Profiling cell types in circulating nucleic acid liquid biopsy
AssigneesThe Board of Trustees of the Leland Stanford Junior University, CZ Biohub SF, LLC
InventorsSevahn K. Vorperian, Mira N. Moufarrej, Stephen R. Quake
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Abstract
Methods and compositions for detecting specific cell types using cell-free RNA (cfRNA) are provided. In some embodiments, methods of evaluating tissue or organ function and methods of treatment are provided comprising detecting specific cell types using cfRNA.
Claims40
A method of evaluating the status of a cell type in a human, the method comprising,
- providing a biological sample from the human,
- detecting from the biological sample the presence, absence or quantity of cell-free RNA (cfRNA) from at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more or all indicative genes, wherein the cell type and indicative genes are selected from any one of Tables 1, 2, 3, 4, or 5;
- and
- generating a score based on detection of the cfRNA from the cell type and indicative genes.
A method of evaluating kidney function in a human, the method comprising,
- providing a biological sample from the human,
- detecting from the biological sample the presence, absence or quantity of cell-free RNA (cfRNA) from at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more or all indicative genes, wherein cell type and indicative genes are provided in any one or more of Tables 1-5 and Table 11;
- generating a score based on detection of the cfRNA from the cell type and indicative genes;
- comparing the score to a control value or a prior score from an earlier-obtained biological sample or from a score for a different cell type from the human, thereby evaluating kidney function in the human.
A method of evaluating brain function in a human, the method comprising,
- providing a biological sample from the human,
- detecting from the biological sample the presence, absence or quantity of cell-free RNA (cfRNA) from at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more or all indicative genes, wherein cell type and indicative genes are provided in any one or more of Tables 1-5, Table 6 and Table 8;
- generating a score based on detection of the cfRNA from the cell type and indicative genes;
- comparing the score to a control value or a prior score from an earlier-obtained biological sample from a score for a different cell type from the human, thereby evaluating brain function in the human.
A method of evaluating liver function in a human, the method comprising,
- providing a biological sample from the human,
- detecting from the biological sample the presence, absence or quantity of cell-free RNA (cfRNA) from at least 3, 4, 5, 6, 7, 8, 9, 10, or all indicative genes, wherein cell type and indicative genes are provided in any one or more of Tables 1-5 and Table 12;
- generating a score based on detection of the cfRNA from the cell type and indicative genes;
- comparing the score to a control value or a prior score from an earlier-obtained biological sample from a score for a different cell type from the human, thereby evaluating liver function in the human.
A non-transitory computer-readable storage device storing computer-executable instructions that, in response to execution, cause a processor to perform operations, the operations comprising:
- receiving data indicating presence, absence or quantity of cell-free RNA (cfRNA) from at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more or all indicative genes for a cell type, wherein cell type and indicative genes are selected from any one of Table 1, 2, 3, 4, or 5;
- generating a score based on detection of the cfRNA from the cell type and indicative genes;
- comparing the score to a control value or a prior score from an earlier-obtained biological sample from the human,
- upon determining that the score is above or below the control value or prior score, generating a classification of disease or prognosis of the human related to the cell type;
- and
- displaying the classification.
Dependencies are inferred from the claim text.