WO2002012434A2 - A global electronic medicine response profile testing network - Google Patents
A global electronic medicine response profile testing network Download PDFInfo
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- WO2002012434A2 WO2002012434A2 PCT/GB2001/003624 GB0103624W WO0212434A2 WO 2002012434 A2 WO2002012434 A2 WO 2002012434A2 GB 0103624 W GB0103624 W GB 0103624W WO 0212434 A2 WO0212434 A2 WO 0212434A2
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Definitions
- the present invention relates to the broad field of healthcare management and specifically to an Internet-facilitated method of improving and applying knowledge of how the genetic make-up of a person affects their response to drug therapy.
- Drug discovery and development is changing at a rapid rate.
- Pharmaceutical companies are adopting key enabling technologies learned from genetics and genomics to streamline the target identification and validation process.
- Validated targets are valued from a commercial perspective as early as possible to ensure that medicines are delivered to the market with superior product profiles.
- Pharmaceutical companies recognise the need to continuously work to improve both the efficacy and safety of drug prescribing.
- One activity that can help with drug safety and efficacy is pharmacogenetics, which has gained enormous momentum with recent advances in molecular genetics and output from the Human Genome Project.
- MRP medicine response profile
- the MRP strategy of the present invention is a fundamental change in how patient healthcare management will be delivered, which is therefore not to be limited solely to use of SNPs as the markers of choice for the practice of the invention.
- the foremost object of the present invention is the development of MRP's which test for panels of gene-based markers, such as, but not limited to, SNPs, insertion-deletion polymorphisms or mutations, or gene duplications.
- Another object of the MRP strategy of the present invention is that the concept of MRP testing will be applicable to any type of pharmacogenetic patient testing in the longer term.
- MRP tests which study marker panels derived from DNA, RNA and/or protein either alone or in different combinations.
- Pharmacogenetic testing dictates that the MRP tests must be used in combination with administration of a therapeutic agent since the purpose of the test is to obtain safety or efficacy information prior to administration of the therapeutic.
- MRP testing is a burgeoning concept within the pharmaceutical and biotech industry. Whilst different groups in the pharmaceutical and biotechnology industries are thinking about how best to implement pharmacogenetic testing, no one that we are aware of has proposed a global MRP testing strategy like the one described and claimed in the present invention.
- An additional feature of the present invention is a centralised testing facility, which is cost-effective for both patient and healthcare provider and affords the medical community the critical information resource necessary to make optimal decisions for individualized therapeutic regimes.
- the invention is a method of using biological markers for the development and prescribing of medicines, such method comprising the steps of obtaining a biological sample from a patient; delivering the sample to a centralized analysis and storage facility; genotyping the sample at the facility, electronically providing the genotype analysis back to said patient upon request by said patient or said patient's healthcare provider in order to enable said healthcare provider to form a judgement as to the most appropriate drug to administer to said patient in view of said patient's genotype; contemporaneously electronically providing the genotype analysis to a peer review body for data analysis and then transmitting such analyzed data to a database so as to enable discovery of one or more associations between a given genotype and a given response to a given drug; and optionally contemporaneously electronically providing the reviewed data and/or the discovered associations back to the facility; and contemporaneously electronically providing the reviewed data and/or discovered associations to one or more healthcare providers upon request by a healthcare provider in order to enable said healthcare provider to form a judgement as to the most appropriate drug to administer to a given patient having a genotype that
- biological sample shall mean a sample of any tissue from a person.
- a preferred biological sample is a blood sample
- centralised analysis and storage facility shall mean one or more facilities that are remote from the place that a sample has been gathered. Such a facility uses a standardised, high throughput (rapid) method of biological sample analysis to determine genotype. Such a facility also has adequate computational means to review and validate such data. If there are more than one facility, then they are connected electronically so as to enable electronic transmission of data via the Internet or via another telecommunication network. Additionally, such a facility may have adequate computational means to enable the observation of associations between genotypes and phenotypes.
- the term "contemporaneously” shall mean that an electronic transmission of data is taking place or capable of taking place as soon as the data has been compiled or created as the result of operation of an algorithm, and the data has been made available for electronic transmission, and a request has been made for the retrieval and/or transmission of such data.
- electrostatically providing shall mean the transmission of data via telecommunication means, including telephone data, voice and or fax lines, satellite transmissions, coaxial cable lines, suitable electromagnetic wavelength transmissions and the like.
- genetic shall mean the study of the inheritance of phenotypic traits.
- genetictype shall mean the information that resides in the genetic information (DNA sequences) and any derivative information thereof, such as, but not limited to, RNA, and protein and/or gene-expression regulation factors influenced by environmental factors, such as, but not limited to, food intake, concurrent medication, and stress factors.
- genotyping shall mean the determination of the nucleic acid sequences and/or genes to be found in a biological sample of interest.
- “genotyping a subject (or DNA sample) for a polymorphic allele at a defined genomic locus” or “determining the genotype at a polymorphic allelic site” also means detecting which forms of the allele are present in a subject (or a sample).
- an individual may be heterozygous or homozygous for a particular allele. More than two forms of an allele may exist, as is the case with microsatellite markers; thus there may be more than three possible genotypes.
- genomic shall mean the study of the effects of alteration of nucleic acid sequence upon phenotype.
