Treatment discovery based on CGH analysis

Abstract

Methods, systems and computer readable media for discovering a combination of treatments to reduce the progress of, or eliminate a tissue malady. Gene expression values of at least one sample of tissue exhibiting the tissue malady and at least one reference sample tissue that does not exhibit the malady are measured using at least one CGH array designed to measure gene sequences and possible variations in gene sequences attributable to the malady. Gene expression signatures are generated from differential expression values of ratios of the measured gene expression values between the at least one sample exhibiting the malady and the at least one reference sample, across all samples, respectively. The tissue samples exhibiting the malady are treated with a treatment, and a treatment-response value is measured with respect to each of the tissue samples treated, as effected by the treatment. A phenotypic signature representing the treatment-response values of each of the tissue samples treated is generated for characterizing the effects of the treatment on the tissues treated. Processing may be repeated with a different treatment at least once so that multiple phenotypic signatures have been generated for multiple treatments. A clustering operation is then based on the gene expression signatures of the differential expression levels and the phenotypic signatures of the treatment-response values together, and treatments are selected by identifying the treatment-response phenotypic signatures caused by those treatments, and which are clustered with gene expression signatures representing differential expression levels representative of the at least one tissue sample exhibiting the malady.

1 . A method for discovering a combination of treatments to reduce the progress of, or eliminate a tissue malady, said method comprising the steps of: 
 (a) measuring gene expression values of at least one sample of tissue exhibiting the tissue malady and at least one reference sample tissue that does not exhibit the malady, using at least one CGH array designed to measure gene sequences and possible variations in gene sequences attributable to the malady;    (b) generating gene expression signatures from differential expression values of ratios of the measured gene expression values between the at least one sample exhibiting the malady and the at least one reference sample, across all samples, respectively;    (c) treating the at least one tissue sample exhibiting the malady with a treatment;    (d) measuring a treatment-response value with respect to each of the tissue samples treated, as effected by the treatment;    (e) generating a phenotypic signature representing the treatment-response values of each of the tissue samples treated;    (f) repeating steps (c)-(e) with a different treatment at least once so that multiple phenotypic signatures have been generated for multiple treatments;    (g) performing a clustering operation based on the gene expression signatures of the differential expression levels and the phenotypic signatures of the treatment-response values together; and    (h) selecting treatments by identifying the treatment-response phenotypic signatures caused by those treatments, and which are clustered with gene expression signatures representing differential expression levels representative of the at least one tissue sample exhibiting the malady.    
     
     
         2 . The method of  claim 1 , further comprising designing the CGH array designed to measure gene sequences and possible variations in gene sequences attributable to the malady; and 
 providing the CGH array for said measuring gene expression values.    
     
     
         3 . The method of  claim 1 , wherein each said treatment is selected from the group consisting of: a drug, a combination of drugs, a compound, a combination of compounds, radiation, a genetic sequence, a combination of genetic sequences, heat, cryogenics and a combination of two or more of any of the previous members in this group.  
     
     
         4 . The method of  claim 1 , further comprising the steps of: 
 labeling the phenotypic signatures as “in phase” signatures;    generating “out of phase” signatures by inverting the “in phase” signatures; and    including the “out of phase” signatures with the “in phase” signatures and the gene expression signatures when performing steps (g) and (h).    
     
     
         5 . The method of  claim 1 , wherein said clustering operation includes finding a density center of a cluster, and calculating distances of the phenotypic signatures, belonging to the cluster, from the density center.  
     
     
         6 . The method of  claim 5 , wherein the selection of treatments is made to address a broad spectrum of genes involved in the process of the malady.  
     
     
         7 . The method of  claim 6 , wherein the treatments are selected by selecting treatment-response signatures within a cluster and having varying distances from the density center.  
     
     
         8 . The method of  claim 1 , wherein said phenotypic signatures are normalized prior to said clustering.  
     
     
         9 . The method of  claim 4 , wherein said phenotypic signatures are normalized prior to said clustering.  
     
     
         10 . The method of  claim 1 , wherein said CGH array is processed on a two-color, two channel microarray apparatus to measure said gene expression values.  
     
     
         11 . The method of  claim 1 , wherein said gene expression values are measured on a single channel microarray apparatus, wherein one of said CGH arrays per sample is used to process each sample exhibiting the malady and one of said CGH arrays per sample is used to process each reference sample.  
     
