Targeted cell free nucleic acid analysis

Abstract

Methods of isolating cell free RNA from individual's bodily fluid and reliably obtain cell free RNA data are presented, preferably by use of high-stability portions and/or use of targeted small amplicons on the cell free RNA.

What is claimed is: 
     
         1 . A method of isolating cell free RNA, comprising:
 obtaining a sample containing cell free RNA from an individual, wherein the cell free RNA comprises a high stability portion located within 200 base pairs from the 5′-end of the cell free RNA;   contacting the sample with a synthetic nucleic acid, wherein the synthetic nucleic acid is configured to bind to at least a portion of 5′-portion of the cell free RNA and form a cell free RNA-synthetic nucleic acid complex; and   isolating the cell free RNA-synthetic nucleic acid complex.   
     
     
         2 . The method of  claim 1 , wherein the sample is a bodily fluid of the individual. 
     
     
         3 . The method of  claim 1 , wherein the cell free RNA is derived from at least one of the following: a cancer-related gene, a cancer-specific gene, a DNA-repair gene, a neoepitope, and a gene not associated with a disease. 
     
     
         4 . The method of  claim 1 , wherein the neoepitope is tumor-specific and individual-specific. 
     
     
         5 . The method of  claim 1 , wherein cell free RNA is a small noncoding RNA. 
     
     
         6 . The method of  claim 1 , wherein the synthetic nucleic acid is a double-stranded DNA, and the cell free RNA-synthetic nucleic acid complex is a DNA-RNA triplex. 
     
     
         7 . The method of  claim 1 , wherein the synthetic nucleic acid is a single-stranded DNA, and cell free RNA-synthetic nucleic acid complex is a DNA-RNA hybrid double helix. 
     
     
         8 . The method of  claim 1 , wherein the synthetic nucleic acid is immobilized on a solid carrier at least by one end of the synthetic nucleic acid. 
     
     
         9 . The method of  claim 8 , wherein the synthetic nucleic acid is immobilized via at least one of a nanoparticle, a magnetic bead, a glass bead, a biotin bead, and a quantum dot. 
     
     
         10 . The method of  claim 8 , wherein the synthetic nucleic acid is immobilized on the solid carrier via a covalent bonding to a surface of the solid carrier. 
     
     
         11 . The method of  claim 1 , wherein the portion of the 5′-portion of the cell free RNA is within 500 or 200 base pairs from 5′-end of the cell free RNA. 
     
     
         12 . The method of  claim 1 , wherein the portion of the 5′-portion of the cell free RNA is within 150 or 120 base pairs from 5′-end of the cell free RNA. 
     
     
         13 . The method of  claim 1 , wherein the isolating comprises separating the RNA-synthetic nucleic acid complex by at least one of a change in molecular weight and a conformational change. 
     
     
         14 . The method of  claim 1 , wherein the synthetic nucleic acid is labeled with a tag, and the isolating comprises separating the RNA-synthetic nucleic acid complex using the tag. 
     
     
         15 . The method of  claim 1 , further comprising amplifying the cell free RNA from the isolated cell free RNA-synthetic nucleic acid complex to obtain the cell free RNA data, wherein the cell free RNA data comprises at least one of RNA sequence data and RNA expression level data. 
     
     
         16 . The method of  claim 15 , wherein the RNA sequence data are selected from the group consisting of mRNA sequence data and splice variant data. 
     
     
         17 . The method of  claim 15 , wherein the RNA expression level data are selected from the group consisting of a quantity of RNA transcript and a quantity of a small noncoding RNA.