Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
1998-01-30
2002-12-31
Marschel, Ardin H. (Department: 1631)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C422S050000, C422S068100, C435S006120, C436S501000, C536S024100, C536S024300, C536S024310, C536S024320, C536S024330
Reexamination Certificate
active
06500938
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 18 known polymorphisms of two human cytochrome p450 genes. These polymorphisms can cause increased drug metabolism, drug resistance or drug toxicity.
DNA-based array technology is especially relevant to 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 affects the 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 genes coding for signaling pathway polypeptides, including different types of receptor, transducer and effector-like polypeptides. The present invention provides for a composition that can be employed in an array-format for detecting changes in expression of a large number of genes coding for different signaling pathway polypeptides.
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 coding for a signaling pathway polypeptide. The plurality of polynucleotide probes can comprise I) first polynucleotide probes, wherein each of said first polynucleotide probes comprises at least a portion of a gene coding for a receptor-like polypeptide; II) second polynucleotide probes, wherein each of said second polynucleotide probes comprises at least a portion of a gene coding for a transducing polypeptide; III) third polynucleotide probes, wherein each of said third polynucleotide probes comprises at least a portion of a gene coding for an effector-like polypeptide; or combinations thereof.
More particularly, in one preferred embodiment the composition comprises a plurality of polynucleotide probes wherein each gene coding for a signaling pathway polypeptide is at least a portion of a sequence selected from the group consisting of SEQ ID Nos: 1-1490. In a second preferred embodiment, the composition comprises a plurality of polynucleotide probes comprising at least a portion of at least 1000 of the sequences of SEQ ID Nos: 1-1490. In a third preferred embodiment, the composition comprises a plurality of polynucleotide probes wherein said polynucleotide probes comprise at least a portion of substantially all the sequences of SEQ ID Nos: 1-1490. The polynucleotide probes can be complementary DNAs, clone DNAs and the like.
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 hybridizable array elements. The microarray of this invention is particularly useful in the diagnosis and treatment of cancer, an immunopathology, a neuropathology and the like.
In another aspect, the present invention encompasses an expression profile that can reflect the levels of a plurality of target polynucleotides in a sample. The expression profile comprises the microarray and a plurality of detectable complexes. Each detectable complex is formed by having at least one of the target polynucleotides hybridizing to at least one of the hybridizable array elements and further comprises a labeling moiety for detection. The expression profile of this invention is particularly useful in the diagnosis and the treatment of cancer, an immunopathology, a neuropathology and the like.
In yet another aspect, the invention provides a method for selecting a plurality of polynucleotide probes, said method comprising (I) obtaining a plurality of query sequences; (II) screening said query sequences against one or more databases comprising annotated sequences to identify sequence hits; and (III) selecting said sequence hits with the highest homology (top hits) to said annotated sequences. The query sequences can be expression sequence tags (ESTs) or full length gene coding sequences, which are electronically screened using preferably the Basic Local Alignment Search Tool (BLAST) algorithm. In one embodiment, the highest homology is identified as a BLAST score equal to or above 100 at a P-value equal to or below 10
−10
against the GenPept database. In a second embodiment, the highest homology is identified as a percent sequence identity equal to or above 80% and a BLAST score equal to or above 250 against the GenBank Primate database. In a third embodiment, the highest homology is identified as a percent identity equal to or above 75% and a BLAST score equal to or above 250 against the GenBank Rodent database. In a fourth embodiment, the highest homology is identified as the match with the lowest P-value when searches are performed against GenPept, GenBank Primate or GenBank Rodent databases.
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 cDNA 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 cDNA library from which the sequence was obtained.
Table 1 is a list of the sequences according to their SEQ ID Nos:. For SEQ ID Nos: 1-1049 (homologous to GenBank sequences) the first column contains Incyte clone numbers. The second column contains a relevant GenBank identification number match, if any. The last column contains an annotation associated with the referenced GenBank identification number along with the genus species or source name. For SEQ ID Nos: 1050-1490 (exact matches to GenBank) the first column contains the GenBank identification number. The second column contains an annotation associated with the referenced GenBank identification number along with the genus species or source name.
Table 2 is a list of the cDNA libraries and a description of the preparation of the cDNA libraries.
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 about 10 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
Au-Young Janice
Seilhamer Jeffrey J.
Incyte Genomics Inc.
Incyte Genomics, Inc.
Marschel Ardin H.
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