Patent 5578443 Issued on November 26, 1996. Estimated Expiration Date: November 26, 2013. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.
435/6, Involving nucleic acid435/15, Involving transferase435/91.1, Polynucleotide (e.g., nucleic acid, oligonucleotide, etc.)435/91.2, Acellular exponential or geometric amplification (e.g., PCR, etc.)435/91.21, Involving the making of multiple RNA copies435/91.5, Acellular preparation of polynucleotide536/23.1, DNA or RNA fragments or modified forms thereof (e.g., genes, etc.)536/24.3, Probes for detection of specific nucleotide sequences or primers for the synthesis of DNA or RNA536/24.33Primers
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.
Other References
Gyllensten in PCR Technology, H. Erlich editor, Stockton Press (1989) at p. 47
Biotechniques, vol. 7, No. 4, issued Apr. 1989, K. B. Gorman et al. "Simplified Method for Selective Amplification and Direct Sequencing of cDNAs" pp. 326-329, see entire document
Proceedings of the National Academy of Science USA, vol. 85, issued Jan. 1988, D. R. Engelke et al., "Direct Sequencing of Enzymatically Amplified Human Genomic DNA", pp. 544-548, see entire document
Clinical Chemistry, vol. 38, No. 11, issued Nov. 1989, L. J. McBride et al., "Automated DNA Sequencing Methods Involving Polymerase Chain Reaction", pp. 2196-2201, see especially pp. 2200-2201
P. Parham, Nature, 350, 111 (1991)
G. Nepom, Immunol. Res., 8, 16 (1989)
E. Stoflet et al., Science, 239, 491 (1988)
G. Thomson, The Handbook of Experimental Immunology, 3, Chapter 102, (1986)
L. Smith et al., The Handbook of Experimental Immunology, 3, Chapter 87 (1986)
Marsh et al., "Nomenclature for factors of the HLA system, 1989", Immunogenetics, 31:131 (1990)
F. Bach et al., "The HLA class II genes and products: the HLA-D region", Immuno. Today, 6:89 (1985)
R. Zinkernagel et al., "Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic chloriomeningitis within a syngeneic or semiallogeneic system", Nature, 248:701 (1974)
F. Bach et al., "The Major Histocompatibility Complex--Genetics and Biology", New Eng. J. of Med., 295:806 (1976)
Bidwell, "DNA-RFLP analysis and genotyping of HLA-DR and DG antigens", Immunology Today, 9:18 (1988)
J. 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 (1988)
P. Erlich, PCR Techniques, (1989)
Todd et al., "HLA-DQ gene contributttes to susceptibility and resistance to insulin-dependent diabetes mellitus", Nature, 329:599 (1987)
Saiki et al., "Enzymatic Amplification of -Globin Genomic Sequences and Restriction Sittte Analysis for Diagnosis of Sickle Cell Anemia", Science, 230:1350 (1985)
K. Mullis et al., "Specific Synthesis of DNA in Vitro via a Polymerase-Catalyzed Chain Reaction", Methods Enzymol., 155:335 (1987)
Saiki et al., "Analysis of enzymatically amplified -globin and HLA-DQA DNA with allele-specific oligonucleotide probes", Nature, 324:163 (1986)
Scharf et al., "Direct Cloning and Sequence Analysis of Enzymatically Amplified Genomic Sequences", Science, 233:1076 (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 (1988)
Brown et al., "Chemical Synthesis and Cloning of a Pyrosine cDNA Gene", Meth. in Enzymol., 68:109 (1979)
Caruthers et al., "Chemical Synthesis of Deoxyoligonucleotides by the Phosphoramidite Method", Methods Enzymol., 154:287 (1987)
