Method for detecting a biological entity in a sample
AssigneeScience Applications International Corporation
InventorsRobert Paul Schaudies, Doreen Robinson
Life of this patent
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Abstract
The invention relates to the detection of a biological entity in a sample. More particularly, the invention relates to detection of specific pathogens from a possible presence of hundreds to thousands of distinct biological species. The invention provides new assays that can detect the presence of one or more biological entity in a sample out of a possible number of hundreds to thousands of distinct biological species. The method according to the invention for detecting a biological entity in a sample comprises randomly amplifying nucleic acids in the sample to produce labeled nucleic acids; hybridizing the labeled nucleic acids to an array of predetermined nucleic acids; and detecting the labeled nucleic acids that have hybridized to the array.
Claims104
A method for detecting one or more biological entities in a sample, comprising:
- (a) combining one or more nucleic acid sequences in a sample with multiple primers comprising randomized nucleotide sequences, said randomized sequences being sufficiently randomized such that substantially all of the nucleic acid sequences of a biological entity are represented among amplification products;
- (b) randomly amplifying the sample nucleic acid sequences to produce nucleic acid amplification products;
- (c) combining the amplification products with an array of predetermined nucleic acid sequences including redundancies which redundancies comprise multiple distinct nucleic acids from the same target entity and such that at least a portion of the amplification products hybridize to the array;
- and
- (d) detecting amplification products that hybridize to the array.
A method for detecting one or more biological entities in a sample, comprising:
- (a) combining one or more nucleic acid sequences in a sample with multiple primers comprising randomized nucleotide sequences, said randomized sequences being sufficiently randomized such that substantially all of the nucleic acid sequences of a biological entity are represented among amplification products;
- (b) randomly amplifying the sample nucleic acid sequences to produce nucleic acid amplification products;
- (c) combining the amplification products with an array of predetermined nucleic acid sequences including positive controls, negative controls and redundancies which redundancies comprises multiple distinct nucleic acids from the same target entity and such that at least a portion of the amplification products hybridize to the array;
- and
- (d) detecting amplification products that hybridize to the array.
A method for detecting one or more biological entities in a sample, comprising:
- (a) combining nucleic acid sequences in a sample with multiple primers comprising randomized nucleotide sequences, said randomized sequences being sufficiently randomized such that substantially all of the nucleic acid sequences of a biological entity are represented among amplification products;
- (b) randomly amplifying the sample nucleic acid sequences to produce nucleic acid amplification products;
- (c) combining the amplification products with an array of predetermined nucleic acid sequences having a know spatial arrangement or relationship to each other and further comprising redundancies which redundancies comprise multiple distinct nucleic acids from the same target entity and such that at least a portion of the amplification products hybridize to the array;
- and
- (d) detecting amplification products that hybridize to the array.
A method for detecting one or more biological entities in a sample, comprising:
- (a) combining nucleic acid sequences in a sample with multiple primers comprising randomized nucleotide sequences, said randomized sequences being sufficiently randomized such that substantially all of the nucleic acid sequences of a biological entity are represented among amplification products;
- (b) randomly amplifying the sample nucleic acid sequences at each cycle of the polymerase chain reaction, to produce nucleic acid amplification products;
- (c) combining the amplification products with an array of predetermined nucleic acid sequences including redundancies which redundancies comprise multiple distinct nucleic acids from the same target entity and such that at least a portion of the amplification products hybridize to the array and wherein the redundancies on the array further comprise more than one copy of the same nucleic acid sequences;
- and
- (d) detecting amplification products that hybridize to the array.
A method for detecting one or more biological entities of a plurality of preselected biological entities potentially present in a sample, comprising:
- (a) combining nucleic acid sequences in a sample with multiple primers comprising randomized nucleotide sequences, said randomized sequences being sufficiently randomized such that substantially all of the nucleic acid sequences of a biological entity are represented among amplification products;
- (b) randomly amplifying the sample nucleic acid sequences to produce nucleic acid amplification products;
- (c) hybridizing the amplification products to an array of predetermined positions on the array in a predetermined pattern, wherein the nucleic acid sequences at the predetermined positions characterize at least one of the plurality of preselected biological entities and wherein the array comprises redundancies which redundancies comprise multiple distinct nucleic acids from the same target entity and
- (d) detecting amplification products that hybridize to the array.
A method for detecting one or more pathogens in a sample, wherein the pathogens are used for the production of biological weapons for terrorism or battlefield use, comprising:
- (a) combining one or more nucleic acid sequences in a sample with multiple primers comprising randomized nucleotide sequences, said randomized sequences being sufficiently randomized such that substantially all of the nucleic acid sequences of a biological entity are represented among amplification products;
- (b) randomly amplifying the sample nucleic acid sequences to produce nucleic acid amplification products;
- (c) combining the amplification products with an array of predetermined nucleic acid sequences including redundancies which redundancies comprise multiple distinct nucleic acids from the same target entity and such that at least a portion of the amplification products hybridize to the array;
- and
- (d) detecting amplification products that hybridize to the array.
Dependencies are inferred from the claim text.