- healthcare provider shall include, but not be limited to, physicians, nurses, physician assistants, medics, child health associates, nurse practitioners, dentists and pharmacists.
- medical data card shall mean an electronic data storage device with built-in security access designed to provide fast access and/or store an individual's medical records.
- genotype review body shall mean any number of individuals qualified by education, experience and training, to review genetic data for completeness, quality, validity and/or for the observation of associations between incidence of a genotype of interest and a phenotype of interest.
- Phenotype shall mean any given physical, biochemical, or physiological state, status or condition of an individual or population of individuals as determined genetically, up to and including the entire makeup of a given individual or population of individuals. Phenotypes can include the outcome(s) of administration of a given drug to a given individual, including efficacy results and including adverse event results.
- a single biological sample is collected from a patient while that patient is in a healthcare provider's office or clinic. Geographic location of the office or clinic has no effect on the operation of the method, making the method globally applicable. Preferably this is the patient's first visit to the healthcare provider, and more preferably, the patient is asymptotic at that time. Conversely, that specific healthcare provider's office or clinic would collect such samples for MRP testing from all patients that use that clinic, who would consent to providing a sample for MRP. Once a biological sample has been collected and has been stored in a central repository, the MRP testing becomes truly applicable on a world-wide scale and sufficiently fast, provided that an Internet link is available.
- the first sample is collected from a patient while they are asymptotic, this sample may be used later as an individual's reference material for determining the individuals healthy baseline reference value for biochemical markers of disease. Therefore, rather than using the reference value of a population to determine if a biochemical marker of disease is increased or decreased, the individual's own healthy baseline reference value could be used.
- the patient's biological sample would be transported to and stored in a safe repository at a centralised laboratory testing facility.
- Biological components contained within the sample (DNA, RNA, protein, specific cell types and so forth) will be isolated, quality controlled and stored at the repository under strictly regulated conditions.
- the healthcare provider Upon a patient's subsequent visit to a healthcare provider, either for a follow-up consultation or with a specific concern or illness, the healthcare provider would request an MRP on-line for the sample in the central laboratory via an on-line request while the patient is waiting there at the healthcare provider's office or clinic.
- MRP information will only be generated on biological samples for which the corresponding individual has given informed consent.
- the MRP information will only be released from the secured database upon the specific consent of the patient.
- the central facility Once the test has been requested, it will be conducted by the central facility and returned to the healthcare provider/healthcare provider preferentially, ideally within 30 minutes.
- the central testing facility could test all incoming samples for all available MRP profiles and store the results in a secure database ready for access upon the healthcare provider/healthcare provider's request.
- test result can furthermore be stored onto a machine readable medical data card that the patient can then take with them to another healthcare provider for data retrieval in the future.
- the patient's medical data card will be used by all healthcare providers/healthcare providers who treat that patient, thereby collecting information that has been requested by multiple healthcare providers.
- the MRP result data is accessed by the healthcare provider, who is then able to correlate the patient's MRP with what is known about prescribing the most appropriate drug for a given genotype.
- the variation in patient response rate to a drug, or the occurrence of adverse events following administration of a drug to certain patients, is mainly due to variation in individual patient's genetic background (genotypes).
- a drug which is known to have a high response rate with little or no risk of an adverse event for a population of patients having a certain genotype may have a significantly decreased response rate or even show a risk of causing an adverse event in another population of patients who have the same disease but who have a different genotype for the target.
- the healthcare provider can make an informed decision and provide the right drug to the right patient and obtain a favorable therapeutic outcome.
- a key feature of the method of the invention is that the patient would have control over access to the sample. Regardless of where the patient is in the world, they can request an MRP test from any healthcare provider using the patient's medical data card which links into the Internet infrastructure, and which manages MRP testing.
- One potential embodiment of the invention would accomplish this by attaching a unique label, such as for example, a bar code or hologram to the initial biological sample (for instance a blood sample), that would correlate to a bar code on the patient's medical data card.
- the patient's medical data card would be needed for the healthcare provider to access the stored data, which the patient would hand over to the healthcare provider for that limited purpose.
- an added level of security can be put in place such that the healthcare provider has to enter a second card into a reader to enable an information update to be made to the patient's record or to request the MRP test.
- a patient could control access to the data, and likewise enable any healthcare provider at any place in the world at any time to access the data on behalf of the patient.
- the card could be used to track the amount of biological sample available for testing, initiating a sample request when the amount of stored biological sample is below a logistical threshold. Any biological sample taken for MRP testing should not be used for any other genetic testing purposes other than for the ones for which consent was given when the sample was obtained.
- biological samples can be collected and acquired from any geographical location throughout the world. All samples will be collated at a few Centralised sites connected via the Internet to their regional locations. Biological sample and data storage would take place at one or more centralized storage facilities. The facilities would be connected electronically via the Internet using an inspected and authorized service provider. Via the Internet, the facilities would receive data from outlying healthcare provider offices or clinics, transmit data to the offices and clinics (when so authorized by the patient by means of their medical data card), transmit data to other storage facilities, and transmit data to one or more pharmaceutical companies for drug discovery and development purposes (if such data had been anonymised after informed consent of the patient made it permissible to do so)
- a consortium of pharmaceutical companies is organized to create a global, centralized repository of biological data that is maintained and updated by data downloads from all consortium members, and that is conversely available for (anonymised) data retrieval by all consortia members for the purposes of drug discovery and development, and for the purpose of healthcare management.
