containing linearly increasing concentrations of a denaturing agent. In this review DGGE and the several modifications of the original protocol are presented. Moreover, its applications in human molecular genetics are summarized together with a preliminary comparison with other mutation detection technologies such as chemical cleavage, RNase protection, and single‐strand conformation polymorphism. © 1994 Wiley‐Liss, Inc.

[1]  K. Kidd,et al.  Variability in nuclear DNA among nonhuman primates: Application of molecular genetic techniques to intra‐ and inter‐species genetic analyses , 1992, American journal of primatology.

[2]  S. Antonarakis,et al.  Use of denaturing gradient gel electrophoresis to detect point mutations in the factor VIII gene. , 1990, Genomics.

[3]  Y. Kan,et al.  Molecular characterization of beta-thalassemia in the Sardinian population. , 1992, American journal of human genetics.

[4]  S. Brusilow,et al.  Use of denaturing gradient gel electrophoresis for detection of mutation and prospective diagnosis in late onset ornithine transcarbamylase deficiency. , 1990, Genomics.

[5]  V. Sheffield,et al.  The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. , 1993, Genomics.

[6]  K. Hiyama,et al.  Variations among Japanese of the factor IX gene (F9) detected by PCR-denaturing gradient gel electrophoresis. , 1993, American journal of human genetics.

[7]  R. Myers,et al.  Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. , 1985, Nucleic acids research.

[8]  K. Hayashi,et al.  PCR-SSCP: a simple and sensitive method for detection of mutations in the genomic DNA. , 1991, PCR methods and applications.

[9]  R. Fodde,et al.  Germline APC mutation familial adenomatous polyposis in Indian family , 1992, The Lancet.

[10]  U. Francke,et al.  Mutation creating a new splice site in the growth hormone receptor genes of 37 Ecuadorean patients with Laron syndrome , 1992, Human mutation.

[11]  J. Gitschier,et al.  Mutations and a polymorphism in the factor VIII gene discovered by denaturing gradient gel electrophoresis. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[12]  W. Bender,et al.  Molecular analysis of recombination events in Drosophila. , 1989, Genetics.

[13]  M. Lathrop,et al.  Exclusion of linkage between the collagenase gene and generalized recessive dystrophic epidermolysis bullosa phenotype. , 1991, The Journal of clinical investigation.

[14]  S. Antonarakis,et al.  Hemophilia A due to mutations that create new N-glycosylation sites. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[15]  S. Antonarakis,et al.  The molecular basis of hemophilia A in man. , 1988, Trends in genetics : TIG.

[16]  Denaturing gradient gel electrophoresis of the alpha 1-antitrypsin gene: application to prenatal diagnosis. , 1991, American journal of medical genetics.

[17]  D. Amadori,et al.  Base transitions are the most frequent genetic changes at P53 in gastric cancer. , 1993, Cancer research.

[18]  S. Friend,et al.  Constant denaturant gel electrophoresis as a rapid screening technique for p53 mutations. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[19]  B. Theophilus,et al.  Comparison of RNase A, a chemical cleavage and GC-clamped denaturing gradient gel electrophoresis for the detection of mutations in exon 9 of the human acid beta-glucosidase gene. , 1989, Nucleic acids research.

[20]  W. Thilly,et al.  Mutational spectrometry: a general approach for hot-spot point mutations in selectable genes. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Fodde,et al.  Denaturing gradient gel electrophoresis and direct sequencing of PCR amplified genomic DNA: a rapid and reliable diagnostic approach to beta thalassaemia , 1990, British journal of haematology.

[22]  K. Hiyama,et al.  An improved method for the detection of genetic variations in DNA with denaturing gradient gel electrophoresis. , 1990, Mutation research.

[23]  M. Robertson,et al.  Mutational analysis of patients with adenomatous polyposis: identical inactivating mutations in unrelated individuals. , 1993, American Journal of Human Genetics.

[24]  J. Lavergne,et al.  Duplication of a methionine within the glycoprotein Ib binding domain of von Willebrand factor detected by denaturing gradient gel electrophoresis in a patient with type IIB von Willebrand disease. , 1991, Blood.

[25]  P. de Knijff,et al.  Characterization of five new mutants in the carboxyl-terminal domain of human apolipoprotein E: no cosegregation with severe hyperlipidemia. , 1993, American journal of human genetics.

