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Tyrosine kinomeRelated Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Nucleic AcidTyrosine kinome description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20070037150, Tyrosine kinome. Brief Patent Description - Full Patent Description - Patent Application Claims
[0002] 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. FIELD OF THE INVENTION [0003] The invention relates to the field of cancer genetics and therapeutics. In particular, it relates to genetic changes that affect protein kinase gene families or other gene families. These genetic changes are useful in diagnostic, prognostic, drug discovery, and clinical drug testing applications. BACKGROUND OF THE INVENTION [0004] Tyrosine kinases (TKs) are central regulators of signaling pathways that control differentiation, transcription, cell cycle progression, apoptosis, motility, and invasion (1). Although genetic alterations in a few TK genes have been linked to human cancer (2), most TK genes have not been directly implicated in tumorigenesis. Additionally, it is not known how many or how often members of the TK gene family are altered in any particular cancer type. BRIEF SUMMARY OF THE INVENTION [0005] In a first embodiment of the invention a method is provided for detecting mutations involved in cancer. Members of a family of genes in a database of human nucleotide sequences are identified based on homology to a known member of the family. Nucleotide sequence differences in a selected region of each of the members of the family of genes are identified in matched pairs of an individual's cancer cells and normal cells. Such differences identify members of heightened interest Additional nucleotide sequence differences in the members of heightened interest are determined, either in one or more additional regions outside of the selected region, or in matched pairs of cancer cells and normal cells of additional individuals, or in both. [0006] Another embodiment of the invention provides a method of screening test substances for use as anti-cancer agents. A test substance is contacted with an activated protein kinase selected from the group consisting of: NTRK3, FES, MCCK/MLK4, EPHA3, NTRK2, INSRR, JAK1, PDGFRA, EPHA7, EPHA8, KDR, FGFR1, and ERBB4. Activity of the activated protein kinase is assayed. A test substance which inhibits the activity of the activated protein kinase is a potential anti-cancer agent. [0007] Another embodiment of the invention provides a method of screening test substances for use as anti-cancer agents. A test substance is contacted with a mutated GUCY2F guanylate cyclase. Activity of the mutated GUCY2F guanylate cyclase is assayed. A test substance which increases the activity of the mutated GUCY2F guanylate cyclase is a potential anti-cancer agent. [0008] Another embodiment of the invention provides an isolated, activated protein kinase. The kinase is selected from the group consisting of: NTRK3, FES, MCCK/MLK4, GUCY2F, EPHA3, NTRK2, INSRR, JAK1, PDGFRA, EPHA7, EPHA8, KDR, FGFR1, and ERBB4. [0009] Another embodiment of the invention provides an isolated, mutated GUCY2F protein. [0010] Still another embodiment of the invention is a method of categorizing cancers. The sequence of one or more protein kinase family members in a sample of a cancer tissue is determined. The one or more members is selected from the group consisting of NTRK3, FES, MCCK/MLK4, EPHA3, NTRK2, INSRR, JAK1, PDGFRA, EPHA7, EPHA8, GUCY2F, KDR, FGFR1, and ERBB4. A somatic mutation of said one or more protein kinase family members is identified in the cancer tissue. The cancer tissue is assigned to a group based on the presence of the somatic mutation. BRIEF DESCRIPTION OF THE DRAWINGS [0011] FIG. 1 shows detection of mutations in tyrosine kinase genes. Representative examples of mutations in NTRK3 (FIG. 1A) and MCCK/MLK4 (FIG. 1B) identified using the Mutation Explorer software package (SoftGenetics, State College, PA). In each case, the top box contains the sequence chromatogram from tumor DNA, the middle box contains the sequence chromatogram from normal tissue from the same patient, and the lower box contains a computed comparison between the tumor and normal traces displaying a peak at the observed alteration. [0012] FIG. 2 shows distribution of mutations in NTRK3, FES, MCCK/MLK4 and GUCY2F. Arrows indicate location of mutations while boxes represent functional domains. [0013] FIG. 3 shows sequence conservation and location of mutations in altered genes. Alignment of amino acid sequences for (FIG. 3A) NTRK3, (FIG. 3B) FES, NTRK2 and EPHA3, and (FIG. 3C) MCCK/MLK4. Conserved residues are indicated by a dot, while nonconserved residues are indicated by a letter. The positions of identified mutations in each gene are highlighted in yellow, while positions of mutations in MET and BRAF are highlighted in blue. Underlined regions represent the activation loop (subdomain VII and VIII). DETAILED DESCRIPTION OF THE INVENTION [0014] Any database can be used in the present invention, whether public, subscription, or proprietary to identify members of a family of genes. Databases can be of nucleotide sequences or protein sequences. They can be of genomic sequences or expressed sequence