- Other potential consortia members can include regulators, patient advocacy groups, and insurers and diagnostics manufacturers.
- the global network of central laboratory facilities will ensure that legal and ethical standards are maintained, will promote sample security and will reduce the risk for misuse of patient information.
- Using a consortium will streamline reimbursement for payers and alleviate the need for profit margins on the manufacture and sale of diagnostic kits.
- Such data enable researchers to locate disease susceptibility genes, locate targets for drug intervention in disease processes, and accumulate enough data to discover associations between certain genotypes and diseases, or between certain genotypes and responses to drugs.
- Each of these key drug discovery activities would be much more rapidly enabled by the invention, since an enormous global pool of diverse patient populations would be transferring MRP test data to the data storage centers, which would be analyzing the data on a real-time basis to generate genotype-phenotype associations, making the data and the analyses available in real time to drug researchers, and. subsequently making the association knowledge available in real time back to healthcare providers to complete the loop.
- the proposed MRP -testing procedure will allow the collection of information about patients' phenotype and drug response. This information could, after peer review, be made available to all healthcare providers to improve and facilitate their decision making for therapeutic intervention and effective disease management.
- the proposed MRP-testing procedure would allow adverse event recording post-marketing of a new drug on a significant scale. Should adverse events be picked up, once a therapeutic has come onto the market, a reference database analyzing existing patient's data, including adverse event reporting would help to identify the seriousness of the problem. Prompt identification of adverse events and peer review of the severity of the effect will help to determine the best course of action. The best action may be, but is not limited to, a simple label change or drug reformulation or renewed market positioning. At its most extreme, an adverse event may dictate that the best course of action is removal of a drug from the market.
- An additional object of the present invention would be to enable new standards of regulatory agency approval for new human drugs that would require submission of data which may tend to identify patients as responders, non-responders or likely sufferers of adverse events, where such data was obtained through practice of the invention as claimed. Again, reducing costs of clinical trials provides the incentive for drug companies to develop drugs with a smaller market potential but for which there is a significant unmet medical need or need for improved likelihood of compliance.
- the method of the invention should use a testing technology that will: take thirty minutes or less or be available in real time on a database; require minimal sampling from the patient; enable availability of the test results to the patient and healthcare provider while the patient is still in the same consultation visit with the healthcare provider; and comply with all applicable international standards and regulations on the storage and testing of samples.
- MRP testing data is to be continually collected, accessed and assessed via a centralized testing facility. Communications to and from distant locations and computers will be to the centralized testing facility by means of the International Network of Computers (the Internet).
- Internet communications software, data management software, database software, bioinformatic software, clinical modeling software are all needed for the method of the invention, and are all readily commercially available. Such availability and applicability, and the operation of such software are all well known to those of ordinary skill in the fields of clinical management, telecommunications, information systems, and management of clinical trials of experimental human drugs.
- the test is ordered in real time from the healthcare provider's computer, and the cost of the MRP test is included in the price of the pharmaceutical and is not billed separately to the patient.
- IBS Irritable Bowel Syndrome
- IBS Irritable Bowel Syndrome
- Antagonism at 5-hydroxytryptamine receptors has been shown to be useful in the treatment of diarrhoea-predominant irritable bowel syndrome.
- Alosetron hydrochloride (CAS registry number: CAS-122852-69-1; see US Patent No. 5,360,800, the entire disclosure of which is incorporated herein by reference) is a 5-HT3 receptor antagonist. Both animal and human studies indicate that 5-HT3 receptor blockade has therapeutic value in the treatment of irritable bowel syndrome, particularly in diarrhea-predominant IBS. (The disclosures of all US patents cited herein are incorporated herein by reference in their entirety.)
- alosetron hydrochloride has been shown to reduce pain and improve bowel function in patients with Irritable Bowel Syndrome (IBS). See Bardhan et al., Aliment Pharmacol Ther 2000 Jan; 14(1): 23-34; Jones et al, Aliment Pharmacol Ther 1999 Nov; 13(11): 1419-27; Camilleri et al., Aliment Pharmacol Ther 1999 Sep; 13(9): 1149-59; Mangel et al, Aliment Pharmacol Ther 1999 May; 13 Suppl 2:77-82. Alosetron has further been indicated as a potential treatment for the symptomatic relief of carcinoid diarrhea. Saslow et al., Gut 1998 May; 42(5): 628- 34.
- 5-hydroxytryptamine (5HT) receptors have been identified and characterized in the gastrointestinal tract, including 5HT3, 5HT4, and 5HTla receptors; these receptors are involved not only in modulating gut motility but also in visceral sensory pathways.
- 5HT3 antagonists e.g., alosetron, granisetron and ondansetron
- Full and partial 5HT4 agonists e.g., HTF919, tegaserod
- these agents may have therapeutic potential in IBS.
- the human 5HTT protein is encoded by a single gene (SLC6A4) found on chromosome 17ql2 (Ramamoorthy et al, Proc. Natl. Acad. Sci. USA 90:2542 (1993); Geemperter et al, Hum. Genet. 95:677 (1995); Lesch et al, J. Neural Transm. 91 :67 (1993).
- the 5HT Transporter regulates the magnitude and duration of serotonergic responses.
