1887

Chapter 136 : Molecular Methods: HLA Alleles

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Molecular Methods: HLA Alleles, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815905/9781555813642_Chap136-1.gif /docserver/preview/fulltext/10.1128/9781555815905/9781555813642_Chap136-2.gif

Abstract:

Molecular biology techniques aimed at identification of HLA polymorphism at the gene level have largely replaced HLA typing assays based on identification of HLA proteins. The HLA genes encode at least six different HLA molecules, HLA-A, -B, and -C (class I molecules) and HLA-DR, -DQ, and -DP (class II molecules). The HLA molecules are encoded by the most polymorphic genetic loci known in humans. Each HLA allele is designated by the name of the gene followed by an asterisk and a four- to eight-digit number indicating the allele. Different HLA alleles defined by DNA typing can specify HLA proteins which are indistinguishable by methods based on protein identification, such as serology. DNA from HLA-characterized reference cells is usually derived from Epstein-Barr virus-transformed B lymphoblastoid cell lines. Molecular biology-based HLA typing methods utilize DNA as a starting material. PCR is used to generate a large number of copies of an HLA gene for rapid detection of HLA types. PCR uses sequence-specific primer pairs (a 5’ [sense] primer and a 3’ [antisense] primer) and polymerase to specifically amplify selected segments of DNA. DNA is negatively charged due to its phosphate composition; thus, amplified DNA will move toward the positively charged pole in an agarose gel matrix. Amplification is used to obtain sufficient copies of a specific HLA gene for analysis by DNA sequencing.

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

DRB1 nucleotide sequences from a few DRB1 alleles. Dashes indicate identity with the sequence of DRB1*0101. The numbers indicate the codons. Only part of the sequence of the DRB1 gene is shown; the polymorphic exon 2 includes codons 5 through 95. Probes identifying polymorphic sequences distinguishing these alleles are boxed.

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Example of two heterozygous allele combinations that cannot be distinguished from one another when both HLA-A alleles are characterized as a heterozygous mixture (i.e., ambiguous combinations). Some of the polymorphic nucleotides that distinguish the alleles and their and associations are diagrammed in the figure. The heterozygous combination A*02010101 and A*6601 (ambiguous combination 1) cannot be distinguished from the alternative, A*023501 and A*2603 (ambiguous combination 2), unless a single allele is isolated and characterized. Identification of the alleles present relies on the laboratory’s ability to link the first polymorphic sequence (located at codons 9-10, TTC ACA) to one of the two alternative second polymorphisms (CAC or CAG at codon 70). If CAC is in (i.e., found on the same DNA strand) with TTC ACA, then the first ambiguous combination is present.

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Primer locations for sequence-based typing of the HLA-B gene. The locations at which amplification and sequencing primers anneal to the HLA-B gene are indicated by arrows. BIn3 includes both BIn3 and BIn3-AC primers. Ex, exon; Int, intron; F, forward; R, reverse.

