Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Patent
1993-08-16
1997-05-13
Wax, Robert A.
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
435 15, 435 911, 435 912, 435 915, 435 9151, 536 2433, 935 8, 935 17, 935 18, 935 77, 935 78, C12Q 168, C12Q 148, C12N 1511
Patent
active
056291493
ABSTRACT:
The present invention provides a process for determining genotypes in highly polymorphic systems by polymerase chain reaction amplification of cDNA or genomic DNA and direct sequencing polymerase chain reaction products using oligonucleotide primers. More specifically, Class II and Class I HLA genotypes can be unambiguously determined in any subject in 16-24 hours by direct sequencing of DRB, DQB, DQA, DPB, DPA, HLA-A, HLA-B and HLA-C- transcripts enzymatically amplified using a limited number of non-allele-specific oligonucleotides. Total cellular RNA from peripheral blood mononuclear cells is reverse transcribed using antisense primers, specific for different locus (DQB, DQA, DPA or DPB) or group of loci (DRB1-5, or HLA-A and HLA-B and HLA-C). The synthesized cDNA molecules are then enzymatically amplified using different combinations of oligonucleotides for each locus and directly sequenced with Taq polymerase using an internal oligonucleotide. The sequenced genes are then analyzed.
REFERENCES:
patent: 4582788 (1986-04-01), Erlich
patent: 4683195 (1987-07-01), Mullis
patent: 4683202 (1987-07-01), Mullis
patent: 4835098 (1989-05-01), Orr
Parham, P. "Bone Marrow Transplantation. Making Just the Right Match [news]," Nature, 350 (6314):111-3, (1991 Mar. 14).
Nepom, G. "Structural Variation Among Major Histocompatibility Complex Class-II Genes Which Predispose to Autoimmunity," Immunologic Research, 8(1):16-38 (1989).
Stoflet, E. et al., "Genomic Amplification With Transcript Sequencing," Science, 239(4839):491-4 (1988 Jan. 29).
Thomson, G., "Human HLA Genetics and Disease Associations", The Handbook of Exp. Immunol. 3:Chap 102 (1986).
Smith, L. et al., "The Major Histocompatibility Complex of the Mouse", The Handbook of Exp. Immunol. 3:Chap 87 (1986).
Merryman, et al., "A Novel Association of DQ-alpha and DQ-beta Genes in the DRw10 Haplotype", J. Immunol. 143: 2068-2073 (1989).
Gyllensten, PCR Technology pp. 47 (1989).
Innes et al., Proc. Natl. Acad. Sci. USA 85:9436-9440.
Anasetti et al., "Effect of HLA Incompatibility on Graft-versus-Host Disease, Relapse, and Survival After Marrow Transplantation for Patients with Leukemia or Lymphoma", Hum. Immunol., 29:70-91 (1990).
Bach et al., "The Major Histocompatibility Complex--Genetics and Biology", N. Engl. J. Med., 295:806-813 (1976).
Bach, "The HLA Class II Genes and Products: the HLA-D Region", Immunol. Today, 6:89-94 (1985).
Bidwell, "DNA-RFLP Analysis and Genotyping of HLA-DR and DQ Antigens", Immunol. Today, 9:18-23 (1988).
Brown et al., "Chemical Synthesis and Cloning of a Tyrosine tRNA Gene", Methods Enzymol., 68:109-151 (1979).
Caruthers, et al., "Chemical Synthesis of Deoxyoligonucleotides by the Phosphoramidite Method", Methods Enzymol., 68:109-151 (1979).
Chirgwin et al., "Isolation of Biologically Active Ribonucleic Acid from Sources Enriched in Ribonuclease", Biochemistry, 18:5294-5299 (1979).
Dupont, "Nomenclature for Factors of the HLA System, 1987", 10th International Histocompatibility Workshop Hum. Immunol., 26:3-14 (1989).
Engelke et al., "Direct Sequencing of Enzymatically Amplified Human Genomic DNA", PNAS-USA, 85:544-548 (Jan. 1988).
Erlich et al., "HLA Class II Gene Polymorphism: DNA Typing, Evolution and Relationship to Disease Susceptibility", PCR Techniques, Chapter 16, pp. 193-208 (1989).
Gorman et al., "Simplified Method for Selective Amplification an Direct Sequencing of cDNAs", Biotechniques, 7:326-329 (Apr. 1989).
Gough, "Rapid and Quantitative Preparation of Cytoplasmic RNA from Small Numbers of Cells", Anal. Biochem., 173:93-95 (1988).
Gregerson et al., "Molecular Diversity of HLA-DR4 Haplotypes", PNAS, 83:2642-46 (1986).
Gyllenstein et al., "Generation of Single-Stranded DNA by the Polymerase Chain Reaction and Its Application to Direct Sequencing of the HLA-DQA Locus", Proc. Natl. Acad. Sci. USA, 85:7652-7656 (1988).
Higuchi, "Simple and Rapid Preparation of Samples for PCR", PCR Technology, pp. 31-38 (1989).
Johns et al., "Purification of Human Genomic DNA from Whole Blood Using Sodium Perchlorate in Place of Phenol", Anal. Biochem., 180:276-278 (1989).
Kao et al., "Molecular Analysis of the HLA Class II Genes in Two DRw6-Related Haplotypes, DRw13 DQw1 and DRw14 DQw3", J. Immunol., 142:1743-1747 (1989).