- An insertion/deletion polymorphism consisting of a 44 base pair segment in the transcriptional control region 5' upstream to the 5HTT coding sequence has previously been identified.
- deletion (or short) allele of this polymorphism is associated with decreased transcription efficiency of the 5HTT gene promoter, decreased gene expression, and decreased 5-hydroxytryptamine uptake.
- polymorphisms in the 5-hydroxytryptamine transporter (5HTT) gene are correlated with the response of subjects with IBS to pharmaceutical therapy More particularly, it was found that an insertion/deletion polymorphism in the 5' non-coding region of the 5HTT gene is a predictor for the response of patients with IBS to treatment with a 5HT antagonist; and there was identified a genetic subset of IBS patients that displays a higher incidence of relief of IBS symptoms and a lower incidence of the side effect of constipation when treated with alosetron (compared to patients with an alternative polymorphism at the same site of the 5HTT gene).
- a further aspect is a method of screening a subject suffering from a gastrointestinal disease that is treatable with a 5-hydroxytryptamine (5HT) ligand, as an aid in predicting the subject's response to treatment with a 5HT ligand.
- the method comprises obtaining a sample of the subject's DNA and determining the genotype of the subject at a polymorphic allelic site in the 5hydroxytryptamine transporter (5HTT) gene, where different genotypes at that site have been associated with different incidences of a phenotypic response to treatment with a 5HT ligand.
- the genotype that is detected in the sample indicates that the subject is likely to have the phenotypic response associated with that genotype.
- Another aspect is a method of screening a subject with irritable bowel syndrome (IBS), as an aid in predicting the subject's response to treatment with a 5HT ligand.
- the method comprises obtaining a sample of the subject's DNA and determining the genotype of the subject at a polymorphic allelic site in the 5hydroxytryptamine transporter (5HTT) gene, where different genotypes at that site have been associated with different incidences of a phenotypic response to treatment with a 5HT ligand.
- 5HTT 5hydroxytryptamine transporter
- a further aspect is a method of screening a 5-hydroxytryptamine (5HT) ligand for variations in a measurable phenotypic effects among genetic subpopulations of subjects with a gastrointestinal disorder.
- the method comprises administering the 5HT ligand to a population of subjects suffering from the gastrointestinal disorder, and obtaining DNA samples from each of the subjects.
- the DNA samples are genotyped for a polymorphic allele of the 5-hydroxytryptamine transporter (5HTT) gene, and correlations between the polymorphic allele genotype and the occurrence of a phenotypic response in the population of subjects are determined.
- 5HTT 5-hydroxytryptamine transporter
- Detection of a genotype that is correlated with an increased or decreased incidence of a desired therapeutic response or a side effect indicates that the effectiveness of the ligand in treating that gastrointestinal disorder varies among genetic subpopulations.
- the genetic samples were obtained from subjects enrolled in clinical trials of alosetron for the treatment of IBS. The genetic samples were screened for an insertion/deletion polymorphism in the 5' non-coding region of the 5-hydroxytryptamine transporter gene (5HTT gene), using polymerase chain reaction (PCR) technology. The alleles were labeled as "del” (deletion) or "ins” (insertion) resulting in three possible genotypes (del/del; del/ins or ins/ins). The insertion polymorphism (allele "ins”) had SEQ ID NO:2:
- TSfon-coding sequences are shown in lowercase typeface Polymorphic bases are shown in bold typeface Base numbering is relative to the sequence shown Polymorphism numbering is relative to the gene cDNA sequences
- the "del" allele represents a deletion of approximately 44 base pairs in the 5' untranslated region of the 5HTT gene. This deletion in the transcriptional regulatory region has been associated with decreased re-uptake of 5HT and therefore an increased 5HT basal level. Therefore, the del/del genotype is postulated to result in a lower transcription efficiency, lower production of 5HTT, and reduced basal 5HT re-uptake (compared to the del/ins or ins/ins genotype).
- del/del, del/ins and ins/ins genotypes were approximately evenly distributed among the subjects. Of 219 subjects, 71 were del/del 5HTT; 75 were del/ins 5HTT; and 73 were ins/ins 5HTT.
- the del/del genotype is associated with an increased incidence of relief of IBS symptoms and a lower frequency of constipation as an effect of treatment with a 5HT3 antagonist, and therefore an increased incidence of favorable therapeutic response to treatment with a 5HT3 antagonist (compared to subjects with the del/ins or ins/ins genotype treated with the same 5HT3 antagonist).
- alosetron was more effective than placebo in relieving IBS symptoms.
- the incidence of relief of IBS symptoms for both alosetron and placebo was increased compared to other 5HTT genotypes.
- Subjects with the del/del genotype also showed a reduced incidence of constipation compared to the del/ins and ins/ins 5HTT genotype groups.
- Subjects with the del/del 5HTT genotype showed an increased incidence of favourable therapeutic response with a higher incidence of relief of IBS symptoms and a lower incidence of the alosetron-induced side effect of constipation, when compared with subjects who had del/ins or ins/ins 5HTT genotypes.
- a subject who suffers from a gastrointestinal disease that is treatable with 5HT ligands can be genetically screened, to aid in predicting their response to such treatment.
- Screening comprises obtaining a sample of DNA from the subject and screening the DNA to determine the genotype (presence/absence of polymorphic alleles) at a predetermined polymorphic site in the 5hydroxytryptamine transporter (5HTT) gene, where different genotypes at that site have previously been associated with different incidences of a phenotypic response to treatment with a 5HT ligand.
