Method of Detecting Genetic Mutations
First Claim
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1. A method of detecting, or determining the frequency of, a mutation or nucleotide modification in a multiplicity of nucleic acid templates comprising:
- i) embedding a multiplicity of nucleic acid templates and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;
ii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;
iii) treating the composition resulting from step (ii) under conditions such that said modified and/or unmodified amplification primers hybridize to said nucleic acid templates to form primed templates;
iv) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates;
v) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support;
vi) hybridizing sequencing primers to said immobilized single stands resulting from step (v) and effecting extension of said hybridized sequencing primers in the presence of at least two nucleotides bearing different detectable labels to form extension products, wherein one of said nucleotides is incorporated into said extension product when said immobilized single strand bears said mutation or nucleotide modification and the other of said nucleotides is incorporated into said extension product when said immobilized single strand does not bear said mutation or modified nucleotide; and
vii) detecting the extension products of the sequencing primers resulting from step (vi), and determining the presence of, or the frequency of, said nucleic acid templates bearing said mutated or modified nucleotide.
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Abstract
The present invention relates, in general, to drug resistance, and, in particular, to a method of detecting drug resistance populations, including minor drug resistance viral populations.
5 Citations
27 Claims
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1. A method of detecting, or determining the frequency of, a mutation or nucleotide modification in a multiplicity of nucleic acid templates comprising:
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i) embedding a multiplicity of nucleic acid templates and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;ii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;iii) treating the composition resulting from step (ii) under conditions such that said modified and/or unmodified amplification primers hybridize to said nucleic acid templates to form primed templates; iv) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates; v) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support; vi) hybridizing sequencing primers to said immobilized single stands resulting from step (v) and effecting extension of said hybridized sequencing primers in the presence of at least two nucleotides bearing different detectable labels to form extension products, wherein one of said nucleotides is incorporated into said extension product when said immobilized single strand bears said mutation or nucleotide modification and the other of said nucleotides is incorporated into said extension product when said immobilized single strand does not bear said mutation or modified nucleotide; and vii) detecting the extension products of the sequencing primers resulting from step (vi), and determining the presence of, or the frequency of, said nucleic acid templates bearing said mutated or modified nucleotide. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method of determining viral load in a patient comprising:
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i) extracting viral DNA from a biological sample from said patient; ii) embedding said DNA and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;iii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;iv) treating the composition resulting from step (iii) under conditions such that said modified and/or unmodified amplification primers hybridize to said DNA to form primed templates, v) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates; vi) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support; vii) hybridizing sequencing primers to said immobilized single stands resulting from step (vi) and effecting extension of said hybridized sequencing primers in the presence of at least one nucleotide bearing a detectable label to form extension products; and viii) detecting labeled extension products resulting from step (vii), and thereby determining said viral load. - View Dependent Claims (19, 20, 21)
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22. A method of determining viral load in a patient comprising:
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i) extracting viral RNA from a biological sample from said patient; ii) reverse transcribing said RNA to produce cDNA and embedding said cDNA and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;iii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;iv) treating the composition resulting from step (iii) under conditions such that said modified and/or unmodified amplification primers hybridize to said cDNA to form primed templates, v) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates; vi) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support; vii) hybridizing sequencing primers to said immobilized single stands resulting from step (vi) and effecting extension of said hybridized sequencing primers in the presence of at least one nucleotide bearing a detectable label to form labeled extension products; and viii) detecting labeled extension products resulting from step (vii), and thereby determining said viral load.
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23. A method of determining viral load in a patient comprising:
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i) extracting viral DNA from a biological sample from said patient; ii) embedding said DNA and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;iii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;iv) treating the composition resulting from step (iii) under conditions such that said modified and/or unmodified amplification primers hybridize to said DNA to form primed templates, v) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates; vi) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support; vii) hybridizing a labeled probe specific for said virus to said immobilized single stands resulting from step (vi) to form a labeled duplex; and viii) detecting the presence of said labeled duplex, and thereby determining said viral load. - View Dependent Claims (24)
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25. A method of determining viral load in a patient comprising:
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i) extracting viral RNA from a biological sample from said patient; ii) reverse transcribing said RNA to form cDNA and embedding said cDNA and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;iii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;iv) treating the composition resulting from step (iii) under conditions such that said modified and/or unmodified amplification primers hybridize to said cDNA to form primed templates, v) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates; vi) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support; vii) hybridizing a labeled probe specific for said virus to said immobilized single stands resulting from step (vi) to form a labeled duplex; and viii) detecting the presence of said labeled duplex, and thereby determining said viral load.
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26. A method of detecting a mutation or nucleotide modification in a multiplicity of nucleic acid templates derived from DNA isolated from a biological sample comprising:
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i) embedding said multiplicity of nucleic acid templates and modified 3′
amplification primers or modified 5′
amplification primers in a semi-solid support under conditions such that said modified amplification primers are immobilized in said semi-solid support;ii) contacting said semi-solid support resulting from step (i) with a polymerase, deoxynucleotide triphosphates (dNTPs), and unmodified 5′
or 3′
amplification primers;iii) treating the composition resulting from step (ii) under conditions such that said modified and/or unmodified amplification primers hybridize to said nucleic acid templates to form primed templates, iv) effecting amplification of said primed templates in said semi-solid support, wherein double-stranded products of said amplification localize around said primed templates; v) denaturing said double-stranded amplification products and removing resulting single strands not immobilized in said semi-solid support; vi) hybridizing sequencing primers to said immobilized single stands resulting from step (v) and effecting extension of said hybridized sequencing primers in the presence of a nucleotide bearing a detectable label, wherein said nucleotide bearing said detectable label is incorporated into said extension product when said immobilized single strand bears said mutation or nucleotide modification so that a labeled extension product is formed; and viii) detecting labeled extension products resulting from step (vii), and thereby determining the presence of said mutation or nucleotide modification. - View Dependent Claims (27)
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Specification