Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2000-01-31
2002-12-10
Brusca, John S. (Department: 1637)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C536S063000, C536S063000
Reexamination Certificate
active
06492505
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to a composition comprising a plurality of polynucleotide sequences 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 may be used to determine whether individuals are carrying mutations that predispose them to cancer. The array has over 50,000 DNA targets 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 to screen expression of a large number of genes rapidly. There is a growing awareness that gene expression is affected in a global fashion and that 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 some of 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 membrane-associated proteins. Proteins which span or are associated with cell membranes include receptors, ion channels and symporters, cytokines and their suppressors, monomeric or heterotrimeric G- and ras-related proteins, lectins such as selectin, oncogenes and their suppressors, and the like. Receptors include G protein coupled, four transmembrane, and tyrosine kinase receptors. Some of these proteins may span a cellular membrane and some may be secreted. The secreted proteins typically include signal sequences that direct them to their final cellular or extracellular destination.
The present invention provides for a composition comprising a plurality of polynucleotide sequences for use in detecting changes in expression of a large number of genes encoding proteins which are membrane-associated proteins, receptors and ion channels. Such a composition can be employed for the diagnosis or treatment of any disease—a pancreatic disease, a cancer, an immunopathology, a neuropathology and the like—where a defect in the expression of a gene encoding membrane-associated proteins is involved.
SUMMARY OF THE INVENTION
In one aspect, the present invention provides a composition comprising a plurality of polynucleotide sequences, wherein each of said polynucleotide sequences comprises at least a fragment of a gene encoding membrane-associated proteins, receptors and ion channels.
In one preferred embodiment, the plurality of polynucleotide sequences comprises at least a fragment of one or more of the sequences, SEQ ID NOs:1-305, presented in the Sequence Listing. In a second preferred embodiment, the composition comprises a plurality of polynucleotide sequences comprising at least a fragment of a gene encoding a membrane-associated protein. In a third preferred embodiment, the composition comprises a plurality of polynucleotide sequences comprising at least a fragment of a gene encoding a receptor. In a fourth preferred embodiment, the composition comprises a plurality of polynucleotide sequences comprising at least a fragment of a gene encoding ion channels. In a fifth preferred embodiment, the composition comprises a plurality of polynucleotide sequences comprising at least a fragment of at least one or more of the sequences of SEQ ID NOs:1-288. In a sixth preferred embodiment, the composition comprises a plurality of polynucleotide sequences comprising at least a fragment of at least one or more of the sequences of SEQ ID NOs:289-294. In a seventh preferred embodiment, the composition comprises a plurality of polynucleotide sequences comprising at least a fragment of at least one or more of the sequences of SEQ ID NOs:295-305. In one aspect, the fragment is selected from the group consisting of SEQ ID NOs:295-297, or SEQ ID NOs:298-305. In an eighth preferred embodiment, the composition is a polynucleotide probe. In one aspect, the composition is immobilized on a substrate. In a ninth preferred embodiment, the composition is an hybridizable array element.
The composition, a hybridizable array element, is useful to monitor the expression of a plurality of expressed polynucleotides. The microarray is used in the diagnosis and treatment of a pancreatic disease, 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 polynucleotide sequences 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 probe polynucleotide sequence to at least one target polynucleotide sequence and further comprises a labeling moiety for detection.
DESCRIPTION OF THE SEQUENCE LISTING, FIGURES, 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 and assembling clone inserts (isolates) from various cDNA libraries. Each sequence is identified by a sequence identification number (SEQ ID NO:) and by clone number.
FIGS
1
A and
1
B are an alignment of SEQ ID NOs:298-302 produced using GELVIEW Fragment Assembly System software (Genetics Computer Group (GCG), Madison Wis.).
FIGS. 2A and 2B
are an alignment of SEQ ID NOs:303-305 produced using GELVIEW Fragment Assembly System software (GCG).
Table 1 is a list of the sequences disclosed herein. By column, the table contains: 1) SEQ ID NO: as shown in the Sequence Listing; 2) Incyte Clone NO; 3) PRINT ID, designation of the relevant PROSITE group; 4) PRINT DESCRIPTION; 5) PRINT STRENGTH, the degree of correlation to the PROSITE group, >1300 is strong and 1000 to 1300 is weak; 6) PRINT SCORE, where >1300 is strong and 1000 to 1300 is suggestive; 7) TM, the presence of at least one transmembrane domain; and 8) SIGNAL PEPTIDE, the presence of a signal peptide. The table is arranged so that SEQ ID NOs:1-305 contain at least a fragment of a gene encoding a membrane-associated protein, some of which are receptors, and some, ion channels.
DESCRIPTION OF THE INVENTION
Definitions
The term “microarray” refers to an ordered arrangement of hybridizable array elements. The elements are arranged so that there are preferably at least one or more different elements, more preferably at least 100 elements, even more preferably at least 1,000 elements, and most preferably at least 10,000 elements on a one cm
2
substrate surface. The maximum number of array elements is unlimited, but is at least 100,000. Furthermore, the hybridization signal from each array element is individually distinguishable. In a preferred embodiment, the array elements comprise polynucleotide sequences.
A “polynucleotide” refers to a chain of nucleotides. Preferably, the chain has from about five to 10,000 nucleotides, more preferably from about 50 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 unde
Au-Young Janice
Guegler Karl J.
Reddy Roopa
Brusca John S.
Incyte Genomics Inc.
Incyte Genomics, Inc.
Kim Young
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