Abstract
Comparison of HLA allelic sequences reveals a patchwork pattern in which individual alleles are defined by unique combinations of sequence motifs. Although each individual motif may be shared with other alleles, only a few alleles have specific sequences that are not present in other alleles (1). Thus the main problem facing conventional methods of human leukocyte antigen (HLA) typing is their inherent inability to determine, in heterozygous individuals, to which allele a particular motif belongs (2). To overcome this problem, allele separation must be performed in some samples prior to typing, making the whole procedure technically labor-intensive and time-consuming (3,4).
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References
Parham P., Lawlor D. A., Lomen C. E., and Ennis P. D. (1989) Diversity and diversification of HLA-A,B,C alleles. J. Immunol. 142, 3937–3950.
Rozemuller E. H. and Tilanus M. G. (1996) A computerized method to predict the discriminatory properties for class II sequencing based typing. Hum. Immunol. 46, 27–34.
Arguello R., Avakian H., Goldman J. M., and Madrigal J. A. (1996) A novel method for simultaneous high resolution identification of HLA-A, HLA-B, and HLA-Cw alleles. Proc. Natl. Acad. Sci. USA 93, 10,961–10,965.
Knapp L. A., Lehmann E., Hennes L., Eberle M. E., and Watkins D. I. (1997) High-resolution HLA-DRB typing using denaturing gradient gel electrophoresis and direct sequencing. Tissue Antigens 50, 170–177.
Orita M., Iwahana H., Kanazawa H., Hayashi K., and Sekiya T. (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86, 2766–2770.
Spinardi L., Mazars R., and Theillet C. (1991) Protocols for an improved detection of point mutations by SSCP. Nucleic Acids Res. 19, 4009.
Sheffield V. C., Beck J. S., Kwitek A. E., Sandstrom D. W., and Stone E. M. (1993) The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics 16, 325–332.
Wood N. A., Clay T. M., and Bidwell J. L. (1991) HLA-DR/Dw matching by PCR fingerprinting: the origin of PCR fingerprints and further applications. Eur J Immunogenet. 18, 147–153.
Zimmerman P. A., Carrington M. N., and Nutman T. B. (1993) Exploiting structural differences among heteroduplex molecules to simplify genotyping the DQA1 and DQB1 alleles in human lymphocyte typing. Nucleic Acids Res. 21, 4541–4547.
Arguello R., Pay A. L., McDermott A., et al. (1997) Complementary strand analysis: a new approach for allelic separation in complex polyallelic genetic systems. Nucleic Acids Res. 25, 2236–2238.
Arguello J. R., Little A-M., Pay A. L., et al. (1998) Mutation detection and typing of polymorphic loci through double-strand conformation analysis. Nat. Genet. 18, 192–194.
Arguello J. R., Little A-M., Bohan E., Goldman J. M, Marsh S. G. E, and Madrigal J. A. (1998) High resolution HLA class I typing by reference strand mediated conformation analysis (RSCA). Tissue Antigens 52, 57–66.
Fischer S. G. and Lerman L. S. (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci U S A 80, 1579–83.
Cereb N., Maye P., Lee S., Kong Y., and Yang S. Y. (1995) Locus-specific amplification of HLA class I genes from genomic DNA: locus-specific sequences in the first and third introns of HLA-A,-B, and-C alleles. Tissue Antigens 45, 1–11.
Fernandez-Vina M. and Bignon J. (1997) Primers and oligonucleotide probes (SSOP) used for DNA typing of HLA class II alleles, in Genetic Diversity of HLA. Functional and Medical Implications. Volume 1 (Charron D., ed.), EDK, Paris, pp. 597–632
Ramon D., Arguello J., Cox S., et al. (1998) Application of RSCA for the typing of HLA-DPB1. Hum. Immunol. 59, 734–747.
Rozemuller E. H., Bouwens A.G., Bast B. E., and Tilanus M. G. (1993) Assignment of HLA-DPB alleles by computerized matching based upon sequence data. Hum. Immunol. 37, 207–212.
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Rafael, J., Pérez-Rodríguez, M., Pay, A., Fisher, G., McWhinnie, A., Alejandro Madrigal, J. (2003). HLA Typing With Reference Strand-Mediated Conformation Analysis. In: Powis, S.H., Vaughan, R.W. (eds) MHC Protocols. Methods in Molecular Biology™, vol 210. Humana Press. https://doi.org/10.1385/1-59259-291-0:173
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DOI: https://doi.org/10.1385/1-59259-291-0:173
Publisher Name: Humana Press
Print ISBN: 978-0-89603-548-5
Online ISBN: 978-1-59259-291-3
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