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US 2003/0194728 A1Published application
Haplotypes of the SLC26A2 gene
AssigneeNone recorded
InventorsStefanie E. Kliem, Beena Koshy, Debra A. Tanguay
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AssigneeNone recorded
InventorsStefanie E. Kliem, Beena Koshy, Debra A. Tanguay
Estimating the term…
Novel genetic variants of the Solute Carrier Family 26, Member 2 (SLC26A2) gene are described. Various genotypes, haplotypes, and haplotype pairs that exist in the general United States population are disclosed for the SLC26A2 gene. Compositions and methods for haplotyping and/or genotyping the SLC26A2 gene in an individual are also disclosed. Polynucleotides defined by the haplotypes disclosed herein are also described.
A method for assigning a haplotype for the solute carrier family 26, member 2 (SLC26A2) gene to an individual, which comprises examing at least one copy of the individual's CTSG gene to identify the phased sequence of nucleotides at each of PS1-PS5 for that copy of the individual's SLC26A2 gene, comparing the phased sequence to the CTSG haplotypes shown in the table immdediately below, and assigning to the individual a SLC26A2 haplotype from the table that is consistent with the phased sequence, wherein the assigned SLC26A2 haplotype comprises a haplotype selected from the group consisting of the SLC26A2 haplotypes shown in the table immediately below:
A method for assigning a haplotype pair for the solute carrier family 26, member 2 (SLC26A2) gene to an individual, which comprises examing both copies of the individual's SLC26A2 gene to identify the phased sequence of nucleotides at PS1-PS5 for each copy of the individual's SLC26A2 gene, comparing each of the pahsed sequences to the CTSG haplotype pairs shown in the table immediately below, and assigning to the individual a SLC26A2 haplotype pair from the table that is consistent with each of the phased sequences, wherein the assigned SLC26A2 haplotype pair comprises a haplotype pair selected from the group consisting of the SLC26A2 haplotype pairs shown in the table immediately below:
A method for genotyping the solute carrier family 26, member 2 (SLC26A2) gene of an individual, comprising determining for the two copies of the SLC26A2 gene present in the individual the identity of the nucleotide pair at one or more polymorphic sites (PS) selected from the group consisting of PS1, PS2, PS3 and PS5, wherein the one or more polymorphic sites (PS) have the position and alternative alleles shown in SEQ ID NO:
A method for haplotyping the solute carrier family 26, member 2 (SLC26A2) gene of an individual which comprises determining, for one copy of the SLC26A2 gene present in the individual, the identity of the nucleotide at two or more polymorphic sites (PS) selected from the group consisting of PS1, PS2, PS3 and PS5, wherein the selected PS have the position and alternative alleles shown in SEQ ID NO:1.
A method for assigning a haplotype pair for the solute carrier family 26, member 2 (SLC26A2) gene to an individual comprising:
A method for identifying an association between a trait and at least one haplotype or haplotype pair of the solute carrier family 26, member 2 (SLC26A2) gene which comprises comparing the frequency of the haplotype or haplotype pair in a population exhibiting the trait with the frequency of the haplotype or haplotype pair in a reference population, wherein the haplotype is selected from haplotypes 1-5 shown in the table presented immediately below:
A method for reducing the potential for bias in a clinical trial of a candidate drug for treating a disease or condition predicted to be associated with SLC26A2 activity, the method comprising determining which of the SLC26A2 haplotypes or SLC26A2 haplotype pairs shown in the tables immediately below is present in each individual that is participating in the trial;
An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:
An isolated fragment of a solute carrier family 26, member 2 (SLC26A2) isogene, wherein the fragment comprises at least 50 nucleotides in one of the regions of SEQ ID NO:1 shown in the table immediately below and wherein the fragment comprises one or more polymorphisms selected from the group consisting of adenine at PS1, guanine at PS2, adenine at PS3 and thymine at PS5, wherein the selected polymorphism has the position set forth in the table immediately below:
An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of
An isolated fragment of a SLC26A2 coding sequence, wherein the fragment comprises at least 50 nucleotides and one or more polymorphisms selected from the group consisting of adenine at a position corresponding to nucleotide 1046, thymine at a position corresponding to nucleotide 2065 in SEQ ID NO:2.
