Systems and Methods for Sequencing of Cell-Free RNA

A method comprising:

• (a) obtaining a sample comprising a plurality of cell-free nucleic acid molecules, the plurality of cell-free nucleic acid molecules comprising a plurality of cell-free RNA molecules from a biological sample of an individual or a plurality of DNA molecules complementary to the plurality of cell-free RNA molecules;
• (b) obtaining a panel of nucleic acid molecules that enriches for nucleic acids from a subset of a whole exome, wherein the subset comprises at least 5% of target genes identified in Table 3, wherein the target genes are rarely abundant as cell-free RNA transcripts within a plurality of control liquid biopsies;
• and
• (c) enriching from the sample for the nucleic acids by contacting the sample with the panel of nucleic acid molecules.

A method comprising:

• (a) obtaining, by a computer system, sequencing read data of a plurality of cell-free RNA molecules from a biological sample of an individual;
• (b) aligning, by the computer system, the sequencing read data to a reference database to identify a first gene expression profile of a plurality of genes from which the plurality of cell-free RNA molecules is transcribed;
• (c) excluding, by the computer system, a gene expression contribution of platelets from the first gene expression profile, thereby generating a second gene expression profile of the plurality of genes that lacks the gene expression contribution from the platelets;
• and
• (d) determining, by the computer system, a gene expression signature of at least one gene within the second gene expression profile, wherein the gene expression signature is associated with a biological condition of the individual.