Intron sequence analysis method for detection of adjacent and remote locus alleles as haplotypes
DCFirst Claim
1. A method for detection of at least one coding region allele of an HLA locus comprising amplifying genomic DNA with a primer pair that spans a non-coding region sequence selected from the group consisting of untranslated sequences between exons, 5'"'"' and 3'"'"' untranslated regions associated with a genetic locus, and spacing sequences between genetic loci, said primer pair defining a DNA sequence, said DNA sequence being in genetic linkage with said HLA locus and containing a sufficient number of said non-coding region sequence nucleotides to produce an amplified DNA sequence characteristic of said allele.
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Abstract
The present invention provides a method for detection of at least one allele of a genetic locus and can be used to provide direct determination of the haplotype. The method comprises amplifying genomic DNA with a primer pair that spans an intron sequence and defines a DNA sequence in genetic linkage with an allele to be detected. The primer-defined DNA sequence contains a sufficient number of intron sequence nucleotides to characterize the allele. Genomic DNA is amplified to produce an amplified DNA sequence characteristic of the allele. The amplified DNA sequence is analyzed to detect the presence of a genetic variation in the amplified DNA sequence such as a change in the length of the sequence, gain or loss of a restriction site or substitution of a nucleotide. The variation is characteristic of the allele to be detected and can be used to detect remote alleles. Kits comprising one or more of the reagents used in the method are also described.
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11 Claims
- 1. A method for detection of at least one coding region allele of an HLA locus comprising amplifying genomic DNA with a primer pair that spans a non-coding region sequence selected from the group consisting of untranslated sequences between exons, 5'"'"' and 3'"'"' untranslated regions associated with a genetic locus, and spacing sequences between genetic loci, said primer pair defining a DNA sequence, said DNA sequence being in genetic linkage with said HLA locus and containing a sufficient number of said non-coding region sequence nucleotides to produce an amplified DNA sequence characteristic of said allele.
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7. A method for detection of at least one allele of an HLA locus comprising:
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A. amplifying genomic DNA with a primer pair that spans a non-coding region sequence selected from the group consisting of untranslated sequences between exons, 5'"'"' and 3'"'"' untranslated regions associated with a genetic locus, and spacing sequences between genetic loci, said primer pair defining a DNA sequence, said DNA sequence being in genetic linkage with said allele and containing a sufficient number of said non-coding region sequence nucleotides to produce an amplified DNA sequence characteristic of said allele; and B. analyzing said amplified DNA sequence to detect the presence of a genetic variation in said amplified sequence. - View Dependent Claims (8, 9, 10, 11)
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Specification