Methods and compositions for enriching non-host sequences in host samples

Abstract

Disclosed are compositions and methods for enriching a non-host sequence from a host sample. Also disclosed are compositions and methods for detecting a non-host sequence in a host sample. For example, a pathogen can be enriched and detected in a sample taken from a human without knowing what the pathogen is.

1 .- 74 . (canceled) 
     
     
         75 . A method of enriching non-human nucleic acids from a human sample comprising selectively amplifying nucleic acids isolated from the human sample using non-human target primers to form an enriched population of non-human nucleic acids, wherein the non-human target primers do not bind to at least the top 1,000 human B cell transcripts. 
     
     
         76 . The method of  claim 75 , wherein the nucleic acids isolated from the human sample are selected from the group consisting of DNA and RNA. 
     
     
         77 . The method of  claim 75  further comprising performing subtractive hybridization against a population of reference human cDNAs, wherein the subtractive hybridization results in a further enriched population of non-human nucleic acids. 
     
     
         78 . The method of  claim 75 , wherein the top 1,000 human B cell transcripts comprise at least 65% of all human B cell transcripts. 
     
     
         79 . The method of  claim 75 , wherein the top 1,000 human B cell transcripts are greater than 200 base pairs in length. 
     
     
         80 . The method of  claim 75 , wherein the non-human target primers do not bind to at least the top 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000 human B cell transcripts or whole human B cell transcriptome. 
     
     
         81 . The method of  claim 75 , wherein the non-human nucleic acids are pathogenic sequences. 
     
     
         82 . The method of  claim 81 , wherein the pathogenic sequences are from viruses, bacteria, fungi, or any infectious agents. 
     
     
         83 . A method of enriching non-human nucleic acids from a human sample comprising hybridizing a set of non-human target primers to total RNA or mRNA isolated from the human sample and selectively reverse transcribing total RNA or mRNA isolated from the human sample to form an enriched population of non-human cDNA strands, wherein the set of non-human target primers do not hybridize to at least the top 1,000 human B cell transcripts. 
     
     
         84 . The method of  claim 83  further comprising performing subtractive hybridization against a population of reference human cDNAs, wherein the subtractive hybridization results in a further enriched population of non-human cDNAs. 
     
     
         85 . The method of  claim 83 , wherein the top 1,000 human transcripts comprise at least 65% of all human B cell transcripts. 
     
     
         86 . The method of  claim 83 , wherein the top 1,000 human B cell transcripts are greater than 200 base pairs in length. 
     
     
         87 . The method of  claim 83 , wherein the non-human target primers do not bind to at least the top 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000 human transcripts or whole human transcriptome. 
     
     
         88 . The method of  claim 83 , wherein the non-human nucleic acids are pathogenic sequences. 
     
     
         89 . The method of  claim 88 , wherein the pathogenic sequences are from viruses, bacteria, fungi, or any infectious agents. 
     
     
         90 . A diagnostic assay, comprising non-human target primers for amplifying nucleic acids from a human sample to form an enriched population of non-human nucleic acids, wherein the non-human target primers do not bind to at least the top 1,000 human B cell transcripts. 
     
     
         91 . The assay of  claim 90 , wherein the top 1,000 human B cell transcripts comprise at least 65% of all human B cell transcripts. 
     
     
         92 . The assay of  claim 90 , wherein the top 1,000 human B cell transcripts are greater than 200 base pairs in length. 
     
     
         93 . The assay of  claim 90 , wherein the non-human target primers do not bind to at least the top 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000 human B cell transcripts or whole human B cell transcriptome. 
     
     
         94 . The assay of  claim 90 , wherein the non-human target primers are at least the oligonucleotides in  FIG. 10  or  FIG. 11 .