heteroduplex analysis


Summary: A method of detecting gene mutation by mixing PCR-amplified mutant and wild-type DNA followed by denaturation and reannealing. The resultant products are resolved by gel electrophoresis, with single base substitutions detectable under optimal electrophoretic conditions and gel formulations. Large base pair mismatches may also be analyzed by using electron microscopy to visualize heteroduplex regions.

Top Publications

  1. Gonzalez M, Gonzalez D, López Pérez R, Garcia Sanz R, Chillon M, Balanzategui A, et al. Heteroduplex analysis of VDJ amplified segments from rearranged IgH genes for clonality assessments in B-cell non-Hodgkin's lymphoma. A comparison between different strategies. Haematologica. 1999;84:779-84 pubmed
    ..b>Heteroduplex analysis represents an attractive approach since it is easy to perform and avoids the use of radioactive substrates ..
  2. Velasco E, Infante M, Duran M, Perez Cabornero L, Sanz D, Esteban Cardeñosa E, et al. Heteroduplex analysis by capillary array electrophoresis for rapid mutation detection in large multiexon genes. Nat Protoc. 2007;2:237-46 pubmed
    b>Heteroduplex analysis (HA) has proven to be a robust tool for mutation detection...
  3. Avila M, Pando M, Carrion G, Peralta L, Salomon H, Carrillo M, et al. Two HIV-1 epidemics in Argentina: different genetic subtypes associated with different risk groups. J Acquir Immune Defic Syndr. 2002;29:422-6 pubmed
    ..One, in heterosexual men and women, is dominated by env subtype F whereas the other, in homosexual men, is dominated by env subtype B, as determined by env HMA. ..
  4. Su Y, Lee C, Hung C, Chen C, Cheng W, Tsao P, et al. Rapid detection of beta-globin gene (HBB) mutations coupling heteroduplex and primer-extension analysis by DHPLC. Hum Mutat. 2003;22:326-36 pubmed
    ..The elution profile for the heteroduplex analysis of DHPLC could be successfully used to identify the common disease-causing mutations of HBB...
  5. Palais R, Liew M, Wittwer C. Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Anal Biochem. 2005;346:167-75 pubmed
    ..In these cases, if DNA of a known reference genotype is added to each unknown before PCR, quantitative heteroduplex analysis can differentiate heterozygous, homozygous, and wild-type genotypes if the fraction of reference DNA is ..
  6. Ponti R, Quaglino P, Novelli M, Fierro M, Comessatti A, Peroni A, et al. T-cell receptor gamma gene rearrangement by multiplex polymerase chain reaction/heteroduplex analysis in patients with cutaneous T-cell lymphoma (mycosis fungoides/Sézary syndrome) and benign inflammatory disease: correlation with clinical, histologi. Br J Dermatol. 2005;153:565-73 pubmed
    ..The finding of a clonal T-cell rearrangement is more closely associated with the histological pattern (in particular with the density and extent of the cell infiltrate) rather than with the MF cutaneous T-score or immunophenotype. ..
  7. Kapoor A, Jones M, Shafer R, Rhee S, Kazanjian P, Delwart E. Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay. J Virol. 2004;78:7112-23 pubmed
    ..The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies. ..
  8. Kitrinos K, Hoffman N, Nelson J, Swanstrom R. Turnover of env variable region 1 and 2 genotypes in subjects with late-stage human immunodeficiency virus type 1 infection. J Virol. 2003;77:6811-22 pubmed
  9. Carr J, Avila M, Gomez Carrillo M, Salomon H, Hierholzer J, Watanaveeradej V, et al. Diverse BF recombinants have spread widely since the introduction of HIV-1 into South America. AIDS. 2001;15:F41-7 pubmed
    ..BF recombinants were temporally and geographically widespread, found as early as 1986-1987 in vertically infected Argentinian children and in Argentina, Uruguay, and Bolivia. ..

More Information


  1. Kozlowski P, Krzyzosiak W. Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection. Nucleic Acids Res. 2001;29:E71 pubmed
    SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost...
