Evidence based system and method for identifying factors of disease

Abstract

A repeatable methodology for generation of a specific biological function library (data pool) and techniques for structuring queries that cluster and parse gene and protein alterations in individual patients and patient cohorts. Method enables analytical distinction between detectable changes in biological function and non-detectable changes in biological function using current diagnostic techniques and technologies.

Claims

1-12. (canceled)

13. A computer implemented method that: receives input of all reference information pertinent to biological functions and input of information for individual patients; information specific to a cohort of patients; and disease specific information.

14. A computer implemented method that: generates a biological function library or data pool incorporating all reference data; and share content with other users if desired; and enables the user to create and/or select additional versions of the biological function library to meet specific objective(s), using various alternate versions of the reference content from the first version of the biological function library, with iterative versions of the content being a different version and/or arrangement of the same content as the first version of the content.

15. A computer implemented method that: provides for display and storage, listing and reference information pertaining to all specific biological function genes and/or proteins altered/mutated in individual patients, a patient cohort and/or a given disease; listing and reference information pertaining to all specific biological function genes and/or proteins not altered/not mutated in individual patients, a patient cohort and/or a given disease; and listing and reference information pertaining to all specific biological function genes and/or proteins not detected in individual patients, a patient cohort and/or a given disease.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0015] This repeatable method is intended to identify the alteration status of genes and/or proteins known to impact specific biological functions in a disease of interest.

[0016] FIG. 1A Overview of repeatable methodology.

[0017] FIG. 1B Process for generating specific biological function gene library or data pool.

[0018] FIG. 1C Query of gene library or data pool with patient cohort data.

[0019] FIG. 1D Identification of disease factors.

DETAILED DESCRIPTION

[0020] FIG. 1A presents one embodiment of the overall methodology. According to an embodiment of the invention, a review of human and animal studies for a disease of interest is done to identify specific biological functions/factors. This review of scientific literature will result in the generation of an initial listing of biological functions in our disease of interest and the genes and proteins that regulate them. For example, the following sources can be used to seed the biological functions list: [0021] Review pathology focused postmortem publications [0022] Review genomics and proteomic focused publications [0023] Review cell signaling focused publications

[0024] In an embodiment of the invention, a next step can be review of an authoritative repository, such as METLIN or KEGG, for a listing of genes pertinent to our initial biological function list. FIG. 1B illustrates how lists such as these are combined to generate our Specific Biological Function Library. An example of four lists our methodology can create: [0025] Functional gene lists extracted from an authoritative repository [0026] Cohort list of patients with gene mutations [0027] Cohort list of patients with genes that have altered expression data [0028] Cohort list of patients with genes that have altered protein expression data

[0029] Other embodiments of this invention, as seen in FIG. 1C, multiple queries can then be generated against this biological function library. For example, three search and sort functions can be run: [0030] Search Patient Cohort list of gene mutations for genes extracted from authoritative repository [0031] Search Patient Cohort list of genes with altered expression for genes extracted from authoritative repository [0032] Search Patient Cohort list of genes with alterations in protein expression data for genes extracted from authoritative repository

[0033] In an embodiment of the invention, any query of the Specific Biological Function Library will return a response with the following three categories: [0034] Name and number of altered genes/proteins detected in patient cohort [0035] Name and number of non-altered genes/proteins detected in patient cohort [0036] Name and number of genes/proteins not detected in patient cohort

[0037] FIG. 1D then reveals analysis that can be conducted using an embodiment of the Specific Biological Function Library to identify gene or protein alterations implicated in a specific disease or patient population. An example of two analytical functions: [0038] Compare results from the above searches to generate a cumulative listing of genes mutated/altered in the disease of interest for a cohort [0039] Compare cumulative listing of genes mutated/altered in the disease of interest for multiple cohorts

[0040] An embodiment of this invention is intended to extract specific biological function information from all existing scientific literature published to create a library that can screen patient data for patterns of gene and/or protein alterations within and across cohort data sets: these patterns can be clusters of patients carrying mutations/alterations for particular genes and/or proteins, or particular mutations/alterations of particular genes and/or proteins in a given disease; or clusters of genes and/or proteins mutated/altered together. As illustrated in FIG. 1D one embodiment of this invention then can be used to determine whether or not a collection of genes that regulate specific biological functions impact individual patient outcome and disease progression.

[0041] The field currently relies on two approaches: 1) detecting sequencing and expression changes in the whole genome and 2) searching the genome for alterations in a small subset of genes or proteins. The results of these analysis are then regarded as the definitive sequence or expression for a given individual and disease. One embodiment of this invention creates a library that combines the information from both of these approaches. Furthermore, diagnostic techniques and analysis are narrowly focused to report only what genetic or proteomic alterations a given test reports. Analysis does not include assessment of functional genes that were not detected. However, knowing the genes or proteins that were not detected but are known to have a role in a specific biological function can provide valuable insight to the researcher such as alerting to potential protocol or diagnostic issues. By querying molecular data for specific functional genes and proteins, my method allows a deeper understanding of what it is our diagnostics are and are not reporting.

[0042] The logic and processes described in this document may be implemented in software, firmware, hardware or any combination thereof. Furthermore, execution of said logic and processes can occur across a distributed architectural environment, a strictly local computing environment or any combination thereof. It is therefore intended that the scope of the invention be limited not by this detailed description, but rather by any claims that issue on an application based hereon. The phrase “in one embodiment” or “in an embodiment” in the specification does not necessarily refer to the same embodiment, nor are separate or alternative embodiments mutually exclusive of other embodiments. Explicit reference to an “embodiment” or the like, steps and functions are described, which may be variously combined and included in some embodiments, but also variously omitted in other embodiments. Consequently, the disclosure of the embodiments of the invention is provided for explanatory purposes, without limiting the scope of the invention, as set forth in the following claims.