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815905.ch136
1. Bozon, M. V.,, J. C. Delgado,, A. Selvakumar,, O. P. Clavijo,, M. Salazar,, M. Ohashi,, S. M. Alosco,, J. Russell,, N. Yu,, B. Dupont, and , E. J. Yunis. 1997. Error rate for HLA-B antigen assignment by serology: implications for proficiency testing and utilization of DNA-based typing methods. Tissue Antigens 50:387394.
2. Bunce, M.,, M. C. Barnardo, and , K. I. Welsh. 1998. The PCR-SSP manager computer program: a tool for maintaining sequence alignments and automatically updating the specificities of PCR-SSP primers and primer mixes. Tissue Antigens 52:158174.
3. Cao, K.,, J. Hollenbach,, X. Shi,, W. Shi,, M. Chopek, and , M. Fernandez-Vina. 2001. Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum. Immunol. 62:10091030.
4. Cereb, N., and , S. Y. Yang. 1997. Dimorphic primers derived from intron 1 for use in the molecular typing of HLA-B alleles. Tissue Antigens 50:7476.
5. Ellexson, M. E.,, G. Z. Zhang,, D. Stewart,, M. Lau,, G. Teresi,, P. Terasaki,, B. Roe, and , W. Hildebrand. 1995. Nucleotide sequence analysis of HLA-B* 1523 and B*8101—dominant a-helical motifs produce complex sero-logic recognition patterns for the HLA-B"DT” and HLAB “NM5” antigens. Hum. Immunol. 44:103110.
6. Flomenberg, N.,, L. A. Baxter-Lowe,, D. L. Confer,, M. Fernandez-Vina,, A. Filipovich,, M. Horowitz,, C. K. Hurley,, C. Kollman,, C. Anasetti,, H. Noreen,, A. Begovich,, W. Hildebrand,, E. Petersdorf,, B. Schmeckpeper,, M. Setterholm,, E. Trachtenberg,, T. Williams,, E. J. Yunis, and , D. Weisdorf. 2004. Impact of HLA class I and class II high resolution matching on outcomes of unrelated donor bone marrow transplantation: HLA-C mismatching is associated with a strong adverse effect on transplant outcome. Blood 104:19231930. [Online.] doi:10.1182/blood-2004-03-0803.
7. Hurley, C. K. 1997. Acquisition and use of DNA-based HLA typing data in bone marrow registries. Tissue Antigens 49:323328.
8. Hurley, C. K.,, L. A. Baxter-Lowe,, B. Logan,, C. Karanes,, C. Anasetti,, D. Weisdorf, and , D. L. Confer. 2003. National Marrow Donor Program HLA-matching guidelines for unrelated marrow transplants. Biol. Blood Marrow Transplant. 9:610615.
9. Hurley, C. K.,, M. Setterholm,, M. Lau,, M. S. Pollack,, H. Noreen,, A. Howard,, M. Fernandez-Vina,, D. KuKuruga,, C. R. Muller,, M. Venance,, J. A. Wade,, M. Oudshoorn,, C. Raffoux,, J. Enczmann,, P. Wernet, and , M. Maiers. 2004. Hematopoietc stem cell donor registry strategies for assigning search determinants and matching relationships. Bone Marrow Transplant. 33:443450.
10. Kosman, C. 2000. HLA class I and class II DNA extraction methods. In A. B. Hahn,, G. A. Land, and , R. M. Strothman (ed.), American Society for Histocompatibility and Immuno-genetics Laboratory Manual. American Society for Histocompatibility and Immunogenetics, Lenexa, Kans.
11. Marsh, S. G. E.,, E. D. Albert,, W. F. Bodmer,, R. E. Bontrop,, B. Dupont,, H. A. Erlich,, D. E. Geraghty,, J. A. Hansen,, B. Mach,, W. R. Mayr,, P. Parham, et al. 2002. Nomenclature for factors of the HLA system, 2002. Eur. J. Immunogenet. 29:463515.
12. McGinnis, M. D.,, M. P. Conrad,, A. G. M. Bouwens,, M. G. J. Tilanus, and , M. N. Kronick. 1995. Automated, solid-phase sequencing of DRB region genes using T7 sequencing chemistry and dye-labeled primers. Tissue Antigens 46:173179.
13. Mickelson, E. M.,, L. A. Guthrie,, R. Etzioni,, C. Anasetti,, P. J. Martin, and , J. A. Hansen. 1994. Role of the mixed lymphocyte culture (MLC) reaction in marrow donor selection: matching for transplants from related haploidentical donors. Tissue Antigens 44:8392.
14. Mickelson, E. M.,, G. Longton,, C. Anasetti,, E. Petersdorf,, P. Martin,, L. A. Guthrie, and , J. A. Hansen. 1996. Evaluation of the mixed lymphocyte culture (MLC) assay as a method for selecting unrelated donors for marrow transplantation. Tissue Antigens 47:2736.
15. Middleton, D. 1999. History of DNA typing for the human MHC. Rev. Immunogenet. 1:135156.
16. Mytilineos, J.,, M. Lempert,, S. Scherer,, V Schwarz, and , G. Opelz. 1998. Comparison of serological and DNA PCR-SSP typing results for HLA-A and HLA-B in 421 black individuals—a collaborative transplant study report. Hum. Immunol. 59:512517.
17. Nepom, G. T., and , H. Erlich. 1991. MHC class-II molecules and autoimmunity. Annu. Rev. Immunol. 9:493525.
18. Noreen, H. J.,, N. Yu,, M. Setterholm,, M. Ohashi,, J. Baisch,, R. Endres,, M. Fernandez-Vina,, U. Heine,, S. Hsu,, M. Kamoun,, Y. Mitsuishi,, D. Monos,, L. Perlee,, S. Rodriguez-Marino,, S. Smith,, S. Y. Yang,, K. Shipp,, J. Hegland, and , C. K. Hurley. 2001. Validation of DNA-based HLA-A and HLA-B testing of volunteers for a bone marrow registry through parallel testing with serology. Tissue Antigens 57:221229.
19. Olerup, O., and , H. Zetterquist. 1992. HLA-DR typing by PCR amplification with sequence specific primers (PCR-SSP) in 2 hours: an alternative to serological DR typing in clinical practice including donor-recipient matching in cadaveric transplantations. Tissue Antigens 39:225235.
20. Opelz, G.,, T. Wujciak,, B. Dohler,, S. Scherer, and , J. Mytilineos. 1999. HLA compatibility and organ transplant survival. Rev. Immunogenet. 1:334342.
21. Parham, R, and , T. Ohta. 1996. Population biology of antigen presentation by MHC class I molecules. Science 272:6774.
22. Robinson, J.,, M. J. Waller,, P. Parham,, J. G. Bodmer, and , S. G. E. Marsh. 2001. IMGT/HLA database—a sequence database for the human major histocompatibility complex. Nucleic Acids Res. 29:210213.
23. Rozemuller, E. H.,, A. G. M. Bouwens,, B. E. J. E. G. Bast, and , M. G. J. Tilanus. 1993. Assignment of HLA-DPB alleles by computerized matching based upon sequence data. Hum. Immunol. 37:207212.
24. Sanger, F.,, S. Nicklen, and , A. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:54635467.
25. Schreuder, G. M. T.,, C. K. Hurley,, S. G. E. Marsh,, M. Lau,, M. Maiers,, C. Kollman, and , H. J. Noreen. 2001. The HLA dictionary 2001: a summary of HLA-A, -B, -C, -DRB1/3/4/5, -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens. Hum. Immunol. 62:826849.
26. Sidney, J.,, H. M. Grey,, R. T. Kubo, and , A. Sette. 1996. Practical, biochemical and evolutionary implications of the discovery of HLA class I supermotifs. Immunol. Today 17:261266.

Tables

Generic image for table
TABLE 1

Comparison of HLA typing methods

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 2

References providing primer strategies (SSP) for determining HLA types

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 3

References providing probe strategies (SSOPH) for determining HLA types

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 4

References for alternate methods of DNA-based testing

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 5

References on direct DNA sequencing (SBT)

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 6

Kits for the isolation of DNA

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 7

Examples of sequence-specific primer typing kits

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136
Generic image for table
TABLE 8

Examples of SSOPH typing kits

Citation: Hurley C, Cao K, Tang T, Steiner N, Lazaro A, Howard C, Ng J. 2006. Molecular Methods: HLA Alleles, p 1198-1214. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch136

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error