  2. Leys E, Smith J, Lyons S, Griffen A. Identification of Porphyromonas gingivalis strains by heteroduplex analysis and detection of multiple strains. J Clin Microbiol. 1999;37:3906-11 pubmed
    b>Heteroduplex analysis has been used extensively to identify allelic variation among mammalian genes. It provides a rapid and reliable method for determining and cataloging minor differences between two closely related DNA sequences...
  3. Williams D, Pittman T, Gillis T, Matsuoka M, Kashiwabara Y. Simultaneous detection of Mycobacterium leprae and its susceptibility to dapsone using DNA heteroduplex analysis. J Clin Microbiol. 2001;39:2083-8 pubmed
    ..The assay should prove useful for drug resistance surveillance in leprosy control programs when combined with similar molecular tests developed for other drug resistance markers. ..
  4. Spink C, Keen L, Middleton P, Bidwell J. Discrimination of suballeles present at the TNFd microsatellite locus using induced heteroduplex analysis. Genes Immun. 2004;5:76-9 pubmed
    ..Some studies have associated the d3 and d4 alleles with disease outcome. We re-analysed one such study cohort using IHG technology and demonstrated a high proportion of incorrectly assigned TNFd3 alleles. ..
  5. Montano S, Sanchez J, Laguna Torres A, Cuchi P, Avila M, Weissenbacher M, et al. Prevalences, genotypes, and risk factors for HIV transmission in South America. J Acquir Immune Defic Syndr. 2005;40:57-64 pubmed
    ..A renewed effort in controlling STIs, especially among MSM groups, could significantly lessen the impact of the HIV epidemic in South America. ..
  6. Saribas Z, Kocagoz T, Alp A, Gunalp A. Rapid detection of rifampin resistance in Mycobacterium tuberculosis isolates by heteroduplex analysis and determination of rifamycin cross-resistance in rifampin-resistant isolates. J Clin Microbiol. 2003;41:816-8 pubmed
    Direct heteroduplex analysis and a universal heteroduplex generator assay were performed to detect rifampin resistance rapidly in Turkish Mycobacterium tuberculosis isolates...
  7. Matousek J, Ptacek J, Dedic P, Schubert J. Analysis of variability of P1 gene region of N strain of potato virus Y using temperature-gradient gel electrophoresis and DNA heteroduplex analysis. Acta Virol. 2000;44:41-6 pubmed
    ..Two of these variants from the hybrid 220-5 (Czech Republic) were sequenced. Both of them differed from the Nicola P1/1 clone by 6 point mutations, which led to several changes at the amino acid level. ..
  8. Romi R, Boccolini D, Di Luca M, La Rosa G, Marinucci M. Identification of the sibling species of the Anopheles maculipennis complex by heteroduplex analysis. Insect Mol Biol. 2000;9:509-13 pubmed
    ..differences in the ITS2 sequences were used to set up a rapid and sensitive diagnostic tool based on heteroduplex analysis. The relative heteroduplex mobility allowed the following seven species to be readily distinguished: An...
  9. Crepin M, Escande F, Pigny P, Buisine M, Calender A, Porchet N, et al. Efficient mutation detection in MEN1 gene using a combination of single-strand conformation polymorphism (MDGA) and heteroduplex analysis. Electrophoresis. 2003;24:26-33 pubmed
    ..Together, these methods provide an efficient screen for MEN1 mutations. ..
  10. Till B, Burtner C, Comai L, Henikoff S. Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res. 2004;32:2632-41 pubmed
    ..We conclude that a variety of sss nucleases and extracts can be effectively used for high-throughput mutation and polymorphism discovery. ..
  11. Esteban Cardeñosa E, Duran M, Infante M, Velasco E, Miner C. High-throughput mutation detection method to scan BRCA1 and BRCA2 based on heteroduplex analysis by capillary array electrophoresis. Clin Chem. 2004;50:313-20 pubmed
    ..shown to be a powerful system to detect mutations by either single-strand conformation polymorphism or heteroduplex analysis (HA)...
