Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1998-12-03
2002-09-17
Horlick, Kenneth R. (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091100, C435S091200, C536S024330, C536S024320, C536S023100
Reexamination Certificate
active
06451525
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to a method for rapidly determining sequence information for a plurality of target polynucleotides in a sample, and to reagents and kits therefor. In a particular embodiment, the invention is directed to a method of determining, in parallel, the presence or absence of a plurality of sequence variants in a sample.
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BACKGROUND OF THE INVENTION
Genetic mutations underlie many disease states and disorders. Some diseases have been traced directly to single point mutations in genomic sequences (e.g., the A to T mutation associated with sickle cell anemia), while others have been correlated with large numbers of different possible polymorphisms located in the same or different genetic loci (e.g., cystic fibrosis). Mutations within the same genetic locus can produce different diseases (e.g., hemoglobinopathies). In other cases, the presence of a mutation may indicate susceptibility to particular condition for a disease but is insufficient to reliably predict the occurrence of the disease with certainty.
Genetic mutations have been found to occur by a variety of mechanisms, such as single base substitutions, deletions of one or more bases, insertions of one or more bases, transpositions, duplications, etc. Single base substitutions (transitions and transversions) within gene sequences can cause missense mutations and nonsense mutations. In missense mutations, an amino acid residue is replaced by a different amino acid residue, whereas in nonsense mutations, stop codons are created that lead to truncated polypeptide products. Mutations that occur within signal sequences for exon/intron splicing of mRNAs can produce defective splice variants with dramatically altered protein sequences. Deletions, insertions, and other mutations can also cause fraameshifts in which contiguous residues encoded downstream of the mutation are replaced with entirely different amino acid residues. Mutations outside of exons can interfere with gene expression and other processes. Most known pathogenic mutations have been localize to gene-coding sequences, splice signals, and regulatory sequences.
The large numbers of potential genetic polymorphisms poses a significant challenge to the development of methods for identifying and characterzing samples and for diagnosing and predicting disease. In light of the increasing quantity of sequence data that has become available for various organisms, and particularly for higher organisms such as humans, there is a need for rapid and convenient methods for simultaneously determining the presence or absence of a plurality of target mutations. Ideally, such a method should have high sensitivity, accuracy, and reproducibility. The method should allow simultaneous detection of large numbers of target mutations.
Accordingly, it is an object of the present invention to provide a precise and reproducible method for detecting a plurality of target polynucleotide sequences in a sample.
It is another object to provide a rapid and convenient method for determining the presence or absence of a plurality of target polynucleotide sequences in parallel.
It is an additional object to provide a method for establishing a sequence profile of one or more samples, which is useful for identifying or distinguishing samples.
It is yet another object to provide a method for determining the zygosity of one or more genetic loci in the sample.
Still another object is to provide a method that is useful in forensics, for establishing a sequence profile for the sample that can be used to help include or exclude a potential suspect from consideration.
It is also an object of the present invention to provide kits and reagents that are useful for practicing the above methods.
SUMMARY OF THE INVENTION
In one aspect, the present invention includes a method for obtaining sequence information from a plurality of target polynucleotides in a sample. In one embodiment, the method involves contacting a plurality of different-sequence primers with a polynucleotide sample under conditions effective for the primers to anneal to primer-complementary regions in one or more target polynucleotides, to form one or more target-primer hybrid(s). Each different-sequence primer contains (i) a target binding segment and (ii) a tag segment having a nucleotide sequence that identifies the target binding segment. The hybrid(s) are contacted with a labeled nucleotide terminator in the presence of a primer-extending reagent under conditions effective to append (covalently link) the base to an end of the annealed primer in the hybrid only when the base is complementary to a base in
Blasband Andrew J.
Koepf Sandy M.
Lowe Adam L.
Horlick Kenneth R.
PE Corporation (NY)
Powers Vincent M
Wilder Cynthia B.
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