`
`CLAIMS
`
`1. A system for generating a report identifying a therapeutic agent for an individual with a cancer
`
`comprising:
`
`a. at least one nucleic acid sequencing device configured to assay a plurality of molecular targets in a
`
`biological sample from the individual to determine a nucleic acid sequence for the each of the
`
`plurality of molecular targets, wherein the plurality of molecular targets comprises AR, BRAF,
`
`CTNNBl, EGFR, ERRBZ, ESRl, KIT, KRAS, MET, MLHl, PDGFRA, PDGFRB, PIK3CA
`
`(PI3K), PTEN, and TOPl,
`
`b.
`
`at least one computer database comprising:
`
`i.
`
`a reference sequence for each of the plurality of molecular targets; and
`
`ii.
`
`a listing of available therapeutic agents with efficacy linked to each of the plurality of
`
`molecular targets;
`
`c.
`
`a computer-readable program code comprising instructions to input the nucleic acid sequences for
`
`the each of the plurality of molecular targets and to compare each of the sequences with a
`
`corresponding reference sequence from the at least one computer database in (b)(i);
`
`d.
`
`a computer-readable program code comprising instructions to access the at least one computer
`
`database and to identify at least one therapeutic agent from the listing of available therapeutic
`
`agents in (b)(ii), wherein the comparison to the reference in (c) indicates a likely benefit of the at
`
`least one therapeutic agent for treating the cancer; and
`
`e.
`
`a computer-readable program comprising instructions to generate a report that comprises a listing
`
`of the molecular targets for which the comparison to the reference sequence indicated a likely
`
`benefit of the at least one therapeutic agent in (d) and the at least one therapeutic agent identified
`
`in (d).
`
`The system of claim 1, wherein the nucleic acid sequences are input into the system from a location
`
`that is remote from the at least one computer database.
`
`The system of claim 1, wherein the nucleic acid sequences are input into the system over an intemet
`
`connection.
`
`-160-
`
`Docket No. 37901-715331
`
`
`
`The system of claim 1, wherein the report is in electronic or paper format.
`
`The system of claim 1, wherein the at least one computer database filI'tl’lCl‘ comprises data
`
`corresponding to at least one clinical trial of a molecular target.
`
`The system of claim 1, wherein the reference sequence for each of the plurality of molecular targets
`
`comprises a wild type nucleic acid sequence for that molecular target.
`
`The system of claim 1, wherein the nucleic acid sequences are determined after the individual has
`
`received drug therapy for the cancer.
`
`The system of claim 1, wherein the nucleic acid sequences are determined by assessing nucleic acid
`
`collected from a cell, a tissue sample, a blood sample or any combination thereof.
`
`The system of claim 1, wherein each reference sequence is obtained from at least one individual
`
`without the cancer.
`
`10.
`
`11.
`
`12.
`
`13.
`
`14.
`
`The system of claim 1, wherein the plurality of molecular targets finther comprises ATRX (RAD54),
`
`CDHl (UVOMORULIN), CDKNlB (p27/kip1), CDKNZA (METASTASIN (MTS-1)), ERBB4,
`
`MYC (c-MYC), RADS 1, and WISP3 (LOST IN INFLAMMATORY BREAST CANCER (LIBC)).
`
`The system of claim 1, wherein the report filI'tl’lCl‘ comprises a listing of at least one additional
`
`molecular target for which the comparison to the reference in (c) indicates a likely lack of benefit of
`
`at least one therapeutic agent and the at least one additional therapeutic agent.
`
`The system of claim 1, filI'tl’lCl‘ comprising a computer-readable program code comprising instructions
`
`to prioritize the list of the at least one therapeutic agent.
`
`The system of claim 12, wherein the report provides a prioritized list of the at least one therapeutic
`
`agent.
`
`The system of claim 1, wherein the individual has been treated by and failed to respond to at least one
`
`cancer therapeutic.
`
`-161-
`
`Docket No. 37901-715331
`
`
`
`15.
`
`16.
`
`17.
`
`The system of claim 1, wherein the at least one device configured to assay the plurality of molecular
`
`targets is configured to perform next generation (NextGen) sequencing.
`
`The system of claim 1, wherein the at least one deVice configured to assay the plurality of molecular
`
`targets is configured to perform at least one of polymerase chain reaction (PCR), pyrosequencing,
`
`real-time PCR, sequencing, NextGen sequencing, methylation specific PCR (MSPCR), restriction
`
`fragment length polymorphism (RFLP analysis), immunohistochemistry (IHC), immunoassay, an
`
`eXpression microarray, a comparative genomic hybridization (CGH) microarray, a single nucleotide
`
`polymorphism (SNP) microarray, in-situ hybridization (ISH), fluorescent in-situ hybridization
`
`(FISH), and a proteomic array.
`
`The system of claim 1, wherein the at least one nucleic acid sequencing deVice is configured to
`
`identify at least one of a mutation, polymorphism, deletion, insertion, substitution, translocation,
`
`fi1sion, break, duplication, amplification or repeat in a nucleic acid sequence corresponding to each of
`
`the plurality of molecular targets
`
`-162-
`
`Docket No. 37901-715331
`
`
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