Arrays of nucleic acid probes for analyzing biotransformation genes

Abstract

The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set. The probes in the second, third and fourth probe sets are identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least three nucleotides thereof that includes the at least one interrogation position, except that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets.

1 . An array comprising one or more array information features.  
     
     
         2 . The array of  claim 1 , wherein said one or more array information features comprises at least 4 features.  
     
     
         3 . The array of  claim 2 , wherein said features are positioned in a defined pattern on said array.  
     
     
         4 . The array of  claim 3 , wherein said defined pattern provides a symbol when specifically bound to target.  
     
     
         5 . The array of  claim 1 , wherein said one or more features provides coded information when specifically bound to target.  
     
     
         6 . The array of  claim 5 , wherein said coded information is binary or non-binary coded information.  
     
     
         7 . A method for providing information about an array, said method comprising: contacting an array of  claim 1  with a sample comprising a target that binds to at least one of said one or more information features to produce at least one signal that provides information about said microarray.  
     
     
         8 . The method of  claim 7 , wherein said target is spiked into said sample prior to contacting of said array with said sample.  
     
     
         9 . The method of  claim 7 , wherein said information is provided by assessing binding of said target to said one or more array information probes.  
     
     
         10 . The method of  claim 9 , wherein said assessing is by determining the presence, absence or level of binding to control levels of binding.  
     
     
         11 . The method of  claim 7 , further comprising determining the presence, absence or level of at least one signal that provides said information.  
     
     
         12 . The method of  claim 11 , wherein said at least one signal provides a binary code, where 0 is represented by no detectable signal and 1 is represented by a detectable signal.  
     
     
         13 . The method of  claim 11 , wherein said at least one signal provides a binary code, where 1 is represented by no detectable signal and 0 is represented by a detectable signal.  
     
     
         14 . The method of  claim 11 , wherein said at least one signal provides a binary code, where 0 is represented by a signal generated by a first label and 1 is represented by a signal generated by a second label that is detectably distinguishable from the first label.  
     
     
         15 . The method of  claim 7 , further comprising determining a level of said at least one signal to provide a non-binary code that provides said information.  
     
     
         16 . The method of  claim 15 , wherein said non-binary code is represented by levels of signal relative to a control level of signal.  
     
     
         17 . A composition comprising a labeled array information target that specifically binds to an array information probe.  
     
     
         18 . A kit comprising: 
 (a) an array information probe; and    (b) a target that binds to said array information probe under specific binding conditions to produce a signal and thereby provide information about an array.    
     
     
         19 . The kit of  claim 18 , further comprising instructions for using said array information probe and said target to provide information about a microarray.  
     
     
         20 . The kit of  claim 19 , wherein said probe is present in one or more array information elements on the surface on an array.  
     
     
         21 . The kit of  claim 18 , wherein said instructions include a protocol for spiking a sample with said target prior to contacting said array with said sample.  
     
     
         22 . A system for providing information about an array, said system comprising: a) an array comprising one or more array information features; and 
 b) a target that specifically binds to at least one of said one or more array information features.    
     
     
         23 . A method of detecting the presence of an analyte in a sample, said method comprising: 
 (a) contacting a sample suspected of containing said analyte with an array of  claim 1 , wherein said array comprises a probe for said analyte;    (b) detecting any resultant binding complexes on the surface of said array to obtain binding complex data to determine whether said analyte is present in said sample.    
     
     
         24 . The method of  claim 23 , further comprising obtaining information about said array by assessing binding of target to said one or more array information features.  
     
     
         25 . The method of  claim 23 , wherein said analyte is a nucleic acid and said array is an array of nucleic acid probes.  
     
     
         26 . A method comprising transmitting a result obtained from a method of  claim 23  from a first location to a second location.  
     
     
         27 . The method of  claim 26 , wherein said second location is a remote location.  
     
     
         28 . A method comprising receiving a result of a method of  claim 23 .  
     
     
         29 . A hybridization assay comprising the steps of: 
 (a) contacting at least one sample containing nucleic acids labeled with a detectable label with a nucleic acid array comprising one or more array information features to produce a hybridization pattern for said nucleic acid sample; and    (b) analyzing said hybridization pattern for each detectable label to produce data on the amounts of said target nucleic acid in said sample and provide information about the array.    
     
     
         30 . A computer readable medium comprising programming to obtain information about an array from data obtained using the array.  
     
     
         31 . A computer-readable medium comprising: information for decoding encoded array information obtained from an array comprising one or more array information features.  
     
     
         32 . The computer readable medium of  claim 31 , wherein said array is an array of nucleic acids.  
     
     
         33 . The computer-readable medium of  claim 31 , wherein said information comprises a table that contains: a list of feature identifiers; and a list of probe identifiers corresponding to said feature identifiers.  
     
     
         34 . The computer-readable medium of  claim 33 , wherein said table indicates that certain features of said array are array information features.  
     
     
         35 . The computer readable medium of  claim 33 , wherein said table indicates which features correspond to which bit of a code.  
     
     
         36 . The computer-readable medium of  claim 31 , wherein said information indicates an executable program for decoding said encoded array information.  
     
     
         37 . The computer-readable medium of  claim 31 , wherein said information is a file that has a unique identifier that corresponds to a unique identifier of an array.  
     
     
         38 . The computer-readable medium of  claim 31 , wherein said array information features encode binary coded information, and said file contains information for decoding said binary coded information.  
     
     
         39 . A method for obtaining information about an array, comprising: reading an array comprising one or more array information features to provide encoded information for said array; and decoding said encoded information using a computer readable medium of  claim 31  to provide information about said array.  
     
     
         40 . The method of  claim 39 , wherein said array is a nucleic acid array.  
     
     
         41 . The method of  claim 39 , wherein said scanning provides a data file comprising feature identifiers and numerical assessments of the brightness of said array information features.  
     
     
         42 . The method of  claim 39 , wherein said decoding comprises identifying an executable program using said file, and executing said program, to decode said encoded information and provide information about said array.  
     
     
         43 . The method of  claim 42 , wherein said executable program is obtained from a remote location.  
     
     
         44 . A method for obtaining information about an array, comprising: encoding information on an array using one or more array information features; and providing information for decoding said encoded information.  
     
     
         45 . The method of  claim 44 , wherein said array information is provided from a location remote to said array.  
     
     
         46 . A method of assaying a sample, said method comprising: 
 (a) contacting said sample with an array comprising one or more array information features,    (b) reading said array with an array scanner to obtain data, and    (c) decoding said data using a computer readable medium of  claim 31  to provide information for said array.    
     
     
         47 . The method according to  claim 46 , wherein said array is a nucleic acid array.  
     
     
         48 . A method comprising transmitting a result obtained from a method of  claim 46  from a first location to a second location.  
     
     
         49 . The method of  claim 48 , where said second location is a remote location.  
     
     
         50 . A method comprising receiving data representing said data obtained by the method of  claim 46 .  
     
     
         51 . A kit for use with an array scanner, said kit comprising: 
 (a) a computer-readable medium according to  claim 31;  and    (b) instructions for operating said scanner according to said programming.    
     
     
         52 . The kit of  claim 51 , further comprising an array.  
     
     
         53 . A kit for use with an array scanner, said kit comprising: (a) an array comprising array information features; and 
 (b) instructions for obtaining information for decoding encoded array information encoded by said array information features.