Knowles, "Structural Polymorphism of the HLA Class II alpha-and beta-Chains: Summary of the 10th Workshop 2-D Gel Analysis", Immunobiology of the HLA, vol. I, pp. 365-380 (1989).
Marsh et al., "Nomenclature for Factors of the HLA System, 1989", Immunogenetics, 31:131-140 (1990).
Marsh et al., "HLA-DRB Nucleotide Sequences, 1990", Immunogenetics, 31:141-144 (1990).
McBride et al., "Automated DNA Sequencing Methods Involving Polymerase Chain Reaction", Clinical Chem., 38:2196-2291 (Nov. 1989).
Merryman et al., "Nucleotide Sequence of a DRw10 beta-Chain cDNA Clone", J. Immunol., 140:2447-2452 (1988).
Merryman et al., "A Novel Association of DQ-alpha and DQ-beta Genes in the DRw10 Haplotype", J. Immunol., 143:2068-2073 (1989).
Mullis et al., "Specific Synthesis of DNA in Vitro via a Polymerase-Catalyzed Chain Reaction", Methods Enzymol., 155;335-350 (1987).
Narang et al., "Improved phosphotriester Method for the Synthesis of Gene Fragments", Methods Enzymol., 68:90-98 (1979).
Saiki et al., "Enzymatic Amplification of beta-Globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia", Science, 230:1350-1354 (1985).
Saiki et al., "Analysis of Enxzymatically Amplified beta-globin and HLA-DG alpha-DNA with Allele-Specific Oligonucleotide Probes", Nature, 324:163-166 (1986).
Scharf et al., "Direct Cloning and Sequence Analysis of Enzymatically Amplified Genomic Sequences", Science, 233:1076-1078 (1986).
Schulhof et al., "The Final Deprotection Step in Oligonucleotide Synthesis Is Reduced to a Mild and Rapid Ammonia Treatment by Using labile Base-Protecting Groups", Nucl. Acids Res., 15:397-416 (1987).
Terasaki et al., "Microdroplet Assay of Human Serum Cytotoxins", Nature, 204:998-1000 (1964).
Tiercy et al., "Identification and Distribution of Three Serologically Undetected Alleles of HLA-DR by Oligonucleotide-DNA Typing Analysis", Proc. Natl. Acad. Sci. USA, 85:198-202 (1988).
Todd et al., "HLA-DQ.sub.beta Gene Contributes to Susceptibility and Resistance to Insulin-Dependent Diabetes Mellitus", Nature 329:599-604 (1987).
Yang, "Description of the Reference Panel of B-Lymphoblastoid Cell Lines for Factors of the HLA System: The B-Cell Line Panel Designed for the Tenth International Histocompatibility Workshop", Immunobiology of HLA, I:11-19 (1989).
Yang, "A Standardized Method for Detection of HLA-A and HLA-B Alleles by One-Dimensional Isoelectric Focusing (IEF) Gel Electrophoresis", Immunobiology of HLA, I:332-335 (1989).
Zinkernagel et al., "Restriction of in Vitro of T Cell-Mediated Cytotoxicity in Lymphocytic Chorio-Meningitis Within a Syngeneic or Semiallogeneic System", Nature, 248:701-702 (1974).
Wong, C. "Characterization of B-thalassuemia mutations . . . "Nature 330: 384-386 (Nov. 1987).
Larhammer, D. et al. Proc. Natl. Acad. Sci 80: 7313-7317 (Dec. 1983).
Briata, P. et al. Proc. Natl. Acad Sci 86:1003-1007 (Feb. 1989).
Scharf, S. J. et al. Proc. Natl. Acad Sci. 86:6215-6219 (Aug. 1989).
Boss, J. M. et al. Proc. Natl. Acad. Sci 81:5199-5203 (Aug. 1984).
Wu, S. et al. Human. Immunol. 27:305-322 (Jul. 1990).
Unju, N. et al. Human Immunol. 24:175-181 (Mar. 1989).
Auffray, C. Proc. Natl. Acad. Sci. 79:6337-6341 (Oct. 1982).
Gyllensten, U.B. et al. Proc. Natl. Acad. Sci. 87:1835-1839 (Mar. 1990).
Moriachi, J. et al. Proc. Natl. Acad. Sci 82:3420-3424 (May 1985).
Schiffenbauer, J. et al. J. Immunology. 139(1) 228-233 (Jul. 1987).
Schenming, L. et al. EMBO J. 3(2) 447-452 (Feb. 1984).
Begovich, A. B. et al. Proc. Natl. Aca. Sci. 86:9489-9493 (Dec. 1989).
Lair, B. et al. J. Immunol. 141(4) 1353-1357 (Aug. 1988).
Lee, J. S. et al. Immunogenetics 29: 346-349 (May 1989).
Bugwan, T. et al. J. Immunol. 141(12) 4024-4030 (Dec. 1988).
Trowsdale, J. et al. Immunological Rev. 85:5-43 (Jul. 1985).
Barbosa Jose J.
Boyce-Jacino Michael T.
Faras Anthony J.
Rich Stephen S.
Santamaria Pedro
Prouty Rebecca
Rae-Venter Barbara
Regents of the University of Minnesota
Wax Robert A.
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