US 2001.0034O23A1. (19) United States (12) Patent Application Publication (10) Pub. No.: US 2001/0034023 A1 Stanton, JR. et al. (43) Pub. Date: Oct. 25, 2001 (54) GENE SEQUENCE VARIATIONS WITH Related U.S. Application Data UTILITY IN DETERMINING THE (63) Continuation-in-part of application No. 09/710,467, TREATMENT OF DISEASE, INGENES filed on Nov. 8, 2000, which is a continuation-in-part RELATING TO DRUG PROCESSING of application No. 09/696,482, filed on Oct. 24, 2000. Non-provisional of provisional application No. 60/131,334, filed on Apr. 26, 1999. Non-provisional (76) Inventors: Vincent P. Stanton JR., Belmont, MA of provisional application No. 60/139,440, filed on (US); Martin Zillmann, Shrewsbury, Jun. 15, 1999. MA (US) (30) Foreign Application Priority Data Correspondence Address: Jan. 20, 2000 (WO)........................... PCT/USOO/O1392 EDWARD O. KRUESSER BROBECK PHLEGER & HARRISON Publication Classification 12390 EL CAMINO REAL (51) Int. Cl. ............................. C12O 1/68; G06F 19/00 SAN DIEGO, CA 92130 (US) (52) U.S. Cl. ................................................... 435/6; 702/20 (57) ABSTRACT (21) Appl. No.: 09/733,000 Methods for identifying and utilizing variances in genes relating to efficacy and Safety of medical therapy and other aspects of medical therapy are described, including methods (22) Filed: Dec. 7, 2000 for Selecting an effective treatment. US 2001/0034023 A1 Oct. 25, 2001 GENE SEQUENCE WARIATIONS WITH UTILITY 0005 For some drugs, over 90% of the measurable IN DETERMINING THE TREATMENT OF interSubject variation in Selected pharmacokinetic param DISEASE, INGENES RELATING TO DRUG eters has been shown to be heritable. For a limited number PROCESSING of drugs, DNA sequence variances have been identified in Specific genes that are involved in drug action or metabo RELATED APPLICATIONS lism, and these variances have been shown to account for the 0001. This application is a continuation-in-part of Stan variable efficacy or safety of the drugs in different individu ton et al., U.S. application Ser. No. 09/710,467, filed Nov. 8, als. AS the Sequence of the human genome is completed, and 2000 entitled GENE SEQUENCE VARIATIONS WITH as additional human gene Sequence variances are identified, UTILITY IN DETERMINING THE TREATMENT OF the power of genetic methods for predicting drug response DISEASE, IN GENES RELATING TO DRUG PROCESS will further increase. This application concerns methods for ING, which is a continuation-in-part of Stanton et al., U.S. identifying and exploiting gene Sequence variances that application Ser. No. 09/696,482, filed Oct. 24, 2000 entitled account for interpatient variation in drug response, particu GENE SEQUENCE VARIATIONS WITH UTILITY IN larly interpatient variation attributable to pharmacokinetic DETERMINING THE TREATMENT OF DISEASE, IN factors and interpatient variation in drug tolerability or GENES RELATING TO DRUG PROCESSING, which is a toxicity. continuation-in-part of U.S. application Ser. No. not yet 0006 The efficacy of a drug is a function of both phar assigned, Attorney Docket No. 030586.0009CIP4, filed Oct. macodynamic effects and pharmacokinetic effects, or bio 6, 2000 entitled GENE SEQUENCE VARIATIONS WITH availability. In the present invention, interpatient variability UTILITY IN DETERMINING THE TREATMENT OF in drug Safety, tolerability and efficacy are discussed in terms DISEASE, IN GENES RELATING TO DRUG PROCESS of the genetic determinants of interpatient variation in ING, which is a continuation-in-part of Stanton et al., U.S. absorption, distribution, metabolism, and excretion, i.e. application Ser. No. 09/639,474, filed Aug. 15, 2000 GENE pharmacokinetic parameters. SEQUENCE VARIATIONS WITH UTILITY IN DETER MINING THE TREATMENT OF DISEASE, IN GENES 0007 Adverse drug reactions are a principal cause of the RELATING TO DRUG PROCESSING, which is a continu low Success rate of drug development programs (less than ation in part of Stanton et al., U.S. application Ser. No. one in four compounds that enters human clinical testing is 09/590,783, filed Jun. 8, 2000 GENE SEQUENCE VARIA ultimately approved for use by the U.S. Food and Drug TIONS WITH UTILITY IN DETERMINING THE TREAT Administration (FDA)). Adverse drug reactions can be cat MENT OF DISEASE, IN GENES RELATING TO DRUG egorized as 1) mechanism based reactions and 2) idiosyn PROCESSING, which is a continuation-in-part of Stanton, cratic, “unpredictable' effects apparently unrelated to the U.S. application Ser. No. 09/501.955, filed Feb. 10, 2000, primary pharmacologic action of the compound. Although which is a continuation-in-part of Stanton, International Some side effects appear Shortly after administration, in Application Ser. No. PCT/US00/01392, filed Jan. 20, 2000, Some instances Side effects appear only after a latent period. Stanton, U.S. application Ser. No. 09/427,835, filed Oct. 26, Adverse drug reactions can also be categorized into revers 1999, and Stanton et al., U.S. application Ser. No. 09/300, ible and irreversible effects. The methods of this invention 747, filed Apr. 26, 1999, and claims the