Systems and methods for detecting biological features

Abstract

A computer having a memory stores instructions for receiving data. The data comprises one or more characteristics for each cellular constituent in a plurality of cellular constituents that have been measured in a test organism of a species or a test biological specimen from an organism of the species. The memory further stores instructions for computing a model in a plurality of models, wherein the model is characterized by a model score that represents the likelihood of a biological feature in the test organism or the test biological specimen. Computation of the model comprises determining the model score using one or more characteristics for one or more cellular constituents in the plurality of cellular constituents. The memory also stores instructions for repeating the instructions for computing one or more times, thereby computing the plurality of models. The memory also stores instructions for communicating computed model scores.

1 . A computer comprising:
 a central processing unit;   a memory, coupled to the central processing unit, the memory storing:
 (i) instructions for receiving data, wherein said data comprises one or more characteristics for each cellular constituent in a plurality of cellular constituents that have been measured in a single test organism of a species or a single test biological specimen from an organism of said species; 
 (ii) instructions for applying a plurality of pre-existing models using said data to produce a model score for each respective pre-existing model in said plurality of pre-existing models thereby obtaining a plurality of model scores, wherein each model score in said plurality of model scores represents the likelihood of a corresponding biological feature being present in the single test organism or the single test biological specimen and wherein applying a respective model in said plurality of models comprises determining said model score for the respective model using one or more characteristics for a sub-plurality of cellular constituents in said plurality of cellular constituents in said data that have been measured in the single test organism or single test biological specimen, the plurality of pre-existing models comprising a first pre-existing model using one or more characteristics of a first sub-plurality of cellular constituents in said plurality of cellular constituents and a second pre-existing model using one or more characteristics of a second sub-plurality of cellular constituents in said plurality of cellular constituents, wherein the first sub-plurality of cellular constituents includes at least one cellular constituent that is not present in the second sub-plurality of cellular constituents; 
 (iii) instructions for communicating each said plurality of model scores. 
   
     
     
         2 . (canceled) 
     
     
         3 . The computer of  claim 1 , wherein
 five or more model scores are communicated by said instructions for communicating and wherein each model score in said five or more model scores corresponds to a different pre-existing model in said plurality of models.   
     
     
         4 . The computer of  claim 1  wherein said instructions for receiving data comprise instructions for receiving said data from a remote computer over a wide area network. 
     
     
         5 . The computer of  claim 4  wherein said wide area network is the Internet. 
     
     
         6 . The computer of  claim 1  wherein said instructions for communicating comprise instructions for transmitting each said model score to a remote computer over a wide area network. 
     
     
         7 . The computer of  claim 6  wherein said wide area network is the Internet. 
     
     
         8 . The computer of  claim 1  wherein
 the single test organism or the single test biological specimen is deemed to have the biological feature represented by a pre-existing model in the plurality of pre-existing models when the model score is in a first range of values; and 
 the single test organism or the single test biological specimen is deemed not to have the biological feature represented by the pre-existing model when the model score is in a second range of values. 
 
     
     
         9 . The computer of  claim 1  wherein each said corresponding biological feature is a disease. 
     
     
         10 . The computer of  claim 9  wherein said disease is cancer. 
     
     
         11 . The computer of claim wherein each corresponding biological feature is independently one of breast cancer, lung cancer, prostate cancer, colorectal cancer, ovarian cancer, bladder cancer, gastric cancer, and rectal cancer. 
     
     
         12 . (canceled) 
     
     
         13 . The computer of  claim 1  wherein a characteristic in said one or more characteristics for one or more cellular constituents used to determine the model score for a pre-existing model in said plurality of pre-existing models comprises an abundance of said one or more cellular constituents in said single test organism of said species or said single test biological specimen from an organism of said species. 
     
     
         14 . The computer of  claim 1  wherein the species is human. 
     
     
         15 . The computer of  claim 1  wherein the single test biological specimen is a biopsy or other form of sample from a tumor, blood, bone, a breast, a lung, a prostate, a colorectum, an ovary, a bladder, a stomach, or a rectum. 
     