[26]  A. Uitterlinden,et al.  Two-dimensional DNA fingerprinting of human individuals. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[27]  J. Saris,et al.  Rapid detection of polymorphism near gene for adult polycystic kidney disease , 1990, The Lancet.

[28]  M. Devoto,et al.  Screening for non-delta F508 mutations in five exons of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in Italy. , 1991, American journal of human genetics.

[29]  W. Thilly,et al.  Molecular analysis of complex human cell populations: mutational spectra of MNNG and ICR-191. , 1990, Mutation research.

[30]  L. Lerman,et al.  DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[31]  V. Sheffield,et al.  Identification of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis. , 1991, American journal of human genetics.

[32]  R. Myers,et al.  Identification of polymorphisms by genomic denaturing gradient gel electrophoresis: application to the proximal region of human chromosome 21. , 1991, Nucleic acids research.

[33]  R. Fodde,et al.  Homozygous beta+ thalassaemia owing to a mutation in the cleavage-polyadenylation sequence of the human beta globin gene. , 1991, Journal of medical genetics.

[34]  K. Kinzler,et al.  Identification of ras oncogene mutations in the stool of patients with curable colorectal tumors. , 1992, Science.

[35]  Margaret Robertson,et al.  Identification and characterization of the familial adenomatous polyposis coli gene , 1991, Cell.

[36]  L. Lerman,et al.  Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. , 1987, Methods in enzymology.

[37]  C. Férec,et al.  Detection of over 98% cystic fibrosis mutations in a Celtic population , 1992, Nature Genetics.

[38]  W. Thilly,et al.  Fidelity of DNA polymerases in DNA amplification. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[39]  E. Smeraldi,et al.  Use of polymerase chain reaction nad denaturing gradient gel electrophoresis to identify polymorphisms in three exons of dopamine D2 receptor gene in schizophrenic and delusional patients. , 1992, Neuropsychobiology.

[40]  S. Antonarakis,et al.  Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[41]  R. Myers,et al.  Detection and localization of single base changes by denaturing gradient gel electrophoresis. , 1987, Methods in enzymology.

[42]  W. Thilly,et al.  Mutational spectra in human B-cells. Spontaneous, oxygen and hydrogen peroxide-induced mutations at the hprt gene. , 1992, Journal of molecular biology.

[43]  R. Fodde,et al.  Rapid identification by denaturing gradient gel electrophoresis of mutations in the γ‐globin gene promoters in non‐deletion type HPFH , 1992, British journal of haematology.

[44]  B. Suter,et al.  Identification of an amber nonsense mutation in the rosy516 gene by germline transformation of an amber suppressor tRNA gene. , 1988, EMBO Journal.

[45]  W. Isaacs,et al.  Androgen receptor gene mutations in human prostate cancer. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[46]  R. Cotton,et al.  Detection of single base changes in nucleic acids. , 1989, The Biochemical journal.

[47]  R. Myers,et al.  Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. , 1985, Nucleic acids research.

[48]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[49]  B. Top A simple method to attach a universal 50-bp GC-clamp to PCR fragments used for mutation analysis by DGGE. , 1992, PCR methods and applications.

[50]  K. Kinzler,et al.  Identification of a gene located at chromosome 5q21 that is mutated in colorectal cancers. , 1991, Science.

[51]  W. Bender,et al.  Mapping point mutations in the Drosophila rosy locus using denaturing gradient gel blots. , 1991, Genetics.

[52]  R. Fodde,et al.  Detection of K-ras mutations by denaturing gradient gel electrophoresis (DGGE): a study on pancreatic cancer. , 1992, Anticancer research.

[53]  E. Girodon,et al.  Psoralen-modified oligonucleotide primers improve detection of mutations by denaturing gradient gel electrophoresis and provide an alternative to GC-clamping. , 1993, Human molecular genetics.

[54]  R. Eeles,et al.  Detection of point mutations in the p53 gene: Comparison of single‐strand conformation polymorphism, constant denaturant gel electrophoresis, and hydroxylamine and osmium tetroxide techniques , 1993, Human mutation.

[55]  E. Hovig,et al.  Screening for mutations in human HPRT cDNA using the polymerase chain reaction (PCR) in combination with constant denaturant gel electrophoresis (CDGE). , 1992, Mutation research.

[56]  F. S. French,et al.  Single base mutations in the human androgen receptor gene causing complete androgen insensitivity: rapid detection by a modified denaturing gradient gel electrophoresis technique. , 1992, Molecular endocrinology.

