Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2001-03-29
2004-02-17
Allen, Marianne P. (Department: 1631)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C702S019000, C702S020000
Reexamination Certificate
active
06692916
ABSTRACT:
TECHNICAL FIELD
Embodiments of the recent invention provide systems and methods for utilizing gene expression analysis for characterizing a biological condition or agent.
BACKGROUND ART
There has been substantial discussion including congressional hearings concerning medical errors. One source of medical errors include errors with medications. Upwards of 98,000 hospitalized patients annually have been documented to be victims of medication errors (Statement of the American Pharmaceutical Association to the Senate Appropriations Committee Labor, health and Human Services Education Subcommittee Hearing on Medical Errors Dec. 13, 1999). These errors include problems arising from drug interactions for a particular patient taking more than one drug, problems concerning the response of an individual to a particular drug and incorrect medication for a particular condition. Medical errors further arise as a result of misdiagnosis. This may occur as a result of insensitive diagnostic techniques or a wide range of interpersonal variability in the manner in which a clinical state is manifest. At present, there are few tools available for optimizing prognosis, diagnosis and treatment of a medical condition taking into account the particular phenotype and genotype of an individual.
There has been increasing interest in herbal drugs or nutraceuticals. These compounds are grown and collected from around the world, and consequently the compounds are subject to regional and temporal differences in collection and preparation that are difficult to control. It is frequently the case that one batch of a nutraceutical may be effective, there is no assurance that a second batch will be effective. Moreover. analysis of nutraceuticals is problematic because these drugs are complex mixtures in which little is known with respect to the active agent.
All new therapeutic agents require some form of clinical trials. It is known that a drug for treating tumor that is tested in a clinical trial using standard recruiting techniques for patients, may in fact show only limited efficacy. If the beneficial effect observed in a clinical population is too small, the drug will not receive approval by the Food and Drug Administration for use in the population at large. However, the small beneficial effect observed may in fact be an artifact of the clinical trial design or the clinical endpoint in the population of patients. It would be desirable to have criteria for screening patients as they enter a clinical trial to ensure that the beneficial effect of a drug if it exists may be detected and quantified.
SUMMARY OF THE INVENTION
In a first embodiment of the invention there is provided a method, for evaluating a biological condition of a subject, that includes: obtaining from the subject a sample having at least one of RNAs and proteins; deriving from the sample a first profile data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In another embodiment, a method is provided for evaluating a biological condition of a subject, that includes obtaining from the subject a first sample having at least one of fluid, cells and active agents; applying the first sample or a portion thereof to a defined population of indicator cells; obtaining from the indicator cells a second sample containing at least one of RNAs or proteins; deriving from the second sample a first profile data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In a another embodiment, a method is provided for evaluating a biological condition affected by an agent, the method including: obtaining, from a target population of cells to which the agent has been administered, a sample having at least one of RNAs and proteins; deriving from the sample a first profile data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition as affected by the agent.
In a another embodiment, a method is provided for evaluating the effect on a biological condition by a first agent in relation to the effect by a second agent, including: obtaining, from first and second target populations of cells to which the first and second agents have been respectively administered, first and second samples respectively, each sample having at least one of RNAs and proteins; deriving from the first sample a first profile data set and from the second sample a second profile data set, the profile data sets each including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing for the panel a first calibrated profile data set and a second profile data set, wherein (i) each member of the first calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a first baseline profile data set for the panel, and (ii) each member of the second calibrated profile data set is a function of a corresponding member of the second profile data set and a corresponding member of a second baseline profile data set for the panel, the calibrated profile data sets providing a measure of the effect by the first agent on the biological condition in relation to the effect by the second agent.
In a further embodiment, a method of conducting a clinical trial of an agent, is provided, including: causing the blind administration of a selected one of a placebo and the agent to each candidate of a pool of subjects; and using quantitative gene expression to monitor an effect of such administration.
In another embodiment, a digital storage medium is provided on which is stored a computer readable calibrated profile data set, wherein: the calibrated profile data set relates to a sample having at least one of RNAs and proteins derived from a target cell population to which an agent has been administered; the calibrated profile data set includes a first plurality of members, each member being a quantitative measure of a change in an amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of a biological condition as affected by administration of the agent.
In another embodiment, a digital storage medium is provided on which is stored a plurality of records R
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relati
Bankaitis-Davis Danute M.
Bevilacqua Michael P.
Cheronis John C.
Tryon Victor
Allen Marianne P.
Bromberg & Sunstein LLP
Source Precision Medicine, Inc.
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