  12. Barros P, Blanco M, Boán F, Gómez Márquez J. Heteroduplex analysis of minisatellite variability. Electrophoresis. 2005;26:4304-9 pubmed
    ..In this report, we have critically assessed and employed heteroduplex analysis (HA) for the identification of different human minisatellite MsH43 alleles...
  13. Shinka T, Naroda T, Tamura T, Sasahara K, Nakahori Y. A rapid and simple method for sex identification by heteroduplex analysis, using denaturing high-performance liquid chromatography (DHPLC). J Hum Genet. 2001;46:263-6 pubmed
    ..This new system may have wide applications in many different fields, such as forensic medicine, prenatal diagnosis, inbreeding of animals, and anthropology. ..
  14. Campagnoli M, Rossi A, Palmqvist L, Flisberg A, Niklasson A, Minchotti L, et al. A novel splicing mutation causes an undescribed type of analbuminemia. Biochim Biophys Acta. 2002;1586:43-9 pubmed
    ..intron sequences of the albumin gene were amplified via PCR and screened for mutations by SSCP and heteroduplex analysis. A mutation in the DNA region encoding exon 1 and its flanking intron was revealed by the presence of a ..
  15. Duan W, Ding H, Zhu W, Srinivasan K, Otterson G, Villalona Calero M, et al. RT-PCR heteroduplex analysis permits differentiation of transgene and host gene expression in a transgenic animal model. Biotechniques. 2002;33:58, 60-2, 64 passim pubmed
    ..The potential for gene silencing may complicate matters further. Here we report the use of RT-PCR heteroduplex analysis to differentiate the expression of a transgene and its homologous wild-type, even when these genes are ..
  16. Galliano M, Campagnoli M, Rossi A, Wirsing von Konig C, Lyon A, Cefle K, et al. Molecular diagnosis of analbuminemia: a novel mutation identified in two Amerindian and two Turkish families. Clin Chem. 2002;48:844-9 pubmed
    ..gene were amplified by PCR and screened for mutations by single-strand conformational polymorphism and heteroduplex analysis. The mutated DNA fragments were sequenced directly...
  17. Kourkine I, Hestekin C, Magnusdottir S, Barron A. Optimized sample preparation for tandem capillary electrophoresis single-stranded conformational polymorphism/ heteroduplex analysis. Biotechniques. 2002;33:318-20, 322, 324-5 pubmed
    ..We also have found that PCR buffers, which are typically used to suspend samples for slab-gel heteroduplex analysis (HA), but which are less suitable for CE because of the presence of extra salt that reduces the efficiency ..
  18. Wittwer C, Reed G, Gundry C, Vandersteen J, Pryor R. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem. 2003;49:853-60 pubmed
    ..The technique requires only the usual unlabeled primers and a generic double-stranded DNA dye added before PCR for amplicon genotyping, and is a promising method for mutation screening. ..
  19. Juliano J, Kwiek J, Cappell K, Mwapasa V, Meshnick S. Minority-variant pfcrt K76T mutations and chloroquine resistance, Malawi. Emerg Infect Dis. 2007;13:872-7 pubmed
    ..Surveillance for minority-variant drug resistant mutations may be useful in making antimalarial drug policy. ..
  20. Caridi G, Dagnino M, Lugani F, Shalev S, Campagnoli M, Galliano M, et al. A novel mutation in the albumin gene (c.1A>C) resulting in analbuminemia. Eur J Clin Invest. 2013;43:72-8 pubmed publisher
    ..The albumin gene was screened by single-strand conformation polymorphism and heteroduplex analysis, and the mutated region was submitted to DNA sequencing...
  21. Connelley T, MacHugh N, Burrells A, Morrison W. Dissection of the clonal composition of bovine alphabeta T cell responses using T cell receptor Vbeta subfamily-specific PCR and heteroduplex analysis. J Immunol Methods. 2008;335:28-40 pubmed publisher
    ..The development and validation of these methods provides for the first time a generic set of molecular tools that can be used to perform detailed analysis of the TCR diversity and clonal composition of bovine T cell responses...