tags or cDNA sequences. Preferably the sequences are human sequences although the same methods can be used for other species. Homology to a known member may be based on limited portions of the known member, such as a catalytic domain or a regulatory domain. Alternatively homology may be based on the whole protein. Any algorithm or program known in the art can be used. Suitable programs are available publicly and commercially, or they can be made by the individual worker in the art. [0015] Nucleotide sequence differences in a family member can be determined between a sample of cancer cells and normal cells. Cancer and normal cells typically are matched pairs, i.e., they are derived from the same individual and optionally from the same organ. Any technique can be used to determine nucleotide sequence differences. Sequencing of genomic DNA or cDNA can be used. Other techniques which detect differences between two sequences can also be used, without limitation. Techniques which detect differences between the encoded proteins can also be used, since a change in the amino acid of a protein indicates that the nucleotide sequence has been changed. [0016] Selected regions of the family members can be initially screened for nucleotide differences. Any basis for selecting a region can be used. Regions can be selected based on knowledge of mutations in similar regions of other proteins, or based on predictions of particularly important domains of the encoded proteins. Examples of important domains include, but are not limited to catalytic domains and regulatory domains. [0017] One method for determining the functional significance of any mutation which is found is to determine the effect that the mutation has on the encoded protein. A synonymous mutation creates no change in the encoded protein and is sometimes termed silent. Such a mutation is less likely to be functionally relevant to cancer than a non-synonymous mutation. One can determine an encoded protein by identifying an mRNA transcribed from a gene containing a mutation and translating the mRNA (or derived cDNA). [0018] Another method for determining functional significance of a mutation is to determine if the mutation affects an evolutionarily conserved amino acid residue. This can be done by aligning sequences of the same protein from different species and assessing which ones are invariant or predominantly so. The mutation is then compared with this determination of evolutionarily conserved residues to identify if the mutation affects such a residue. [0019] Another method for attributing functional significance to a mutation is to determine if it affects an important domain of the protein. Such domains include but are not limited to catalytic domains and regulatory domains. Another index of functional significance of a new mutation can be found by comparing the amino acid residue affected by the new mutation with equivalent residues in other proteins. If mutations have been found affecting the equivalent residues and those mutations have been determined to be associated with disease, then the new mutation is more likely to be functionally significant. The equivalent mutation may be in the positionally equivalent amino acid residue, or in a close neighbor, perhaps within 5, within 3, within 2, or within 1 residue of the positionally equivalent amino acid residue. [0020] The identified protein kinase family members which have been found to harbor cancer-associated mutations can be used to screen test substances for use as anti-cancer agents. The encoded mutant proteins can be isolated from cells and used in vitro in a cell-free assay. Alternatively, cancer cell lines harboring the mutant protein kinase family members can be used. Cells which have been genetically modified to express the encoded mutant protein can also be used. Regardless of the form in which the mutant protein is presented, it can be contacted with a test substance and the affect on enzymatic activity assessed. If the mutant protein is an activated protein kinase, then test substances will desirably inhibit the activity. If the mutant protein is enzymatically less active than its wild-type cognate, then the test substance will desirably restore activity. Although the family members were selected as being homologous to a tyrosine kinase, all family members are not tyrosine kinases. Some phosphorylate other residues of proteins, such as serine and/or threonine. Others contain inactive kinase domains and have other catalytic domains, such as guanylate cyclase activity. Assays for tyrosine, serine, or threonine kinase activity are well known in the art. See, e.g., the HitHunter.TM. Enzyme Fragment Complementation Assay of Applied Biosystems, Foster City, Calif., Tyrosine Kinase Assay Kits, (Green or Red) of Panvera, Madison Wis. Any such assay can be used. Assays for guanylate cyclase are also well known. One commercially availably assay kit which may be used is a cGMP RIA assay (Amersham, Bucks., UK). Continue reading about Tyrosine kinome... Full patent description for Tyrosine kinome Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Tyrosine kinome patent application. ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. 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