Arrays of nucleic acid probes for analyzing biotransformation genes and methods of using the same

An array of oligonucleotide probes immobilized on a solid support, the array comprising at least four sets of nucleic acid probes,

• (1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least six nucleotides exactly complementary to a subsequence of a reference sequence, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence,
• (2) second, third and fourth probe sets, each comprising a corresponding probe for each probe in the first probe set, the probes in the second, third and fourth probe sets being identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least six 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;
• provided the array does not consist of a complete set of probes of a given length wherein a complete set is all permutations of nucleotides A, C, G and T/U;
• wherein the reference sequence is from a biotransformation gene.

A block of nucleic acid probes immobilized on a solid support, comprising:

• a perfectly matched probe comprising a segment of at least six nucleotides exactly complementary to a subsequence of a reference sequence, the segment having a plurality of interrogation positions respectively corresponding to a plurality of nucleotides in the reference sequence,
• for each interrogation position, three mismatched probes, each identical to a sequence comprising the perfectly matched probe or a subsequence of at least six nucleotides thereof including the plurality of interrogation positions, except in the interrogation position, which is occupied by a different nucleotide in each of the three mismatched probes and the perfectly matched probe;
• provided the array does not consist of a complete set of probes of a given length, wherein a complete set is all permutations of nucleotides A, C, G and T/U;
• wherein the reference sequence is from a biotransformation gene.

An array of nucleic acid probes immobilized on a solid support, the array comprising at least four probes:

• a first probe comprising first and second segments, each of at least three nucleotides and exactly complementary to first and second subsequences of a reference sequence, the segments including at least one interrogation position corresponding to a nucleotide in the reference sequence, wherein either (1) the first and second subsequences are noncontiguous, or (2) the first and second subsequences are contiguous and the first and second segments are inverted relative to the complement of the firsthand second subsequences in the reference sequence;
• second, third and fourth probes, identical to a sequence comprising the first probe or a subsequence thereof comprising at least three nucleotides from each of the first and second segments, except in the at least one interrogation position, which differs in each of the probes;
• provided the array does not consist of a complete set of probes of a given length, wherein a complete set is all permutations of nucleotides A, C, G and T/U;
• wherein the reference sequence is from a biotransformation gene.

A method of comparing a target nucleic acid with a reference sequence comprising a predetermined sequence of nucleotides, the method comprising:

• (a) hybridizing a sample comprising the target nucleic acid to an array of nucleic acid probes immobilized on a solid support, the array comprising:
• (1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least six nucleotides exactly complementary to a subsequence of the reference sequence, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence, wherein the reference sequence is from a biotransformation gene;
• (2) a second probe set comprising a corresponding probe for each probe in the first probe set, the corresponding probe in the second probe set being identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least six 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 two corresponding probes from the first and second probe sets;
• wherein, the probes in the first probe set have at least three interrogation positions respectively corresponding to each of at least three nucleotides in the reference sequence, and
• (b) comparing the relative specific hybridization of two corresponding probes from the first and second probe sets;
• (c) assigning a nucleotide in the target sequence as the complement of the interrogation position of the probe having the greater specific binding;
• (d) repeating (b) and (c) by comparing the relative specific hybridization of a further two corresponding probes from the first and second probe sets until each nucleotide of interest in the target sequence has been assigned.

A method of comparing a target nucleic acid with a reference sequence comprising a predetermined sequence of nucleotides, the method comprising:

• (a) hybridizing the target nucleic acid to an array of oligonucleotide probes immobilized on a solid support, the array comprising:
• a perfectly matched probe comprising a segment of at least six nucleotides exactly complementary to a subsequence of a reference sequence, the segment having a plurality of interrogation positions respectively corresponding to a plurality of nucleotides in the reference sequence, wherein the reference sequence is from a biotransformation gene;
• for each interrogation position, three mismatched probes, each identical to a sequence comprising the perfectly matched probe or a subsequence of at least six nucleotides thereof including the plurality of interrogation positions, except in the interrogation position, which is occupied by a different nucleotide in each of the three mismatched probes and the perfectly matched probe;
• (b) for each interrogation position,
• (1) comparing the relative specific hybridization of the three mismatched probes and the perfectly matched probe;
• (2) assigning a nucleotide in the target sequence as the complement of the interrogation position of the probe having the greatest specific hybridization.

A method of screening a patient for capacity to metabolize a drug, the method comprising:

• (a) hybridizing a tissue sample from the patient containing a target nucleic acid to an array of oligonucleotide probes immobilized on a solid support, the array comprising:
• (1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of the reference sequence from a biotransformation gene which metabolizes the drug, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence,
• (2) a second probe set comprising a corresponding probe for each probe in the first probe set, the corresponding probe in the second probe set being 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 two corresponding probes from the first and second probe sets;
• wherein, the probes in the first probe set have at least three interrogation positions respectively corresponding to each of at least three nucleotides in the reference sequence, and
• (b) determining which probes, relative to one another, in the first and second probe sets specifically hybridize to the target nucleic acid, the relative specific hybridization of corresponding probes in the first and second probe sets indicating whether the target sequence contains a mutation relative to the reference sequence, which, if present, impairs the capacity of the patient to metabolize the drug.

A method of conducting a clinical trial on a drug, the method comprising:

• (a) obtaining a tissue sample containing a target nucleic acid from each of a pool of patients;
• (b) for each tissue sample, hybridizing the target nucleic acid to an array of oligonucleotide probes immobilized on a solid support, the array comprising:
• (1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of the reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence,
• (2) a second probe set comprising a corresponding probe for each probe in the first probe set, the corresponding probe in the second probe set being 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 two corresponding probes from the first and second probe sets;
• wherein, the probes in the first probe set have at least three interrogation positions respectively corresponding to each of at least three nucleotides in the reference sequence;
• (c) determining which probes, relative to one another, in the first and second probe sets specifically hybridize to the target nucleic acid, the relative specific hybridization of corresponding probes in the first and second probe sets indicating whether the target sequence contains a mutation relative to the reference sequence
• selecting a subpool of patients having a target sequence free of the mutation;
• and
• (d) administering the drug to the subpool of patients to determine efficacy.