  22. Surovaia A, Grokhovskii S, Burkhardt G, Fritzsche H, Zimmer C, Gurskii G. [Effect of DNA local conformation on the affinity and binding specificity of bis-netropsins to DNA]. Mol Biol (Mosk). 2002;36:901-11 pubmed
    ..The minimal strong binding site for <--Nt-Pt(NH3)-Nt--> and <--Nt-(CH2)5-Nt--> binding as a hairpin has been found to be DNA duplex 5'-CGTATACG-3'. ..
  23. Chateigner Boutin A, Small I. A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res. 2007;35:e114 pubmed
    ..This new method will be easily applicable to RNA from any organism and should greatly accelerate the study of the role of RNA editing in physiological processes as diverse as plant development or human health. ..
  24. Flisikowski K, Zwierzchowski L. Polymerase chain reaction-heteroduplex (PCR-HD) polymorphism within the bovine STAT5A gene. J Appl Genet. 2003;44:185-9 pubmed
    ..The frequency of allele A varied between 0.91 and 0.77. Animals of genotype BB were found in Charolaise and Limousine breeds only. ..
  25. Wedderburn L, King D. Analysis of the T-cell receptor repertoire of synovial T-cells. Methods Mol Med. 2007;136:97-116 pubmed
    ..Two alternative molecular methods to analyse TCR diversity, identify clonal expansions, and track specific T-cell populations over both time and location are also detailed. ..
  26. Bobkov A, Kazennova E, Sukhanova A, Bobkova M, Pokrovsky V, Zeman V, et al. An HIV type 1 subtype A outbreak among injecting drug users in Kazakhstan. AIDS Res Hum Retroviruses. 2004;20:1134-6 pubmed
    ..94 +/- 1.92 (range 0.79-8.48). The data presented thus confirm the spreading of the same IDU subtype A virus in the former Soviet Union. ..
  27. Han X, Jiang Y, Shang H. [Genetic subtyping of HIV-1 in Liaoning province of China]. Zhonghua Liu Xing Bing Xue Za Zhi. 2001;22:432-4 pubmed
    ..There have been several subtypes of HIV-1 existed in Liaoning province, demonstrating the complexity of HIV epidemology in Liaoning province and the difficulty conducting prevention and treatment. ..
  28. Hiruki C, Wang K. Clover proliferation phytoplasma: 'Candidatus Phytoplasma trifolii'. Int J Syst Evol Microbiol. 2004;54:1349-53 pubmed
    ..On the basis of unique properties of the DNA from clover proliferation phytoplasma, the name 'Candidatus Phytoplasma trifolii' is proposed for the CP group. ..
  29. Amini Nekoo A, Futers T, Moia M, Mannucci P, Grant P, Ariëns R. Analysis of the tissue factor pathway inhibitor gene and antigen levels in relation to venous thrombosis. Br J Haematol. 2001;113:537-43 pubmed
    ..0001). These results provide evidence for a relationship between venous thrombosis and total TFPI level as a possible risk factor, whereas they do not support a link between DVT and mutations in the nine exons of the TFPI gene. ..
  30. Moore P, Woo J, Vernau W, Kosten S, Graham P. Characterization of feline T cell receptor gamma (TCRG) variable region genes for the molecular diagnosis of feline intestinal T cell lymphoma. Vet Immunol Immunopathol. 2005;106:167-78 pubmed
    ..It is proposed that assessment of TCRG V--J junctional diversity for the detection of clonality represents an important adjunctive tool for the diagnosis of T cell lymphoma in the cat. ..
  31. Neschastnova A, Gasanova V, Belitskiĭ G, Iakubovskaia M, Dolinnaia N. [Chemical cleavage of DNA with single base mismatches for detection of mutations of unknown localization]. Mol Biol (Mosk). 2007;41:535-43 pubmed
  32. Onay T, Zielenski J, Topaloglu O, Gokgoz N, Kayserili H, Apak M, et al. Cystic fibrosis mutations and associated haplotypes in Turkish cystic fibrosis patients. Hum Biol. 2001;73:191-203 pubmed
    ..The mutation spectrum of CF in Turkey and its associated haplotypes indicated the presence of a major Mediterranean component in the contemporary Turkish population. ..