     
         12 . The method of  claim 1 , wherein each treatment-response value comprises a concentration level or amount of the treatment used to block or retard the progress of the malady by a predetermined percentage over a predetermined period of time after treatment.  
     
     
         13 . The method of  claim 1 , wherein each treatment-response value comprises a value characterizing the amount of blocking or retardation of the malady over a predetermined period of time after treatment with a fixed amount of the treatment.  
     
     
         14 . The method of  claim 1 , further comprising generating at least one phenotypic signature representing treatment-response values of each of the tissue samples exhibiting the malady, resultant from treating the tissue samples exhibiting the malady, with at least one treatment having known undesirable characteristics for treatment of the tissues exhibiting the malady; 
 including that at least one phenotypic signature resulting from said treatment having known undesirable characteristics with all other signatures included in performing the clustering step (g); and    discarding any phenotypic signature representing treatment-response values from candidacy for the selection step (h) when the phenotypic signature is less than or equal to a predefined distance from a location of the at least one phenotypic signature resulting from treatment with a treatment having known undesirable characteristics.    
     
     
         15 . The method of  claim 14 , wherein said known undesirable characteristics comprise an unacceptable level of toxicity.  
     
     
         16 . The method of  claim 14 , wherein said known undesirable characteristics comprise an insufficient efficacy.  
     
     
         17 . A method for screening a combination of treatments to select treatments for tissue exhibiting a malady, said method comprising the steps of: 
 (a) providing differential expression levels of tissue samples exhibiting the malady relative to at least one reference tissue sample from respective features of CGH arrays designed to measure gene sequences and possible variations in gene sequences attributable to the malady;    (b) for respective differential expression levels from respective features of respective CGH arrays for each tissue sample exhibiting the malady, providing a gene expression signature representing the differential expression level for each tissue sample for gene expression levels from that feature, respectively;    (c) providing a treatment-response value, for each tissue sample exhibiting the malady having been treated with a treatment, as effected by the treatment;    (d) generating a phenotypic signature representing the treatment-response values of each of the tissue samples having been treated;    (e) repeating steps (c)-(d) with a different treatment at least once so that multiple phenotypic signatures have been generated for multiple treatments;    (f) performing a clustering operation based on the gene expression signatures of the differential expression levels and the phenotypic signatures of the treatment-response values together; and    (g) selecting treatments by identifying the treatment-response phenotypic signatures caused by those treatments, and which are clustered with gene expression signatures representing differential expression levels representative of the tissue samples exhibiting the malady.    
     
     
         18 . A method of augmenting an original or existing single treatment or treatment combination for a disease with at least one additional treatment that covers gene activity of the disease not addressed by the original or existing treatment, said method comprising the steps of: 
 (a) providing differential expression levels of diseased tissue samples relative to at least one reference tissue for respective features of CGH arrays designed to measure gene sequences and possible variations in gene sequences attributable to the disease;    (b) for respective features of respective CGH arrays for each diseased tissue sample, providing a gene expression signature representing the differential expression level for each tissue sample for that feature, respectively;    (c) treating the diseased tissue samples with the original or existing single treatment or combination treatment;    (d) measuring a treatment-response value with respect to each of the diseased tissue samples as effected by the original or existing single or combination treatment;    (e) generating a phenotypic signature representing the treatment-response values of each of the diseased tissue samples as effected by the original or existing single or combination treatment;    (f) treating the diseased tissue samples with a treatment that is not included in the original or existing single or combination treatment;    (g) measuring a treatment-response value with respect to each of the diseased tissue samples as effected by the treatment that is not included in the original or existing single or combination treatment;    (h) generating a phenotypic signature representing the treatment-response values of each of the diseased tissue samples as effected by the treatment that is not included in the original or existing single or combination treatment;    (i) repeating steps (f)-(h) with a different treatment that is also not included in the original or existing single or combination treatment at least once so that multiple phenotypic signatures have been generated for multiple treatments not included in the original or existing single or combination treatment;    (j) performing a clustering operation based on the gene expression signatures of the differential expression levels and the phenotypic signatures of the treatment-response values together; and    (k) selecting at least one treatment by identifying the treatment-response phenotypic signatures caused by the at least one treatment, and which are clustered with phenotypic signatures identifying the treatment-response phenotypic signatures caused by the treatment or treatments in the original treatment, as well as with gene expression signatures representing differential expression levels representative of the diseased tissue samples, but separated from the phenotypic signatures identifying the treatment-response phenotypic signatures caused by the treatment or treatments in the original treatment, so as to address disease-gene activity not currently addressed by the treatment or treatments in the original or existing treatment.    
     