- the presence of a particular genotype therefore indicates an increased likelihood that the individual subject will exhibit the associated phenotype.
- genotyping a subject as described herein will be an aid in predicting the response a subject will have to treatment with a 5HT ligand, and thus assist in the treatment decision.
- genotyping a subject (or DNA sample) for a polymorphic allele at a defined genomic locus or "determining the genotype at a polymorphic allelic site,” means detecting which forms of the allele are present in a subject (or a sample).
- an individual may be heterozygous or homozygous for a particular allele. More than two forms of an allele may exist, as is the case with microsatellite markers; thus there may be more than three possible genotypes.
- a subject that is "predisposed to" a particular phenotypic response based on genotyping of a polymorphic allele will be more likely to display that phenotype than an individual with a different genotype at that polymorphic allele.
- the phenotypic response is based on a biallelic polymorphism, the response may differ among the three possible genotypes (Eg. For 5HTT: del/del, del/ins and ins/ins).
- a "genetic subset" of a population consists of those members of the population having a particular genotype.
- a population can potentially be divided into three subsets: homozygous for allele 1, heterozygous, and homozygous for allele 2.
- a gastrointestinal disease 'treatable with 5HT ligands' is one in which the administration of a 5HT ligand (in an appropriate pharmaceutical formulation, and in a therapeutically effective amount) has been shown to reduce or alleviate symptoms, without causing unacceptable side effects.
- Regulatory Authority e.g. FDA, EMEA
- Therapeutically effective amounts of such compounds can be readily determined by those skilled in the art using, e.g., dose-response studies.
- ⁇ 5HT ligand' encompasses antagonists and agonists of 5HT receptors, including partial agonists and drugs that interact with 5HTT (e.g. selective serotonin re-uptake inhibitors, SSRTs).
- 5HT ligands may bind to any subtype of the 5HT receptor, including 5HT3 and 5HT4 receptors; the ligands rriay be specific for a particular receptor subtype.
- 5HT-related compounds include 5HT3 antagonists (e.g., ondansetron, granisetron, tropisetron, dolasetron, mirtazapine, itasetron, pancopride, zatosetron, azasetron, cliansetron, YM-144 (Yamanouchi) and RSI 7017 (Roche)).
- 5HT3 antagonists e.g., ondansetron, granisetron, tropisetron, dolasetron, mirtazapine, itasetron, pancopride, zatosetron, azasetron, cliansetron, YM-144 (Yamanouchi) and RSI 7017 (Roche)
- 5HT4 agonists are also known, including tegaserod, prucalopride, norcisapride and the 4- amino-5-chloro-2-methoxy-N- (1 -substituted piperidin-4-yl) benzamide known as Y- 34959 (Yoshitomi Pharmaceuticals), and buspirone.
- 5HT4 antagonists include piboserod (SmithKline Beecham).
- Dual 5HT3 and 5HT4 agonists include renzapride (SmithKline Beecham) and E3620 (Eisai).
- a 5HTla agonist is also known, LY315535 (Eli Lilly).
- Selective serotonin re-uptake inhibitors include fluoxetine, etc.
- a side effect is an undesirable response to the administration of a therapeutic compound, i.e., and an effect that is not directed to alleviating the symptoms or cause of the disease being treated. Side effects range from minor inconveniences to more serious events.
- a compound with 5HT-ligand activity may be screened for variation in its effects among genetic subpopulations of subjects with a gastrointestinal disorder.
- Such methods involve administering the compound to a population of subjects suffering from a 5HT-mediated gastrointestinal disorder, obtaining DNA samples from the subjects (which may be done either prior to or after administration of the compound), genotyping a polymorphic allelic site in the 5HTT gene, and correlating the genotype of the subjects with their phenotypic responses (both favorable and unfavorable) to the treatment.
- the method may be used to determine the correlation of a known 5HTT polymorphic allele with the response of subjects with gastrointestinal disorders (such as IBS) to treatment with a 5HT ligand.
- the population of subjects with the disease of interest is stratified according to genotype for the particular polymorphic allele, and their response to a therapeutic agent is assessed (either prospectively or retrospectively) and compared among the genotypes.
- the response to the therapeutic agent may include either, or both, desired therapeutic responses (e.g., the alleviation of signs or symptoms) and undesirable side effects.
- desired therapeutic responses e.g., the alleviation of signs or symptoms
- undesirable side effects may be identified.
- a non-responder will be a subject displaying a defined degree of decreased incidence of therapeutic efficacy, possibly displaying no therapeutic efficacy at all.
- a non-responder can be categorized as a subject displaying a defined degree of increased incidence of a side effect of interest, ranging from relatively benign side effects to those that are potentially life-threatening.
- Polymorphisms are variant sequences within the human genome that may or may not have a functional consequence. These variants can be used in all aspects of genetic investigation including the analysis and diagnosis of genetic disease, forensics, evolutionary and population studies. Two types of genetic analyses are typically performed: linkage and association studies.
- a linkage study provides genetic map information where there is no prior knowledge or assumption about the function of a gene.
- a linkage study one uses DNA polymorphisms to identify chromosomal regions that are identical between affected relatives with the expectation that allele sharing frequencies will be higher for a marker (polymorphism) whose chromosomal location is close to that of the disease allele.