  33. Hofman Bang J, Christiansen M. Single temperature endonuclease-enhanced single-strand conformation polymorphism/heteroduplex mutation analysis: evaluation of the method. Scand J Clin Lab Invest. 2004;64:605-7 pubmed
  34. Dehkordi F, Rashki A, Bagheri N, Chaleshtori M, Memarzadeh E, Salehi A, et al. Study of VSX1 mutations in patients with keratoconus in southwest Iran using PCR-single-strand conformation polymorphism/heteroduplex analysis and sequencing method. Acta Cytol. 2013;57:646-51 pubmed publisher
    ..PCR-single-strand conformational polymorphism/heteroduplex analysis was performed, followed by DNA sequencing to confirm the identified motility shifts...
  35. Machado D, Delwart E, Diaz R, de Oliveira C, Alves K, Rawal B, et al. Use of the sensitive/less-sensitive (detuned) EIA strategy for targeting genetic analysis of HIV-1 to recently infected blood donors. AIDS. 2002;16:113-9 pubmed
  36. Kwiek J, Russell E, Dang K, Burch C, Mwapasa V, Meshnick S, et al. The molecular epidemiology of HIV-1 envelope diversity during HIV-1 subtype C vertical transmission in Malawian mother-infant pairs. AIDS. 2008;22:863-71 pubmed publisher
    ..These data suggest that the predominant mechanism(s) of HIV-1 subtype C mother-to-child transmission differs by the timing of transmission and is unlikely to be explained by a simple stochastic model. ..
  37. Merrill L, Richardson J, Kuske C, Dunbar J. Fluorescent heteroduplex assay for monitoring Bacillus anthracis and close relatives in environmental samples. Appl Environ Microbiol. 2003;69:3317-26 pubmed
    ..The results show that fluorescent heteroduplex analysis is an effective profiling technique for detection and differentiation of sequences representing small ..
  38. Ray K, Wang W, Czarnecki J, Zhang Q, Acland G, Aguirre G. Strategies for identification of mutations causing hereditary retinal diseases in dogs: evaluation of opsin as a candidate gene. J Hered. 1999;90:133-7 pubmed
    ..We conclude that mutations in the rod opsin gene are not associated with PRA or CSNB in the 11 different dog breeds tested. ..
  39. Chen X, Liu Y, Li J, Chen L, Xu Y, Pan Y, et al. [Study on exons 3 and 4 of alpha-synuclein gene in Chinese familial Parkinson disease patients]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2003;20:536-8 pubmed
    ..chain reaction-single strand conformational polymorphism (PCR-SSCP) and polymerase chain reaction-heteroduplex analysis(PCR-HA) were employed to detect the abnormal mobilization in the familial Parkinson disease and sporadic ..
  40. Kaleebu P, Yirrell D, French N, Lyagoba F, Rutebemberwa A, Cheingsong Popov R, et al. An improved algorithm for determining HIV type 1 subtypes in a primary laboratory in Uganda. AIDS Res Hum Retroviruses. 2000;16:621-5 pubmed
    ..This proposed approach is suitable for epidemiological studies in Uganda and other regions with a predominance of A and D subtypes. ..
  41. Weston M, Eudy J, Fujita S, Yao S, Usami S, Cremers C, et al. Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa. Am J Hum Genet. 2000;66:1199-210 pubmed
    ..search of 57 independent USHIIa probands was performed with a combination of direct sequencing and heteroduplex analysis of PCR-amplified exons. Fifteen new mutations were found...