An isolated polypeptide comprising a naturally occurring human SLC26A2 protein variant that has sulfate transporter activity, wherein the CTSG protein variant comprises SEQ ID NO:3 and wherein the combination of amino acids at 349, 574, and 689 are selected from the protein variants shown in the table immediately below:
An isolated fragment of a SLC26A2 protein variant, wherein the fragment is at least 6 amino acids in length and comprises one or more variant amino acids selected from the group consisting of tyrosine at a position corresponding to amino acid position 349, serine at a position corresponding to amino acid position 689 in SEQ ID NO:3.
A method for screening for compounds targeting the SLC26A2 protein to treat a condition or disease predicted to be associated with SLC26A2 activity, the method comprising;
A method for validating the SLC26A2 protein as a candidate target for treating a medical condition predicted to be associated with SLC26A2 activity, the method comprising:
An isolated oligonucleotide designed for detecting a polymorphism in the solute carrier family 26, member 2 (SLC26A2) gene at a polymorphic site (PS) selected from the group consisting of PS1, PS2, PS3 and PS5, wherein the oligonucleotide contains or is located one to several nucleotides downstream of the selected PS, wherein the oligonucleotide has a length of 15 to 100 nucleotides, and wherein the selected PS has the position and alternative alleles shown in SEQ ID NO:1.
A kit for haplotyping or genotyping the solute carrier family 26, member 2 (SLC26A2) gene of an individual, which comprises a set of oligonucleotides designed to haplotype or genotype each of polymorphic sites (PS) PS1, PS2, PS3 and PS5, wherein the selected PS have the position and alternative alleles shown in SEQ ID NO:1.
A genome anthology for the solute carrier family 26, member 2 (SLC26A2) gene which comprises two or more SLC26A2 isogenes selected from the group consisting of isogenes 1-5 shown in the table immediately below, and wherein each of the isogenes comprises the regions of SEQ ID NO:1 shown in the table immediately below and wherein each of the isogenes 1-5 is further defined by the corresponding sequence of polymorphisms whose positions and alleles are set forth in the table immediately below:
Dependencies are inferred from the claim text.
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Involving nucleic acids: nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
From vertebrates: from mammals
Oligonucleotides characterized by their use: polymorphic or mutational markers
Measuring or testing processes involving enzymes, nucleic acids or microorganisms
Term end not estimated
This invention relates to variation in genes that encode pharmaceutically-important proteins. In particular, this invention provides genetic variants of the human solute carrier family 26, member 2 (SLC26A2) gene and methods for identifying which variant(s) of this gene is/are possessed by an individual.
Current methods for identifying pharmaceuticals to treat disease often start by identifying, cloning, and expressing an important target protein related to the disease. A determination of whether an agonist or antagonist is needed to produce an effect that may benefit a patient with the disease is then made. Then, vast numbers of compounds are screened against the target protein to find new potential drugs. The desired outcome of this process is a lead compound that is specific for the target, thereby reducing the incidence of the undesired side effects usually caused by activity at non-intended targets. The lead compound identified in this screening process then undergoes further in vitro and in vivo testing to determine its absorption, disposition, metabolism and toxicological profiles. Typically, this testing involves use of cell lines and animal models with limited, if any, genetic diversity.
What this approach fails to consider, however, is that natural genetic variability exists between individuals in any and every population with respect to pharmaceutically-important proteins, including the protein targets of candidate drugs, the enzymes that metabolize these drugs and the proteins whose activity is modulated by such drug targets. Subtle alteration(s) in the primary nucleotide sequence of a gene encoding a pharmaceutically-important protein may be manifested as significant variation in expression, structure and/or function of the protein. Such alterations may explain the relatively high degree of uncertainty inherent in the treatment of individuals with a drug whose design is based upon a single representative example of the target or enzyme(s) involved in metabolizing the drug. For example, it is well-established that some drugs frequently have lower efficacy in some individuals than others, which means such individuals and their physicians must weigh the possible benefit of a larger dosage against a greater risk of side effects. Also, there is significant variation in how well people metabolize drugs and other exogenous chemicals, resulting in substantial interindividual variation in the toxicity and/or efficacy of such exogenous substances (Evans et al., 1999, Science 286:487-491). This variability in efficacy or toxicity of a drug in genetically-diverse patients makes many drugs ineffective or even dangerous in certain groups of the population, leading to the failure of such drugs in clinical trials or their early withdrawal from the market even though they could be highly beneficial for other groups in the population. This problem significantly increases the time and cost of drug discovery and development, which is a matter of great public concern.