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. Acid Res., 15:397 (1987)
Dupont, Hum. Immunol., 26:3 (1984)
Chirgwin et al., "Isolation of Biologically Active Ribonucleic Acid from Sources Enriched in Ribonuclease", Biochemistry, 18:5247 (1979)
Gough, "Rapid and Quantitative Preparation of Cytoplasmic RN from Small Numbers of Cells", Anal. Biochem, 173:93 (1988)
Knowles, Immunobiology of the HLA, vol. I, 365-380 (1989)
Gregerson et al., Proc. Nat'l Acad. Sci., 83, 2642-46 (1986)
Kao et al., J. Immunol., 142, 1743 (1989)
Merryman et al., J. Immunol., 140, 2447-52 (1988)
Merryman et al., J. Immunol., 143, 2068-73 (1989)
S. Marsh et al., "HLA-DRB nucleotide sequences, 1990", Immunogenetics, 31:141 (1990)
Johns et al., "Purification of Human Genomic DNA from Whole Blood Using Sodium Percholorate in Place of Phenol", Anal. Biochem., 180:276 (1989)
R. Higuchi, "Simple and Rapid Preparation of Samples for PCR", PCR Technology, (1989)
M. A. Innis et al. Proc. Natl. Acad. Sci. 85:9436-9440 (Dec. 1988)
U. B. Gyllensten. Proc. Natl. Acad. Sci 85:7652-7656 (1988)
Begovich, A. B. et al. "A specific HLA-DPB allele is associated . . . " Proc. Natl. Acad. Sci. 86:9489-9493 (Dec. 1989)
Bugawan, T. L. et al. "Analysis of HLA-DP Allelic . . . " J. Immunology 141(12):4024-4030 (Dec. 1988)
Lee, J. S. et al. "Sequence polymorphism of HLA-DP . . . " Immunogenetics 29:346-349 (May 1989)
Lair, B. et al. "A newly characterized HLA-DPB Chain Allele." J. Immunology 141(4) 1353-1357 (Aug. 1988)
Gyllensten, U. B. et al. "Allelic diversification at the Class I . . . " Proc. Natl. Acad. Sci 87:1835-1839 (Mar. 1990)
Auffray, C. et al. "cDNA clone for the heavy chain . . . " Proc. Natl. Acad. Sci 79:6337-6341 (Oct. 1982)
Uryu, N. et al. "No Difference in the Nucleotide Sequence . . . " Human Immunology 24:175-181 (Mar. 1989)
Wai, S. et al. "Full length DQB cDNA Sequences of . . . " Human Immunology 27:305-322 (Jul. 1990)
Boss, J. M. "Cloning and sequence analysis of the . . . " Proc. Natl. Acad. Sci 81:5199-5203 (Aug. 1984)
Scharf, S. J. et al. "Specific HLA-DQB and HLA-DRBI . . . " Proc. Natl. Acad. Sci. 86:6215-6219 (Aug. 1989)
Briata, P. et al. "Alternative splicing of HLA-DQB transcripts . . . " Proc. Natl. Acad. Sci 86:1003-1007 (Feb. 1989)
Larhammar, D. et al. "Exon-intron organization and complete . . . " Proc. Natl. Acad. Sci 80:7313-7317 (Dec. 1983)
Schenning et al. "Both and ଲ chains of HLA-DC Class II . . . " EMBO J. 3(2): 447-452 (Feb. 1984)
Schiffenbauer, J. et al. "Complete Sequence of the HLA DQ . . . " J. Immunology 139:228-233 (Jul. 1987)
Morinchi, J. et al. "Nucleotide sequence of an HLA DQ chain . . . " Proc. Natl. Acad. Sci 82:3420-3424 (May 1985)
Trousdale, J. "Structure, Sequence and Polymorphism in . . . " Immunological Rev. 85:5-43 (Jul. 1985)
Gorman, K. B. et al. "Simplified Method for Selective Amplification . . . " Biotechniques 7(4):326-329 (Apr. 1989)
McBride, L. J. et al. "Automated DNA Sequencing Methods . . . " Clinical Chemistry 35(11):2196-2201 (Nov. 1989)
Engelke, D. R. et al. "Direct Sequencing of enzymatically . . . " Proc. Natl. Acad. Sci 85:544-548 (Jan. 1988)
Wong, C. et al. "Characterization of ଲ-thalassaemia mutations . . . " Nature 320:384-386 (Nov.(1987
November 26, 2013. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.