- Physical cloning of a linkage region narrows down the DNA sequence that could harbor the candidate disease gene. While linkage analysis locates the disease locus to a specific chromosome or chromosome region, the region of DNA in which to search for the gene is typically large, on the order of several million base pairs.
- association shows the coexistence of a polymorphism and a disease phenotype in a population.
- association studies are based upon linkage disequilibrium, a phenomenon that occurs between a marker and a disease phenotype if the marker polymorphism is situated in close proximity to the functional (disease)-causing causing variant. Since the marker and disease-causing variant are in close proximity, it requires many generations of recombination to separate them in a population. Thus they tend to co-exist together on the same chromosome at a higher than expected frequency.
- a marker (polymorphism) is said to be associated with a specific phenotype when its frequency is significantly higher among one phenotype group compared to its frequency in another. In general, the closer a marker is to the functionally polymorphic site, the stronger the association.
- Polymorphisms that are in linkage disequilibrium with each other can be spaced over large regions. Linkage disequilibrium has been reported in regions as small as lkb or as large as 500 kb. Polymorphisms throughout a gene can be in linkage disequilibrium with each other, such that it is valuable to study the whole genome structure - introns, exons, promoters and transcriptional regulatory regions, and 3' and 5' untranslated regions.
- a marker that is in linkage disequilibrium with a functional polymorphism can be used as the basis of a test that correlates that polymorphism with a phenotype of interest.
- a polymorphism in the 5HTT gene plays a role in the response of subjects to pharmaceutical treatment of IBS, and thus the genotyping of the 5HT Transporter (5HTT) gene (either directly or via its expression product) is useful in identifying therapeutic compounds with measurable effects that vary among 5HTT genotypes.
- the effect to be measured will depend on the particular gastrointestinal condition, therapeutic compound, and patient population, as will be apparent to one skilled in the art.
- the measurable effect may be the relief of, or change in, a pathologic sign or symptom or the occurrence of a side effect related to compound administration. Measurement may be objective or subjective (e.g., by patient self-reporting).
- the association of a 5HTT genotype with a therapeutic response will provide a method of determining the probability that an individual subject will respond in a particular way to treatment with 5HT ligands.
- the characteristic that is typically measured is one that can be influenced by a polymorphism in the gene or its expression product.
- polymorphism includes Single Nucleotide Polymorphisms (SNPs), insertion/deletion polymorphisms; microsatellite polymorphisms; and variable number of tandem repeat (VNTR) polymorphisms.
- Polymorphic alleles are typically detected by directly determining the presence of the polymorphic sequence in a polynucleotide or protein from the subject, using any suitable technique that is known to those of ordinary skill in the art.
- a polynucleotide is typically genomic DNA, or a polynucleotide derived from this polynucleotide, such as in a library made using genomic material from the individual (e.g. a cDNA library).
- genomic DNA or a polynucleotide derived from this polynucleotide, such as in a library made using genomic material from the individual (e.g. a cDNA library).
- the presence of the polymorphism is determined in a method that comprises contacting a polynucleotide or protein of the individual with a specific binding agent for the polymorphism and determining whether the agent binds to the polynucleotide or protein, where the binding indicates that the polymorphism is present.
- the binding agent may also bind to flanking nucleotides and amino acids on one or both sides of the polymorphism, for example at least 2, 5, 10, 15 or more flanking nucleotide or amino acids in total or on each side.
- the agent is able to bind the corresponding wild-type sequence by binding the nucleotides or amino acids which flank the polymorphism position, although the manner of binding will be different than the binding of a polymorphic polynucleotide or protein, and this difference will be detectable (for example this may occur in sequence specific PCR as discussed below).
- the presence of the polymorphism is being determined in a polynucleotide it may be detected in the double stranded form, but is typically detected in the single stranded form.
- the binding agent may be a polynucleotide (single or double stranded) typically with a length of at least 10 nucleotides, for example at least 15, 20, 30, or more polynucleotides.
- the agent may be a molecule that is structurally similar polynucleotides, comprising units (such as purines or pyrimidines) that are able to participate in Watson-Crick base pairing.
- the agent may be a protein, typically with a length of at least 10 amino acids, such as at least 20, 30, 50, 100 amino acids.
- the agent may be an antibody (including a fragment of such an antibody that is capable of binding the polymorphism).
- a polynucleotide agent which is used in the method will generally bind to the polymorphism of interest, and the flanking sequence, in a sequence specific manner (e.g. hybridize in accordance with Watson-Crick base pairing) and thus typically has a sequence which is fully or partially complementary to the sequence of the polymorphism and flanking region.
- a binding agent is used as a probe.
- the probe may be labeled or may be capable of being labeled indirectly.
- the detection of the label may be used to detect the presence of the probe on (and hence bound to) the polynucleotide or protein of the individual.
- the binding of the probe to the polynucleotide or protein may be used to immobilize either the probe or the polynucleotide or protein (and thus to separate it from one composition or solution).
- the polynucleotide or protein of the individual is immobilized on a solid support and then contacted with the probe.
- the presence of the probe immobilized to the solid support (via its binding to the polymorphism) is then detected, either directly by detecting a label on the probe or indirectly by contacting the probe with a moiety that binds the probe.
