Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1999-03-25
2001-02-06
Houtteman, Scott W. (Department: 1655)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C536S024300
Reexamination Certificate
active
06183968
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to a composition comprising a plurality of polynucleotide probes for use in research and diagnostic applications.
BACKGROUND OF THE INVENTION
DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 tumor suppressor gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. The array has over 50,000 DNA probes to analyze more than 400 distinct mutations of p53. A cytochrome p450 gene array is useful to determine whether individuals have one of a number of specific mutations that could result in increased drug metabolism, drug resistance, or drug toxicity.
DNA-based array technology is especially relevant for the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease, or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases the interactions may be expected, such as where the genes are part of the same signaling pathway. In other cases, such as when the genes participate in separate signaling pathways, the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affect the coregulation and expression of a large number of genes.
It would be advantageous to prepare DNA-based arrays that can be used for monitoring the expression of a large number of proteins associated with cell proliferation or receptors. Proteins associated with cell proliferation include cytokines, hormones, growth and differentiation factors, G and ras-related proteins, lectins, oncogenes and their suppressors, and the like. Receptors include G protein coupled, four transmerrmbrane, tyrosine kinase, and nuclear receptors. Some of these proteins may be secreted and typically include signal sequences that direct proteins to their cellular or extracellular destination.
The present invention provides for a composition comprising a plurality of polynucleotide probes for use in detecting changes in expression of a large number of genes which encode proteins associated with cell proliferation and receptors. Such a composition can be employed for the diagnosis and for monitoring the treatment of any disease—a cancer, an immunopathology, a neuropathology and the like—where a defect in the expression of a gene which encodes a protein associated with cell proliferation or a receptor is involved.
SUMMARY OF THE INVENTION
In one aspect, the present invention provides a composition comprising a plurality of polynucleotide probes, wherein each of said polynucleotide probes comprises at least a portion of a gene which encodes a protein associated with cell proliferation or a receptor.
In one preferred embodiment, the plurality of polynucleotide probes can comprise at least a portion of one or more of the sequences (SEQ ID NOS:1-134) presented in the Sequence Listing. In a second preferred embodiment, the composition comprises a plurality of polynucleotide probes comprising at least a portion of a gene coding for a protein associated with cell proliferation. In a third preferred embodiment, the composition comprises a plurality of polynucleotide probes comprising at least a portion of a gene coding for a receptor. In a fourth preferred embodiment, the composition comprises a plurality of polynucleotide probes comprising at least a portion of at least one or more of the sequences of SEQ ID NOS:1-22. In a fifth preferred embodiment, the composition comprises a plurality of polynucleotide probes comprising at least a portion of at least one or more of the sequences of SEQ ID NOS:23-134.
The composition is particularly useful as hybridizable array elements in a microarray for monitoring the expression of a plurality of target polynucleotides. The microarray comprises a substrate and the hybridizable array elements. The microarray can be used, for example, in the diagnosis and treatment of a cancer, an immunopathology, a neuropathology, and the like.
In another aspect, the present invention provides an expression profile that can reflect the expression levels of a plurality of target polynucleotides in a sample. The expression profile comprises a microarray and a plurality of detectable complexes. Each detectable complex is formed by hybridization of at least one of said target polynucleotides to at least one of said polynucleotide probes and further comprises a labeling moiety for detection.
DESCRIPTION OF THE SEQUENCE LISTING AND TABLES
A portion of the disclosure of this patent document contains material which is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent file or records, but otherwise reserves all copyright rights whatsoever.
The Sequence Listing is a compilation of nucleotide sequences obtained by sequencing clone inserts (isolates) of different DNA libraries. Each sequence is identified by a sequence identification number (SEQ ID NO), by the clone number from which it was obtained and by the DNA library from which the sequence was obtained.
Table 1 is a list of the exemplary sequences disclosed herein. By column, the first (3rd, 5th, and 7th) page of the table contains: 1) SEQ as shown in the Sequence Listing; 2) Incyte CLONE number as shown in the Sequence Listing; 3) PRINT reflects the designation of the relevant PROSITE group, 4) the SIGNATURE of that group; 5) the SCORE to the group, where >1300 is strong and 1000 to 1300 is suggestive; 6) STRENGTH reports the degree of correlation to the group, >1300 is strong and 1000 to 1300 is weak; and 7) HITS, number of similar molecules in the group. The second (4th, 6th and 8th) page of the table contains: 8) SEQ (repeated); 9) DESCRIPTION of the molecule/ORGANISM; 10) GenBank identifier; 11) p value; and 12) designation as cell proliferation or receptor category as determined using PRINTS and/or BLAST. The table is arranged so that SEQ ID NOS:1-22 contain at least a portion of a gene coding for a cell proliferation protein and SEQ ID NOS:23-134 contain at least a portion of a gene coding for a receptor.
DESCRIPTION OF THE INVENTION
Definitions
The term “microarray” refers to an ordered arrangement of hybridizable array elements. The array elements are arranged so that there are preferably at least one or more different array elements, more preferably at least 100 array elements, and most preferably at least 1,000 array elements, on a 1 cm
2
substrate surface. The maximum number of array elements is unlimited, but is at least 100,000 array elements. Furthermore, the hybridization signal from each of the array elements is individually distinguishable. In a preferred embodiment, the array elements comprise polynucleotide probes.
A “polynucleotide” refers to a chain of nucleotides. Preferably, the chain has from about 50 to 10,000 nucleotides, more preferably from about 100 to 3,500 nucleotides. The term “probe” refers to a polynucleotide sequence capable of hybridizing with a target sequence to form a polynucleotide probe/target complex. A “target polynucleotide” refers to a chain of nucleotides to which a polynucleotide probe can hybridize by base pairing. In some instances, the sequences will be complementary (no mismatches) when aligned. In other instances, there may be up to a 10%. mismatch.
A “plurality” refers preferably to a group of at least one or more members, more preferably to a group of at least about 100, and even more preferably to a group of at least about 1,000, members. The maximum number of members is unlimited, but is at least about 100,000 members.
A “portion” means a stretch of at least about 100
Bandman Olga
Baughn Mariah R.
Guegler Karl J.
Hillman Jennifer L.
Lal Preeti
Houtteman Scott W.
Incyte Genomics, Inc.
Incyte Pharmaceuticals Inc.
Murry Lynn E.
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