Compositions and methods for metagenome biomarker detection
AssigneeThe Trustees of the University of Pennsylvania
InventorsErle S. Robertson, James Alwine
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Abstract
The present invention provides compositions and methods for the multiplex detection of biomarkers in an environmental, non-biological or biological sample. Compositions and methods are provided for simultaneously detecting and identifying multiple pathogens, including viruses, bacteria, fungi, protozoa and helminths, present in a sample.
Claims6
A method of detecting one or more target nucleic acid molecules in a sample, comprising the use of a set of probes, the set of probes made by a method comprising:
- generating a metagenome in silico by compiling individual genomes, genes and partial sequences present in the sample into a local database and masking low complexity sequences, wherein the metagenome comprises a plurality of nucleic acid sequences;
- comparing each sequence in the metagenome against all others;
- and
- selecting nucleic acid probes that specifically target a unique nucleic acid sequence in the metagenome,
- wherein each unique target nucleic acid sequence is a 250-300 bp region with no more than 50 contiguous nucleotides having 70% or greater sequence homology to any other sequence in the metagenome or to the human genome;
- wherein the set of probes comprises at least 60,000 probes specific for pathogens selected from the group consisting of viral, bacterial, fungal, helminth, and protozoan pathogens;
- the method comprising hybridizing one or more sample nucleic acid molecules to the set of probes, wherein the sample nucleic acid molecules are labeled with a detectable moiety;
- and
- detecting a signal from the hybridizing of the nucleic acid probe with the sample nucleic acid molecule labeled with the detectable moiety, as compared to a reference.
A method of detecting one or more target nucleic acid molecules in a sample, comprising the use of a set of probes, the set of probes made by a method comprising:
- generating a metagenome in silico by compiling individual genomes, genes and partial sequences present in the sample into a local database, and concatenating the individual genomes, genes and partial sequences into a single metagenome, wherein the metagenome comprises a plurality of nucleic acid sequences;
- comparing each sequence in the metagenome against all others;
- and
- selecting nucleic acid probes that specifically target a unique nucleic acid sequence in the metagenome,
- wherein each unique target nucleic acid sequence is a 250-300 bp region with no more than 50 contiguous nucleotides having 70% or greater sequence homology to any other sequence in the metagenome or to the human genome;
- wherein the set of probes comprises at least 60,000 probes specific for pathogens selected from the group consisting of viral, bacterial, fungal, helminth, and protozoan pathogens;
- the method comprising hybridizing one or more sample nucleic acid molecules to the set of probes, wherein the sample nucleic acid molecules are labeled with a detectable moiety;
- and
- detecting a signal from the hybridizing of the nucleic acid probe with the sample nucleic acid molecule labeled with the detectable moiety, as compared to a reference.
Dependencies are inferred from the claim text.