Genetic Attribute Analysis

Abstract

A method and system for genetic attribute analysis are presented in which non-identical sets of genetic attributes comprising nucleotide sequence are compared to determine whether proteins encoded by those nucleotide sequences are functionally equivalent, and therefore whether genetic information contained in the sets of genetic attributes can be considered to be the same. A determination of equivalence between two sets of genetic attributes can enable the compression of thousands of individual DNA nucleotide attributes into a single categorical genetic attribute, which is useful for methods such as attribute discovery, predisposition prediction and predisposition modification where a reduction in the amount of genomic data can enhance processing efficiency. Sets of genetic attributes are determined to be equivalent based on whether they are able to satisfy one or more equivalence rules.

1 . A computer based method for genetic attribute analysis, comprising:
 a) accessing a first set of genetic attributes, associated with an individual, comprising a first nucleotide sequence containing an open reading frame encoding a protein;   b) accessing a second set of genetic attributes, associated with one or more individuals, comprising a second nucleotide sequence containing the open reading frame encoding the protein, wherein one or more nucleotides of the second nucleotide sequence differ from one or more nucleotides of the first nucleotide sequence;   c) identifying whether the first nucleotide sequence and the second nucleotide sequence are equivalent based on an equivalence rule for comparison of non-identical protein-encoding nucleotide sequences;   d) generating, if the first nucleotide sequence and the second nucleotide sequence were identified to be equivalent, a determination indicating that the first set of genetic attributes associated with the individual is identical to the second set of genetic attributes associated with the one or more individuals; and   e) storing the determination.   
   
   
       2 . The computer based method of  claim 1 , wherein the first set of genetic attributes contains an attribute combination associated with the individual and the second set of genetic attributes contains an attribute combination associated with the one or more individuals, and wherein the one or more individuals comprise a group of individuals associated with a query attribute. 
   
   
       3 . The computer based method of  claim 2 , further comprising:
 f) computing, based on the determination, the frequency of occurrence of the attribute combination for the group of individuals.   
   
   
       4 . The computer based method of  claim 2 , further comprising:
 f) computing, based on the determination, a statistical result indicating the strength of association of the attribute combination with the query attribute.   
   
   
       5 . The computer based method of  claim 2 , further comprising:
 f) generating, based on the determination, one or more statistical predictions indicating the potential association between the individual and the query attribute.   
   
   
       6 . The computer based method of  claim 1 , further comprising:
 f) generating, based on the determination, a categorical attribute that can be associated with the individual.   
   
   
       7 . The computer based method of  claim 6 , further comprising:
 g) storing the categorical attribute in association with an attribute profile of the individual to create an expanded attribute profile for the individual.   
   
   
       8 . The computer based method of  claim 1 , further comprising:
 f) linking the determination to at least one of: an attribute combination, a set of attributes, an attribute profile of an individual, a dataset, and a record in a database.   
   
   
       9 . The computer based method of  claim 1 , further comprising:
 f) transmitting the determination to at least one of the set of: a user, a computer readable memory, a computer readable medium, a database, a dataset, a computer processor, a computer on a network, a visual display, and a wireless receiver.   
   
   
       10 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more nucleotides within the open reading frame that do not alter the amino acid sequence of the protein. 
   
   
       11 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more nucleotides within the open reading frame that result in conservative amino acid substitutions within the amino acid sequence of the protein. 
   
   
       12 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more nucleotides within the open reading frame that result in conservative amino acid substitutions occurring anywhere within the protein except for enzymatic, transmembrane and antigen-recognition domains. 
   
   
       13 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more nucleotides within the open reading frame that result in silent amino acid substitutions within the protein. 
   
   
       14 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more conservative missense mutations within the open reading frame. 
   
   
       15 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more conservative missense mutations occurring anywhere within the open reading frame encoding the protein except for those regions of the open reading frame that encode enzymatic, transmembrane or antigen-recognition domains of the protein. 
   
   
       16 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by one or more silent mutations occurring within the open reading frame. 
   
   
       17 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by the locations of nonsense mutations within the open reading frame that occur within a same domain of the protein. 
   
   
       18 . The computer based method of  claim 1 , wherein the equivalence rule requires that two protein-encoding nucleotide sequences are equivalent if they encode the same protein and differ only by the locations of frameshift mutations within the open reading frame that occur within a same domain of the encoded protein. 
   
   
       19 . A computer based system for genetic attribute analysis, comprising:
 a) a first data accessing subsystem for accessing a first set of genetic attributes, associated with an individual, comprising a first nucleotide sequence containing an open reading frame encoding a protein;   b) a second data accessing subsystem for accessing a second set of genetic attributes, associated with one or more individuals, comprising a second nucleotide sequence containing the open reading frame encoding the protein, wherein one or more nucleotides of the second nucleotide sequence differ from one or more nucleotides of the first nucleotide sequence;   c) a data processing subsystem comprising:
 i) a data comparison subsystem for identifying whether the first nucleotide sequence and the second nucleotide sequence are equivalent based on an equivalence rule for comparison of non-identical protein-encoding nucleotide sequences; 
 ii) a data generating subsystem for generating, if the first nucleotide sequence and the second nucleotide sequence were identified to be equivalent, a determination indicating that the first set of genetic attributes associated with the individual is identical to the second set of genetic attributes associated with the one or more individuals; and 
   d) a data storage subsystem for storing the determination.   
   
   
       20 . The computer based system of  claim 19  further comprising:
 e) a communications subsystem for transmitting the determination to at least one of the set of: a user, a computer readable memory, a computer readable medium, a database, a dataset, a computer processor, a computer on a network, a visual display, and a wireless receiver.