System for indentification of pathogens
First Claim
1. A system for identifying a pathogen, said system comprising:
- a.) an automatic fluidics control system configured to receive two or more amplification products of nucleic acid of said pathogen, said two or more amplification products produced with two or more primer pairs wherein at least one of said two or more primer pairs hybridizes to conserved coding regions of a nucleic acid gene sequence wherein said conserved regions flank at least one variable coding region of said nucleic acid gene sequence of said pathogen;
b.) a mass spectrometer configured to directly receive said two or more amplification products from said fluidics control system and configured to provide two or more molecular masses of said two or more amplification products;
c.) a computer program stored on a computer readable medium configured to receive and convert said two or more molecular masses to two or more base compositions wherein said base compositions identify the number but not the nucleic acid gene sequence order of A residues, C residues, T residues, G residues, U residues, analogues thereof or mass tag residues thereof in said two or more amplification products without sequencing said two or more amplification products;
d.) a database stored on a computer readable medium, said database comprising, for at least 19 known pathogens, base compositions of amplification products each indexed to a corresponding primer pair and a pathogen, wherein said amplification products have a variable region flanked by conserved coding regions and wherein at least one of said two or more primer pairs hybridizes to said conserved coding region; and
,e.) a pathogen identification module configured to receive said two or more base compositions from said computer program, and configured to query said received two or more base compositions against said database and configured to determine a match between said two or more base compositions and a member of said at least nineteen base compositions of said database.
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Abstract
The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.
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Citations
25 Claims
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1. A system for identifying a pathogen, said system comprising:
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a.) an automatic fluidics control system configured to receive two or more amplification products of nucleic acid of said pathogen, said two or more amplification products produced with two or more primer pairs wherein at least one of said two or more primer pairs hybridizes to conserved coding regions of a nucleic acid gene sequence wherein said conserved regions flank at least one variable coding region of said nucleic acid gene sequence of said pathogen; b.) a mass spectrometer configured to directly receive said two or more amplification products from said fluidics control system and configured to provide two or more molecular masses of said two or more amplification products; c.) a computer program stored on a computer readable medium configured to receive and convert said two or more molecular masses to two or more base compositions wherein said base compositions identify the number but not the nucleic acid gene sequence order of A residues, C residues, T residues, G residues, U residues, analogues thereof or mass tag residues thereof in said two or more amplification products without sequencing said two or more amplification products; d.) a database stored on a computer readable medium, said database comprising, for at least 19 known pathogens, base compositions of amplification products each indexed to a corresponding primer pair and a pathogen, wherein said amplification products have a variable region flanked by conserved coding regions and wherein at least one of said two or more primer pairs hybridizes to said conserved coding region; and
,e.) a pathogen identification module configured to receive said two or more base compositions from said computer program, and configured to query said received two or more base compositions against said database and configured to determine a match between said two or more base compositions and a member of said at least nineteen base compositions of said database.
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2. A method for identifying a pathogen comprising:
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a.) providing a system, said system comprising; i.) an automatic fluidics control system configured to receive two or more amplification products of nucleic acid of said pathogen, said two or more amplification products produced with two or more primer pairs; ii.) a mass spectrometer configured to directly receive said two or more amplification products from said fluidics control system and configured to provide two or more molecular masses of said two or more amplification products; iii.) a computer program stored on a computer readable medium configured to receive and convert said two or more molecular masses to two or more base compositions wherein said base compositions identify the number but not the nucleic acid gene sequence order of A residues, C residues, T residues, G residues, U residues, analogues thereof or mass tag residues thereof in said two or more amplification products without sequencing said two or more amplification products; iv.) a database stored on a computer readable medium, said database comprising, for at least 19 known pathogens, base compositions of amplification products each indexed to a corresponding primer pair and a pathogen, wherein said amplification products have a variable region flanked by conserved coding regions and wherein at least one of said two or more primer pairs hybridizes to said conserved coding region; v.) a pathogen identification module configured to receive said two or more base compositions from said computer program, and configured to query said received two or more base compositions against said database and configured to determine a match between said two or more base compositions and a member of said at least nineteen base compositions of said database; and vii.) a display interface configured to produce a pathogen identification report from said match; b.) obtaining nucleic acid of said pathogen; c.) amplifying said nucleic acid with said two or more primer pairs to obtain two or more amplification products, wherein at least one of said two or more primer pairs hybridizes to conserved coding regions of a nucleic acid gene sequence wherein said conserved regions flank at least one variable coding region of said nucleic acid gene sequence of said pathogen; d.) transferring said two or more amplification products to said mass spectrometer using said automated fluidics control system; e.) measuring two or more molecular masses of said two or more amplification products using said mass spectrometer; f.) converting said two or more molecular masses to two or more base compositions using said computer program without sequencing said two or more amplification products; and g.) determining a match between said two or more base compositions and a member of said plurality of base compositions of said database using said pathogen identification module, wherein said member of said at least nineteen base compositions is a known amplification product of a known pathogen produced with said two or more primer pairs, and wherein said match identifies said pathogen. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A system for identifying a pathogen, said system comprising:
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a.) an automatic fluidics control system configured to receive two or more amplification products of nucleic acid of said pathogen, said two or more amplification products produced with two or more primer pairs wherein at least one of said two or more primer pairs hybridizes to conserved coding regions of a nucleic acid gene sequence wherein said conserved regions flank at least one variable coding region of said nucleic acid gene sequence of said pathogen; b.) a mass spectrometer configured to directly receive said two or more amplification products from said fluidics control system and configured to provide two or more molecular masses of said two or more amplification products; c.) a computer program stored on a computer readable medium configured to receive and convert said two or more molecular masses to two or more base compositions wherein said base compositions identify the number but not the nucleic acid gene sequence order of A residues, C residues, T residues, G residues, U residues, analogues thereof or mass tag residues thereof in said two or more amplification products without sequencing said two or more amplification products; d.) a database stored on a computer readable medium, said database comprising, for at least 19 known pathogens, base compositions of amplification products each indexed to a corresponding primer pair and a pathogen, wherein said amplification products have a variable region flanked by conserved coding regions and wherein at least one of said two or more primer pairs hybridizes to said conserved coding region; e.) a pathogen identification module configured to receive said two or more base compositions from said computer program, and configured to query said received two or more base compositions against said database and configured to determine a match between said two or more base compositions and a member of said at least nineteen base compositions of said database; and f.) a display interface configured to produce a pathogen identification report from said match. - View Dependent Claims (15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
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Specification