     
         16 . The computer of  claim 1  wherein said one or more characteristics comprises cellular constituent abundance and said data comprises cellular constituent abundances of at least one hundred cellular constituents in said single test organism of said species or said single test biological specimen from said organism of said species. 
     
     
         17 . The computer of  claim 1  wherein said one or more characteristics comprises cellular constituent abundance and said data comprises cellular constituent abundances of at least five hundred cellular constituents in said single test organism of said species or said single test biological specimen from said organism of said species. 
     
     
         18 . The computer of  claim 1  wherein said one or more characteristics comprises cellular constituent abundance and said data comprises cellular constituent abundances of at least five thousand cellular constituents in said single test organism of said species or said single test biological specimen from said organism of said species. 
     
     
         19 . The computer of  claim 1  wherein said one or more characteristics comprises cellular constituent abundance and said data comprises cellular constituent abundances of between one thousand and twenty thousand cellular constituents in said single test organism of said species or said single test biological specimen from said organism of said species. 
     
     
         20 . The computer of  claim 1  wherein a cellular constituent in said plurality of cellular constituents is mRNA, cRNA or cDNA. 
     
     
         21 . The computer of  claim 1  wherein a cellular constituent in said one or more cellular constituents is a nucleic acid or a ribonucleic acid and a characteristic in said one or more characteristics of a cellular constituent in said plurality of cellular constituents is obtained by measuring a transcriptional state of all or a portion of said cellular constituent in said single test organism or said single test biological specimen. 
     
     
         22 . The computer of  claim 1  wherein a cellular constituent in said plurality of cellular constituents is a protein and a characteristic in said one or more characteristics of a cellular constituent in said plurality of cellular constituents is obtained by measuring a translational state of said cellular constituent in said single test organism or said single test biological specimen. 
     
     
         23 . The computer of  claim 1  wherein a characteristic in the one or more characteristics of a cellular constituent in the plurality of cellular constituents is determined using isotope-coded affinity tagging followed by tandem mass spectrometry analysis of the cellular constituent using a sample obtained from the single test organism or the single test biological specimen. 
     
     
         24 . The computer of  claim 1  wherein a characteristic in the one or more characteristics of a cellular constituent in the plurality of cellular constituents is determined by measuring an activity or a post-translational modification of the cellular constituent in a sample obtained from the single test organism or in the single test biological specimen. 
     
     
         25 . The computer of  claim 1  wherein said corresponding biological feature is sensitivity to a drug. 
     
     
         26 . The computer of  claim 1  wherein the plurality of models for which model scores are computed collectively represent the likelihood of each of two or more biological features. 
     
     
         27 . The computer of  claim 26  wherein each biological feature in said two or more biological features is a cancer origin. 
     
     
         28 . The computer of  claim 26  wherein said two or more biological features comprises a first disease and a second disease. 
     
     
         29 . The computer of  claim 1  wherein the plurality of models for which model scores are computed collectively represent the likelihood of each of five or more biological features. 
     
     
         30 . The computer of  claim 29  wherein each biological feature in said five or more biological features is a cancer origin. 
     
     
         31 . The computer of  claim 29  wherein said five or more biological features comprises a first disease and a second disease. 
     
     
         32 . The computer of  claim 1  wherein the plurality of models for which model scores are computed collectively represent the independent likelihood of between two and twenty biological features. 
     
     
         33 . The computer of  claim 32  wherein each biological feature in said between two and twenty biological features is a cancer origin. 
     
     
         34 . The computer of  claim 32  wherein said between two and twenty biological features comprises a first disease and a second disease. 
     
     
         35 - 139 . (canceled) 
     
     
         140 . The computer of  claim 1 , wherein the plurality of cellular constituents have been measured in a single test organism of the species, the method further comprising:
 (iv) communicating instructions for treating the single test organism for a biological feature associated with the model score representing that there is a high likelihood that the biological feature is present in the single test organism.