Personalized crispr profiling for cancer

A method of treating cancer in a subject in need thereof, the method comprising administering to the subject a therapeutic molecule selected from a compilation of therapeutic molecules;

• wherein the cancer in the subject has been determined to be susceptible to the selected therapeutic molecule by a method comprising:
• a) contacting a sample of cancer cells from the subject with a library of gene modulatory reagents to generate a plurality of modified cancer cells, wherein each modified cancer cell harbors one or more of the gene modulatory reagents, wherein the one or more of the gene modulatory reagents are capable of knocking down the function of a gene that encodes a protein target of a therapeutic molecule in the library of therapeutic molecules, wherein the one or more of the gene modulatory reagents does not cleave DNA, and
• b) sequencing the plurality of modified cancer cells, wherein a gene modulatory reagent that impairs cell viability or proliferation rate will have fewer sequence reads than a gene modulatory reagent that does not impair cell viability of proliferation rate, wherein the one or more of the gene modulatory reagents capable of knocking down the function of the gene comprise a sequence complementarity to a gene that encodes for the protein targeted by the selected therapeutic molecule.

A method of perturbing gene function in a plurality of modified cancer cells from a subject having cancer, the method comprising delivering a library of gene modulatory reagents to a sample of cancer cells from the subject to generate the plurality of modified cancer cells;

• wherein each modified cancer cell harbors one or more of the gene modulatory reagents, and each gene modulatory reagent is capable of perturbing the function of a gene that encodes a protein target from a compilation of protein targets.

A compilation comprising a plurality of modified cancer cells, wherein each modified cancer cell harbors one or more gene modulatory reagents, and each gene modulatory reagent is capable of knocking down the function of a gene that encodes a protein target from a compilation of protein targets.

A method of evaluating the functional effect of perturbing gene activity in cancer cells from a subject, the method comprising:

• sequencing a plurality of modified cancer cells, wherein each modified cancer cell harbors one or more gene modulatory reagents, each gene perturbation reagent capable of knocking down the function of a gene that encodes a protein target in a library of protein targets;
• and wherein a gene perturbation reagent that impairs cell viability or proliferation rate will have fewer sequence reads than a gene perturbation reagent that does not impair cell viability or proliferation rate.

A library comprising a plurality of gene perturbation reagents, each gene perturbation reagent capable of knocking down the function of a gene that encodes a protein target from a library of protein targets.

A CRISPR interference (CRISPRi) system comprising a single vector transfer plasmid system comprising:

• a) a first promoter operably linked to a first nucleotide sequence encoding a catalytically inactive RNA-directed nuclease fused to a transcriptional repressor;
• and b) a second promoter operably linked to a second nucleotide sequence encoding a single-guide RNA (sgRNA) sequence comprising a CRISPR RNA (crRNA) sequence having complementarity to at least a portion of a gene that encodes a protein target and a trans-activating CRISPR RNA (tracrRNA) sequence.