- the solid support is generally made of nitrocellulose or nylon.
- the method may be based on an ELIS A system, the techniques of which are well known to those of ordinary skill in the art.
- Detection methods may be based on an oligonucleotide ligation assay in which two oligonucleotide probes are used. These probes bind to adjacent areas on the polynucleotide which contains the polymorphism, allowing (after binding) the two probes to be ligated together by an appropriate ligase enzyme. However the two probes will only bind (in a manner which allows ligation) to a polynucleotide that contains the polymorphism, and therefore the detection of the ligated product may be used to determine the presence of the polymorphism.
- the probe is used in a heteroduplex analysis-based system to detect polymorphisms.
- a heteroduplex structure can be detected by the use of an enzyme that is single or double strand specific.
- the probe is an RNA probe and the enzyme used is RNAse H that cleaves the heteroduplex region, thus allowing the polymorphism to be detected by means of the detection of the cleavage products.
- a detection method may be based on fluorescent chemical cleavage mismatch analysis which is described for example in PCR Methods and Applications 3:268-71 (1994) and Proc. Natl. Acad. Sci. 85:4397-4401 (1998).
- the polynucleotide agent is able to act as a primer for a PCR reaction only if it binds a polynucleotide containing the polymorphism (i.e. a sequence- or allele- specific PCR system). Hence a PCR product will only be produced if the polymorphism is present in the polynucleotide of the individual. Thus the presence of the polymorphism may be determined by the detection of the PCR product.
- the region of the primer which is complementary to the polymorphism is at or near the 3 ' end the primer.
- the polynucleotide agent will bind to the wild-type sequence but will not act as a primer for a PCR reaction.
- Detection may be via a Restriction Fragment Length Polymorphism (RFLP) based system.
- RFLP Restriction Fragment Length Polymorphism
- This can be used if the presence of the polymorphism in the polynucleotide creates or destroys a restriction site that is recognized by a restriction enzyme.
- treatment of a polynucleotide with such a polymorphism will lead to different products being produced compared to the corresponding wild-type sequence.
- the detection of the presence of particular restriction digest products can be used to determine the presence of the polymorphism.
- the presence of the polymorphism may alternatively be determined based on the change that the presence of the polymorphism makes to the mobility of the polynucleotide or protein during gel electrophoresis.
- SSCP polynucleotide single-stranded conformation polymorphism
- DGGE Denaturing gradient gel electrophoresis
- the presence of the polymorphism may be determined using a fluorescent dye and quenching agent-based PCR assay such as the Taqman PCR detection system.
- this assay uses an allele specific primer comprising the sequence around, and including, the polymorphism.
- the specific primer is labeled with a fluorescent dye at its 5' end, a quenching agent at its 3' end and a 3' phosphate group preventing the addition of nucleotides to it. Normally the fluorescence of the dye is quenched by the quenching agent present in the same primer.
- the allele specific primer is used in conjunction with a second primer capable of hybridizing to either allele 5' of the polymorphism.
- Taq DNA polymerase adds nucleotides to the nonspecific primer until it reaches the specific primer. It then releases polynucleotides, the fluorescent dye and quenching agent from the specific primer through its endonuclease activity. The fluorescent dye is therefore no longer in proximity to the quenching agent and fluoresces.
- the mismatch between the specific primer and template inhibits the endonuclease activity of Taq and the fluorescent dye in not released from the quenching agent. Therefore by measuring the fluorescence emitted the presence or absence of the polymorphism can be determined.
- a polynucleotide comprising the polymorphic region is sequenced across the region, which contains the polymorphism to determine the presence of the polymorphism.
- Hybridization based solid phase hybridization (dot blots, MASDA, reverse dot blots, oligonucleotide arrays (chips)); solution phase hybridization (Taqman, Molecular Beacons);
- a method for screening a subject diagnosed with IBS or another gastrointestinal disorder treatable by 5HT ligands, to determine the likelihood they will respond in a particular way to treatment with a 5HT ligand, more particularly a 5HT3 antagonist, and more particularly alosetron.
- Subjects are mammalian, and preferably humans.
- the method comprises screening the subject for a polymorphism in the 5HTT gene that has previously been associated with a high or low incidence of a particular desirable therapeutic outcome (compared to the incidence in subjects with other genotypes), or associated with a high or low incidence of an undesired side effect (compared to the incidence in subjects with other genotypes), and then classifying the subject as a responder, a partial responder or a non-responder.
- Treatment of a subject with a 5HT ligand comprises administration of an effective amount of the pharmaceutical agent to a subject in need thereof.
- the dose of agent is determined according to methods known and accepted in the pharmaceutical arts, and can be determined by those skilled in the art.
- a suitable dosage range and plasma concentration for alosetron are provided in the disclosure of US Patent Number 5,360,800, the entire disclosure of which is hereby incorporated herein by reference.
- Example 2 Assay of insertion/deletion polymorphism in 5HTT gene
- the insertion/deletion marker was in the 5' untranslated region of the 5HTT gene.
- the deletion polymorphism (allele "del”) had SEQ ID NO: 1; the insertion polymorphism (allele “ins”) had SEQ ID NO: 2 (insertion shown in bold typeface):
- the deleted segment comprised nucleotides 161- 204 of SEQ ID NO: 2.
- PCR primer sequences are in underlined typeface.