[57]  M. Wapenaar,et al.  The X chromosome shows less genetic variation at restriction sites than the autosomes. , 1986, American journal of human genetics.

[58]  M. Robertson,et al.  Identification of APC gene mutations in Italian adenomatous polyposis coli patients by PCR-SSCP analysis. , 1993, American journal of human genetics.

[59]  R. Myers,et al.  Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA:DNA duplexes. , 1985, Science.

[60]  S. Orkin,et al.  Linkage of β-thalassaemia mutations and β-globin gene polymorphisms with DNA polymorphisms in human β-globin gene cluster , 1982, Nature.

[61]  R. Fodde,et al.  Eight novel inactivating germ line mutations at the APC gene identified by denaturing gradient gel electrophoresis. , 1992, Genomics.

[62]  L. Lerman,et al.  Comprehensive detection of single base changes in human genomic DNA using denaturing gradient gel electrophoresis and a GC clamp. , 1990, Genomics.

[63]  L. Lerman,et al.  Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis , 1979, Cell.

[64]  V. Sheffield,et al.  Glutaric acidemia type II. Heterogeneity in beta-oxidation flux, polypeptide synthesis, and complementary DNA mutations in the alpha subunit of electron transfer flavoprotein in eight patients. , 1992, The Journal of clinical investigation.

[65]  T. Sekiya,et al.  Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[66]  G. Thomas,et al.  Germ-line mutations in the first 14 exons of the adenomatous polyposis coli (APC) gene. , 1993, American journal of human genetics.

[67]  W. Noll,et al.  Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[68]  A. Brøgger,et al.  Detection of base mutations in genomic DNA using denaturing gradient gel electrophoresis (DGGE) followed by transfer and hybridization with gene-specific probes. , 1988, Mutation research.

[69]  E. Bonora,et al.  Detection of Mutations in Insulin Receptor Gene by Denaturing Gradient Gel Electrophoresis , 1992, Diabetes.

[70]  W. Thilly,et al.  Use of gradient denaturing gels to determine mutational spectrum in human cells. , 1986, Basic life sciences.

[71]  R. Weiss,et al.  Rapid localization of mutations in the thyroid hormone receptor-beta gene by denaturing gradient gel electrophoresis in 18 families with thyroid hormone resistance. , 1992, The Journal of clinical endocrinology and metabolism.

[72]  M. Vidaud,et al.  Mutations in the catalytic domain of human coagulation factor IX: rapid characterization by direct genomic sequencing of DNA fragments displaying an altered melting behavior. , 1989, Genomics.

[73]  G. Condorelli,et al.  NIDDM Associated With Mutation in Tyrosine Kinase Domain of Insulin Receptor Gene , 1992, Diabetes.

[74]  A. Brøgger,et al.  Constant denaturant gel electrophoresis, a modification of denaturing gradient gel electrophoresis, in mutation detection. , 1991, Mutation research.

[75]  R. Fodde,et al.  Rapid detection of the highly polymorphic beta globin framework by denaturing gradient gel electrophoresis. , 1992, Journal of medical genetics.

[76]  V. Sheffield,et al.  Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Neal F. Cariello,et al.  Analysis of mutations using PCR and denaturing gradient gel electrophoresis , 1991, Environmental and molecular mutagenesis.

[78]  S. Cai,et al.  Identification of the multiple beta-thalassemia mutations by denaturing gradient gel electrophoresis. , 1990, The Journal of clinical investigation.

[79]  W. Thilly,et al.  Resolution of a missense mutant in human genomic DNA by denaturing gradient gel electrophoresis and direct sequencing using in vitro DNA amplification: HPRT Munich. , 1988, American journal of human genetics.

[80]  S. Antonarakis,et al.  Molecular characterization of mild-to-moderate hemophilia A: detection of the mutation in 25 of 29 patients by denaturing gradient gel electrophoresis. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[81]  B. Vogelstein,et al.  A genetic model for colorectal tumorigenesis , 1990, Cell.

[82]  R. Myers,et al.  Detection of single base substitutions in total genomic DNA , 1985, Nature.

[83]  A New Strategy for Direct Detection of β‐Thalassemia Mutations , 1990 .

[84]  Henry A. Erlich,et al.  Analysis of enzymatically amplified β-globin and HLA-DQα DNA with allele-specific oligonucleotide probes , 1986, Nature.