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`CLAIMS
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`1. A system for generating a report identifying a therapeutic agent for an individual with a cancer
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`comprising:
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`a. at least one nucleic acid sequencing device configured to assay a plurality of molecular targets in a
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`biological sample from the individual to determine a nucleic acid sequence for the each of the
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`plurality of molecular targets, wherein the plurality of molecular targets comprises AR, BRAF,
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`CTNNBl, EGFR, ERRBZ, ESRl, KIT, KRAS, MET, MLHl, PDGFRA, PDGFRB, PIK3CA
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`(PI3K), PTEN, and TOPl,
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`b.
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`at least one computer database comprising:
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`i.
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`a reference sequence for each of the plurality of molecular targets; and
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`ii.
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`a listing of available therapeutic agents with efficacy linked to each of the plurality of
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`molecular targets;
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`c.
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`a computer-readable program code comprising instructions to input the nucleic acid sequences for
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`the each of the plurality of molecular targets and to compare each of the sequences with a
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`corresponding reference sequence from the at least one computer database in (b)(i);
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`d.
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`a computer-readable program code comprising instructions to access the at least one computer
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`database and to identify at least one therapeutic agent from the listing of available therapeutic
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`agents in (b)(ii), wherein the comparison to the reference in (c) indicates a likely benefit of the at
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`least one therapeutic agent for treating the cancer; and
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`e.
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`a computer-readable program comprising instructions to generate a report that comprises a listing
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`of the molecular targets for which the comparison to the reference sequence indicated a likely
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`benefit of the at least one therapeutic agent in (d) and the at least one therapeutic agent identified
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`in (d).
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`The system of claim 1, wherein the nucleic acid sequences are input into the system from a location
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`that is remote from the at least one computer database.
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`The system of claim 1, wherein the nucleic acid sequences are input into the system over an intemet
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`connection.
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`-160-
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`Docket No. 37901-715331
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`The system of claim 1, wherein the report is in electronic or paper format.
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`The system of claim 1, wherein the at least one computer database filI'tl’lCl‘ comprises data
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`corresponding to at least one clinical trial of a molecular target.
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`The system of claim 1, wherein the reference sequence for each of the plurality of molecular targets
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`comprises a wild type nucleic acid sequence for that molecular target.
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`The system of claim 1, wherein the nucleic acid sequences are determined after the individual has
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`received drug therapy for the cancer.
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`The system of claim 1, wherein the nucleic acid sequences are determined by assessing nucleic acid
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`collected from a cell, a tissue sample, a blood sample or any combination thereof.
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`The system of claim 1, wherein each reference sequence is obtained from at least one individual
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`without the cancer.
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`10.
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`11.
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`12.
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`13.
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`14.
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`The system of claim 1, wherein the plurality of molecular targets finther comprises ATRX (RAD54),
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`CDHl (UVOMORULIN), CDKNlB (p27/kip1), CDKNZA (METASTASIN (MTS-1)), ERBB4,
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`MYC (c-MYC), RADS 1, and WISP3 (LOST IN INFLAMMATORY BREAST CANCER (LIBC)).
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`The system of claim 1, wherein the report filI'tl’lCl‘ comprises a listing of at least one additional
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`molecular target for which the comparison to the reference in (c) indicates a likely lack of benefit of
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`at least one therapeutic agent and the at least one additional therapeutic agent.
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`The system of claim 1, filI'tl’lCl‘ comprising a computer-readable program code comprising instructions
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`to prioritize the list of the at least one therapeutic agent.
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`The system of claim 12, wherein the report provides a prioritized list of the at least one therapeutic
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`agent.
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`The system of claim 1, wherein the individual has been treated by and failed to respond to at least one
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`cancer therapeutic.
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`Docket No. 37901-715331
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`15.
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`16.
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`17.
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`The system of claim 1, wherein the at least one device configured to assay the plurality of molecular
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`targets is configured to perform next generation (NextGen) sequencing.
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`The system of claim 1, wherein the at least one deVice configured to assay the plurality of molecular
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`targets is configured to perform at least one of polymerase chain reaction (PCR), pyrosequencing,
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`real-time PCR, sequencing, NextGen sequencing, methylation specific PCR (MSPCR), restriction
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`fragment length polymorphism (RFLP analysis), immunohistochemistry (IHC), immunoassay, an
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`eXpression microarray, a comparative genomic hybridization (CGH) microarray, a single nucleotide
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`polymorphism (SNP) microarray, in-situ hybridization (ISH), fluorescent in-situ hybridization
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`(FISH), and a proteomic array.
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`The system of claim 1, wherein the at least one nucleic acid sequencing deVice is configured to
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`identify at least one of a mutation, polymorphism, deletion, insertion, substitution, translocation,
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`fi1sion, break, duplication, amplification or repeat in a nucleic acid sequence corresponding to each of
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`the plurality of molecular targets
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`-162-
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`Docket No. 37901-715331
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