- the present 5HTT genotypes were approximately evenly distributed. Of the 219 subjects genotyped for the 5HTT marker, 71 (32.4%) were del/del 5HTT, 75 (34.2%) were del/ins 5HTT and 73 (33.3%) were ins/ins 5HTT.
- the "del” allele represents a deletion of approximately 44 base pairs in the 5' untranslated region of the 5HTT gene.
- the del/del genotype results in a lower transcription efficiency, lower production of 5HTT, and reduced basal 5HT re-uptake (compared to the del/ins or ins/ins genotype).
- the response of subjects to treatment with alosetron in the clinical trial was stratified according to genotype.
- del/del 5HTT genotype showed an increased incidence of favourable therapeutic response, with higher incidence of relief of IBS symptoms and lower incidence of constipation, when compared with subjects with del/ins and ins/ins 5HTT genotypes.
- the del/del 5HTT genotype can thus be considered as a responder group, leaving the del/ins and ins/ins 5HTT genotype groups being considered as qualified responders or non-responders.
- DNA samples are obtained from a population of subjects with gastrointestinal disease, and genomic DNA is extracted using standard procedures (automated extraction or using kit formats). The genotypes of the subjects, and any control individuals utilized, are determined for polymorphisms within the 5HTT gene sequence, using either PCR, PCR- RFLP, Taqman allelic discrimination assays, or any other suitable technique as is known in the art.
- a simple size discrimination assay can be employed to determine the genotype of an individual.
- two primers are employed to specifically amplify the gene of interest in a region surrounding the site of the polymorphism.
- PCR amplification is carried out, generating products, which differ in length, dependent on the genotype (insertion or deletion) they possess.
- the differently sized products are separated, visualized, and the specific genotypes interpreted directly.
- PCR-RFLP polymerase chain reaction - restriction fragment length polymorphism
- a PCR-RFLP assay employs two gene-specific primers to anneal to, and specifically amplify a segment of genomic DNA surrounding the polymorphic site of interest.
- specific restriction endonuclease enzymes are employed to digest the PCR products produced.
- the enzyme utilized for an assay is selected due to its specific recognition sequence, which it requires to bind to, and cleave the PCR product in the presence/absence of the polymorphism, yielding fragments diagnostic of the specific base present at the polymorphic site.
- gel electrophoresis is employed to separate and visualize the fragments produced.
- Taqman assays may also be utilized to identify polymorphisms.
- the allelic discrimination assay uses two allele specific probes labeled with a different fluorescent dye at their 5' ends but with a common quenching agent at their 3' ends. Both probes have a 3' phosphate group so that Taq polymerase cannot add nucleotides to them.
- the allele specific probes comprising the sequence encompassing the polymorphic site and will differ only in the sequence at this site (this is not necessarily true, the allele-specific probes can be shifted relative to each other such that they are not identical in length or composition. However, where they cover the same DNA region they are identical apart from the polymorphic site of interest).
- the allele specific probes are only capable of hybridizing without mismatches to the appropriate site.
- the allele specific probes are used in conjunction with two primers, one of which hybridizes to the template 5' of the two specific probes, whilst the other hybridizes to the template 3' of the two probes. If the allele corresponding to one of the specific probes is present, the specific probe will hybridize perfectly to the template.
- the Taq polymerase extending the 5' primer, will then remove the nucleotides from the specific probe, releasing both the fluorescent dye and the quenching agent. This will result in an increase in the fluorescence from the dye no longer in close proximity to the quenching agent.
- the mismatch at the polymorphic site will inhibit the 5' to 3' endonuclease activity of Taq and hence prevent release of the fluorescent dye.
- the ABI7700 sequence detection system is used to measure the increase in the fluorescence from each specific dye at the end of the thermal cycling PCR directly in PCR reaction tubes. The information from the reactions is then analyzed. If an individual is homozygous for a particular allele only fluorescence corresponding to the dye from that specific probe will be released, but if the individual is heterozygous, then both dyes will fluoresce.
- the genotypes of the individuals can then be correlated with their phenotypic response to treatment with a 5HT ligand. Responses that vary among the genetic subpopulations are identified as either responders, partial responders or non-responders. Once the non- responder population has been identified, it is assumed that a different genotype is present in that population, which is expressing one or more different proteins that comprise a different biochemical pathway that is the underlying cause of the disease as it is seen in the clinic. Hence the non-responder population becomes the focus of a subsequent clinical trial, in which a drug candidate is administered that has been shown to interact with one or more targets thought to be part of the disease pathway in this population that did not respond to the drug administered in the first trial.
- the second trial demonstrates that the second drug candidate elicits a favorable response in the entire population that did not respond to the drug candidate in the first drug trial, then it is apparent that the entire population of patients that started the trials in the first place are now the beneficiaries of safe and effective drug treatments for that clinical definition of disease. It is believed that in many cases, there will be more then two iterations of such clinical trials, reflecting that there are a like number of alternative genotypes that manifest that clinical definition of disease. For example, there may be as many as six distinct genotypes that manifest the disease classified as non-insulin dependant diabetes mellitus.
- any number of iterations of clinical trials can be run, centered around the method of the invention, that is, that in any given iteration that produces a population of non-responders, the population of non-responders represents a whole new group of patients that likely have a different genotype that is treatable by a drug that is different from the drug tested in the previous iteration of clinical trial.
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