     
         19 . The method of  claim 18 , wherein each said treatment is selected from the group consisting of: a drug, a combination of drugs, a compound, a combination of compounds, radiation, a genetic sequence, a combination of genetic sequences, heat, cryogenics and a combination of two or more of any of the previous members in this group.  
     
     
         20 . The method of  claim 18 , further comprising the steps of: 
 labeling the phenotypic signatures as “in phase” signatures;    generating “out of phase” signatures by inverting the “in phase” signatures; and    including the “out of phase” signatures with the “in phase” signatures and the gene expression signatures when performing steps (j) and (k).    
     
     
         21 . A system for discovering a combination of treatments to reduce the progress of, or eliminate a tissue malady, said system comprising: 
 means for generating a gene expression signature representing differential expression levels of each of a plurality of tissue samples exhibiting the malady, relative to at least one reference tissue from gene expression values determined from respective features of CGH arrays designed to measure gene sequences of the tissues and possible variations in gene sequences attributable to the malady;    means for measuring a treatment-response value with respect to each of the tissue samples exhibiting the malady, after treating each tissue sample exhibiting the malady with a treatment;    means for generating a phenotypic signature representing the treatment-response values of each of the tissue samples having been treated; and    means for performing a clustering operation while considering the gene expression signatures of the differential expression levels and the phenotypic signatures of the treatment-response values together.    
     
     
         22 . The system of  claim 21 , further comprising at least one of said CGH arrays designed to measure gene sequences of the tissues and possible variations in gene sequences attributable to the malady.  
     
     
         23 . The system of  claim 21 , further comprising microarray apparatus for processing the tissue samples exhibiting the malady and the at least one reference tissue to obtain the differential expression levels of the diseased tissues relative to the at least one reference tissue.  
     
     
         24 . The system of  claim 21 , wherein multiple treatments are successively and independently applied to treat the tissues exhibiting the malady, with respective treatment-response values measured for each and a treatment-response phenotypic signature is generated for each treatment applied.  
     
     
         25 . The system of  claim 21 , further comprising means for generating out-of-phase phenotypic signatures by inverting said phenotypic signatures.  
     
     
         26 . The system of  claim 25 , wherein said means for clustering includes said out-of-phase phenotypic signatures with said gene expression signatures said phenotypic signatures of the treatment-response values when performing said clustering operation.  
     
     
         27 . The system of  claim 21 , further comprising means for determining a center of density of a cluster identified by said means for clustering, and means for determining a distance of a phenotypic signature found to belong to said cluster, from said center of density.  
     
     
         28 . A computer readable medium carrying one or more sequences of instructions for discovering a combination of treatments to reduce the progress of, or eliminate a tissue malady, wherein execution of one or more sequences of instructions by one or more processors causes the one or more processors to perform the steps of: 
 (a) measuring gene expression values of at least one sample of tissue exhibiting the tissue malady and at least one reference sample tissue that does not exhibit the malady, using at least one CGH array designed to measure gene sequences and possible variations in gene sequences attributable to the malady;    (b) generating gene expression signatures from differential expression values of ratios of the measured gene expression values between the at least one sample exhibiting the malady and the at least one reference sample, across all samples, respectively;    (c) treating the at least one tissue sample exhibiting the malady with a treatment;    (d) measuring a treatment-response value with respect to each of the tissue samples treated, as effected by the treatment;    (e) generating a phenotypic signature representing the treatment-response values of each of the tissue samples treated;    (f) repeating steps (c)-(e) with a different treatment at least once so that multiple phenotypic signatures have been generated for multiple treatments;    (g) performing a clustering operation based on the gene expression signatures of the differential expression levels and the phenotypic signatures of the treatment-response values together; and    (h) selecting treatments by identifying the treatment-response phenotypic signatures caused by those treatments, and which are clustered with gene expression signatures representing differential expression levels representative of the at least one tissue sample exhibiting the malady.