FIG. 1 illustrates a reference sequence for the SLC26A2 gene (Genaissance Reference No. 3758668; contiguous lines), with the start and stop positions of each region of coding sequence indicated with a bracket ([or]) and the numerical position below the sequence and the polymorphic site(s) and polymorphism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymorphic site in the sequence. SEQ ID NO:1 is equivalent to FIG. 1, with the two alternative allelic variants of each polymorphic site indicated by the appropriate nucleotide symbol (R=G or A, Y=T or C, M=A or C, K=G or T, S=G or C, and W=A or T; WIPO standard ST.25). SEQ ID NO:26 is a modified version of SEQ ID NO:1 that shows the context sequence of each polymorphic site, PS1-PS5, in a uniform format to facilitate electronic searching. For each polymorphic site, SEQ ID NO:26 contains a block of 60 bases of the nucleotide sequence encompassing the centrally-located polymorphic site at the 30th position, followed by 60 bases of unspecified sequence to represent that each PS is separated by genomic sequence whose composition is defined elsewhere herein.
FIG. 2 illustrates a reference sequence for the SLC26A2 coding sequence (contiguous lines; SEQ ID NO:2), with the polymorphic site(s) and polymorphism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymorphic site in the sequence.
FIG. 3 illustrates a reference sequence for the SLC26A2 protein (contiguous lines; SEQ ID NO:3), with the variant amino acid(s) caused by the polymorphism(s) of FIG. 2 positioned below the polymorphic site in the sequence.
The present invention is based on the discovery of novel variants of the SLC26A2 gene. As described in more detail below, the inventors herein discovered 5 isogenes of the SLC26A2 gene by characterizing the SLC26A2 gene found in genomic DNAs isolated from an Index Repository that contains immortalized cell lines from one chimpanzee and 93 human individuals. The human individuals included a reference population of 79 unrelated individuals self-identified as belonging to one of four major population groups: Caucasian (21 individuals), African descent (20 individuals), Asian (20 individuals), or Hispanic/Latino (18 individuals). To the extent possible, the members of this reference population were organized into population subgroups by their self-identified ethnogeographic origin as shown in Table 1 below. In addition, the Index Repository contains three unrelated indigenous American Indians (one from each of North, Central and South America), one three-generation Caucasian family (from the CEPH Utah cohort) and one two-generation African-American family. 1 TABLE 1 Population Groups in the Index Repository Population Group Population Subgroup No. of Individuals African descent 20 Sierra Leone 1 Asian 20 Burma 1 China 3 Japan 6 Korea 1 Philippines 5 Vietnam 4 Caucasian 21 British Isles 3 British Isles/Central 4 British Isles/Eastern 1 Central/Eastern 3 Eastern 3 Central/Mediterranean 2 Scandinavian 2 Hispanic/Latino 18 Caribbean 8 Caribbean (Spanish Descent) 2 Central Americazn (Spanish 1 Descent) Mexican American 4 South American (Spanish 3 Descent)
The SLC26A2 isogenes present in the human reference population are defined by haplotypes for 5 polymorphic sites in the SLC26A2 gene, 4 of which are believed to be novel. The SLC26A2 polymorphic sites identified by the inventors are referred to as PS1-PS5 to designate the order in which they are located in the gene (see Table 3 below), with the novel polymorphic sites referred to as PS1, PS2, PS3 and PS5. Using the genotypes identified in the Index Repository for PS1-PS5 and the methodology described in the Examples below, the inventors herein also determined the pair of haplotypes for the SLC26A2 gene present in individual human members of this repository. The human genotypes and haplotypes found in the repository for the SLC26A2 gene include those shown in Tables 4 and 5, respectively. The polymorphism and haplotype data disclosed herein are useful for validating whether SLC26A2 is a suitable target for drugs to treat osteochondrodysplasias, screening for such drugs and reducing bias in clinical trials of such drugs.
In the context of this disclosure, the following terms shall be defined as follows unless otherwise indicated: