Methods for rapid identification and quantitation of nucleic acid variants
First Claim
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1. A method for analyzing a nucleic acid comprising the steps of:
- (a) obtaining a sample comprising nucleic acid for base composition analysis;
(b) selecting at least two primer pairs that will generate overlapping amplification products of at least two sub-segments of the nucleic acid;
(c) amplifying at least two nucleic acid sequences of a region of the nucleic acid designated as a target for base composition analysis using the at least two primer pairs, thereby generating at least two overlapping amplification products;
(d) determining base compositions of the amplification products by;
(i) measuring molecular masses of one or more of the amplification products generated in step (c) using a mass spectrometer; and
(ii) converting one or more of the measured molecular masses to base compositions;
(e) comparing one or more of the base compositions with a source of reference base composition data for the nucleic acid sequence; and
(f) identifying the presence of a particular nucleic acid sequence or variant thereof.
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Abstract
There is a need for nucleic acid analysis which is both specific and rapid, and in which no nucleic acid sequencing is required. The present invention addresses this need, among others by providing a method of nucleic acid amplification of overlapping sub-segments of a nucleic acid followed by molecular mass measurement of resulting amplification products by mass spectrometry, and determination of the base compositions of the amplification products.
158 Citations
36 Claims
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1. A method for analyzing a nucleic acid comprising the steps of:
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(a) obtaining a sample comprising nucleic acid for base composition analysis;
(b) selecting at least two primer pairs that will generate overlapping amplification products of at least two sub-segments of the nucleic acid;
(c) amplifying at least two nucleic acid sequences of a region of the nucleic acid designated as a target for base composition analysis using the at least two primer pairs, thereby generating at least two overlapping amplification products;
(d) determining base compositions of the amplification products by;
(i) measuring molecular masses of one or more of the amplification products generated in step (c) using a mass spectrometer; and
(ii) converting one or more of the measured molecular masses to base compositions;
(e) comparing one or more of the base compositions with a source of reference base composition data for the nucleic acid sequence; and
(f) identifying the presence of a particular nucleic acid sequence or variant thereof. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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29. A method for identifying a human comprising the steps of:
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(a) obtaining a sample comprising mitochondrial DNA of the human for base composition analysis;
(b) selecting at least two primer pairs that will generate overlapping amplification products representing sub-segments of the mitochondrial DNA;
(c) amplifying at least two nucleic acid sequences of a region of the mitochondrial DNA designated as a target for base composition analysis using the at least two primer pairs, thereby generating at least two overlapping amplification products;
(d) determining base compositions of the amplification products by;
(i) measuring molecular masses of one or more of the amplification products generated in step (c) using a mass spectrometer; and
(ii) converting one or more of the measured molecular masses to base compositions;
(e) comparing one or more of the base compositions with a source of reference base composition data for the nucleic acid sequence thereby identifying the human. - View Dependent Claims (30, 31, 32, 33, 34, 35)
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36. A method for characterizing heteroplasmy in mitochondrial DNA comprising the steps of:
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(a) obtaining a sample comprising mitochondrial DNA for base composition analysis;
(b) selecting at least two primer pairs that will generate overlapping amplification products representing sub-segments of the mitochondrial DNA;
(c) amplifying at least two nucleic acid sequences of a region of the mitochondrial DNA designated as a target for base composition analysis using the at least two primer pairs, thereby generating at least two overlapping amplification products;
(d) determining base compositions of the amplification products by;
(i) measuring molecular masses of one or more of the amplification products generated in step (c) using a mass spectrometer; and
(ii) converting one or more of the measured molecular masses to base compositions;
(e) comparing one or more of the base compositions with one or more base compositions of reference sub-segments of a reference sequence; and
(f) identifying at least two distinct amplification products with distinct base compositions obtained by the same pair of primers, thereby characterizing the heteroplasmy.
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Specification