benefit of U.S. are useful for identifying the genetic basis of both mecha Provisional Patent Application, Stanton & Adams, Ser. No. nism based and idiosyncratic toxic effects, whether revers 60/131,334, filed Apr. 26, 1999, and U.S. Provisional Patent ible or not. Methods for identifying the genetic sources of Application, Stanton, Ser. No. 60/139,440, filed Jun. 15, interpatient variation in efficacy and mechanism based tox 1999, which are hereby incorporated by reference in their icity may be initially directed to analysis of genes affecting entireties, including drawings and tables. pharmacokinetic parameters, while the genetic causes of idiosyncratic adverse drug reactions are more likely to be BACKGROUND OF THE INVENTION attributable to genes affecting variation in pharmacody namic responses or immunological responsiveness. 0002 This application concerns the field of mammalian therapeutics and the Selection of therapeutic regimens uti 0008 Absorption is the first pharmacokinetic parameter lizing host genetic information, including gene Sequence to consider when determining the causes of interSubject variances within the human genome in human populations. variation in drug response. The relevant genes depend on the route of administration of the compound being evaluated. 0003. The information provided below is not admitted to For orally administered drugs the major Steps in absorption be prior art to the present invention, but is provided Solely may occur during exposure to Salivary enzymes in the to assist the understanding of the reader. mouth, exposure to the acidic environment of the Stomach, 0004. Many drugs or other treatments are known to have exposure to pancreatic digestive enzymes and bile in the highly variable safety and efficacy in different individuals. A Small intestine, exposure to enteric bacteria and exposure to consequence of Such variability is that a given drug or other cell Surface proteins throughout the gastrointestinal tract. treatment may be effective in one individual, and ineffective For example, uptake of a drug that is absorbed acroSS the or not well-tolerated in another individual. Thus, adminis gastrointestinal tract by facilitated transport may vary on tration of Such a drug to an individual in whom the drug account of allelic variation in the gene encoding the trans would be ineffective would result in wasted cost and time porter protein. Many drugs are lipophilic (a property which during which the patient's condition may significantly promotes passive movement across biological membranes). worsen. Also, administration of a drug to an individual in Variation in levels of Such drugs may depend, for example, whom the drug would not be tolerated could result in a direct on the enterohepatic circulation of the drug, which may be worsening of the patient's condition and could even result in affected by genetic variation in liver canalicular transporters, the patient's death. or intestinal transporters, alternatively renal reabsorbtion US 2001/0034023 A1 Oct. 25, 2001 mechanisms may vary among patients as a consequence of the compound. Experimental means of assessing relevant gene Sequence variances. If a compound is delivered biotransformation Systems are also described. parenterally then absorption is not an issue, however tran 0012 Drug-induced disease or toxicity presents a unique Scutaneous administration of a compound may be Subject to Series of challenges to drug developers, as these reactions genetically determined variation in skin absorptive proper are often not predictable from preclinical Studies and may ties. not be detected in early clinical trials involving Small 0009. Once a drug or candidate therapeutic intervention numbers of subjects. When such effects are detected in later is absorbed, injected or otherwise enters the bloodstream it Stages of clinical development they often result in termina is distributed to various biological compartments via the tion of a drug development program because, until now, blood. The drug may exist free in the blood, or, more there have been no effective tools to seek the determinants commonly, may be bound with varying degrees of affinity to of Such reactions. When a drug is approved despite Some plasma proteins. One classic Source of interpatient variation toxicity, its clinical use is frequently Severely constrained by in drug response is attributable to amino acid polymor the possible occurrence of adverse reactions in even a Small phisms in serum albumin, which affect the binding affinity of group of patients. The likelihood of Such a compound drugs. Such as warfarin. Consequent interpatient variation in becoming first line therapy is Small (unless there are no levels of free warfarin have a significant effect on the degree competing products). Thus, clinical trials that lead to detec of anticoagulation. From the blood a compound diffuses into tion of genetic causes of adverse events and Subsequently to and is retained in interstitial and cellular fluids of different the creation of genetic tests to identify and Screen out organs to different degrees.