  42. Ruibal I, Díaz H, de Armas M, Noa E. On HIV genetic diversity in Cuba. AIDS. 2003;17:2274-5; author reply 2275-6 pubmed
  43. Cabral V, Cunha C, Magalhaes E, Pinto Neto L, Couto Fernandez J, Dietze R, et al. Human immunodeficiency virus type-1 subtypes of infected patients in Espírito Santo, Brazil. Mem Inst Oswaldo Cruz. 2006;101:881-5 pubmed
  44. Arko B, Prezelj J, Kocijancic A, Komel R, Marc J. Association of the osteoprotegerin gene polymorphisms with bone mineral density in postmenopausal women. Maturitas. 2005;51:270-9 pubmed
    ..By our approach we detected eight polymorphisms in the OPG gene. According to our analysis polymorphism 1181G>C is associated with BMD and could therefore be considered as an element of genetic susceptibility to osteoporosis. ..
  45. Thiart R, Scholtz C, Vergotine J, Hoogendijk C, de Villiers J, Nissen H, et al. Predominance of a 6 bp deletion in exon 2 of the LDL receptor gene in Africans with familial hypercholesterolaemia. J Med Genet. 2000;37:514-9 pubmed
    ..Detection of the 6 bp deletion in Xhosa, Pedi, and Tswana FH patients suggests that it is an ancient mutation predating tribal separation approximately 3000 years ago. ..
  46. Vianello F, Lombardi A, Dal Bello F, Zanon E, Cabrio L, Girolami A. Conformation sensitive gel electrophoresis for detection of factor X gene mutations. Thromb Res. 2002;107:51-4 pubmed
    ..CSGE may be an effective and simple procedure for screening factor X gene mutations. ..
  47. Thiselton D, Alexander C, Taanman J, Brooks S, Rosenberg T, Eiberg H, et al. A comprehensive survey of mutations in the OPA1 gene in patients with autosomal dominant optic atrophy. Invest Ophthalmol Vis Sci. 2002;43:1715-24 pubmed
    ..unrelated white patients of European origin with adOA by single-strand conformational polymorphism (SSCP)-heteroduplex analysis and direct sequencing...
  48. Schroeder T, Burger H, Weiser B, Bengualid V, Kimani J, Anzala A, et al. Characterization of intersubtype recombinant HIV type 1 genomes using a nonradioactive heteroduplex tracking assay. AIDS Res Hum Retroviruses. 2005;21:314-8 pubmed
    ..This method is suitable for studies of HIV-1 diversity and recombination in areas of the world where multiple subtypes are found. ..
  49. Lei X, Zhu Y, Tomkinson A, Sun L. Measurement of DNA mismatch repair activity in live cells. Nucleic Acids Res. 2004;32:e100 pubmed
    ..This method is potentially useful in comparing and monitoring MMR activity in live cells under various growth conditions. ..
  50. Glaser R, Jiang W, Boyadjiev S, Tran A, Zachary A, Van Maldergem L, et al. Paternal origin of FGFR2 mutations in sporadic cases of Crouzon syndrome and Pfeiffer syndrome. Am J Hum Genet. 2000;66:768-77 pubmed
    ..A total of 4,374 bases between introns IIIa and 11 of the FGFR2 gene were sequenced and were assayed by heteroduplex analysis, to identify polymorphisms...
  51. Griffiths S, Thompson P, Frayling I, Upadhyaya M. Molecular diagnosis of neurofibromatosis type 1: 2 years experience. Fam Cancer. 2007;6:21-34 pubmed
  52. Zhong P, Burda S, Konings F, Urbanski M, Ma L, Zekeng L, et al. Genetic and biological properties of HIV type 1 isolates prevalent in villagers of the Cameroon equatorial rain forests and grass fields: further evidence of broad HIV type 1 genetic diversity. AIDS Res Hum Retroviruses. 2003;19:1167-78 pubmed
    ..This study further reveals the complexity of HIV-1 infection in rural Cameron and points to the future of the global epidemic, which may be characterized by more genetically diverse viruses. ..
  53. Sakuraba Y, Gondo Y. [ENU mouse mutagenesis and advanced reverse genetics]. Tanpakushitsu Kakusan Koso. 2004;49:2642-8 pubmed