Compositions and methods for oncology precision assays

Abstract

Provided are methods and compositions for preparing a library of target nucleic acid sequences that are useful for assessing gene mutations for oncology biomarker profiling of samples. In particular, a target-specific primer panel is provided that allows for selective amplification of oncology biomarker target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with oncology biomarkers from two or more sample types. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants of one or more targeted sequences associated with oncology.

1 - 20 . (canceled) 
     
     
         21 . A composition for a single stream multiplex determination of actionable oncology biomarkers in a sample, the composition comprising a plurality of sets of primer pair reagents directed to a plurality of target sequences to detect low level targets in the sample, wherein the target genes consist of the following functions: DNA hotspot mutation genes, copy number variation (CNV) genes, inter-genetic fusion genes, and intra-genetic fusion genes; and wherein the plurality of sets of primer pair reagents comprise two or more primers of any of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         22 . The composition of  claim 21 , wherein the one or more actionable target genes in a sample determines a change in oncology activity in the sample indicative of a potential diagnosis, prognosis, candidate therapeutic regimen, and/or adverse event. 
     
     
         23 . The composition of  claim 21 , wherein the target genes comprise one or more of AKT1, AKT2, AKT3, ALK, AR, ARAF, BRAF, CDK4, CD274, CDKN2A, CHEK2, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MET, MTOR, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PIK3CA, PTEN, RAF1, RET, ROS1, RSPO2, RSPO3, SMO, and TP53. 
     
     
         24 . The composition of  claim 21 , wherein the target genes comprise AKT1, AKT2, AKT3, ALK, AR, ARAF, BRAF, CDK4, CD274, CDKN2A, CHEK2, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MET, MTOR, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PIK3CA, PTEN, RAF1, RET, ROS1, RSPO2, RSPO3, SMO, and TP53. 
     
     
         25 . The composition of  claim 21 , wherein the plurality of target sequences comprise one or more of the amplicon sequences detected by the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         26 . The composition of  claim 21 , wherein the plurality of target sequences comprise each of the amplicon sequences detected by the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         27 . The composition of  claim 21 , wherein the plurality of sets of primer pair reagents comprise the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         28 . The composition of  claim 21 , wherein the plurality of sets of primer pair reagents consist of each of the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         29 . A multiplex assay comprising the composition of  claim 25 . 
     
     
         30 . A test kit comprising the composition of  claim 25 . 
     
     
         31 . A method for determining the presence of one or more actionable oncology biomarkers in a biological sample, comprising:
 multiplex amplification of a plurality of target oncology sequences from the biological sample, wherein amplifying comprises contacting at least a portion of the sample with the composition of  claim 21  and a polymerase under amplification conditions, thereby producing amplified target oncology sequences;   detecting each of the plurality of target oncology sequences, wherein detection of one or more actionable oncology biomarkers as compared with a control sample determines a change in oncology activity in the sample indicative of a potential diagnosis, prognosis, candidate therapeutic regimen, and/or adverse event.   
     
     
         32 . The method of  claim 31 , wherein target genes are selected from the group consisting of DNA hotspot mutation genes, copy number variation (CNV) genes, inter-genetic fusion genes, and intra-genetic fusion genes. 
     
     
         33 . The method of  claim 31 , wherein the target genes comprise one or more of AKT1, AKT2, AKT3, ALK, AR, ARAF, BRAF, CDK4, CD274, CDKN2A, CHEK2, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MET, MTOR, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PIK3CA, PTEN, RAF1, RET, ROS1, RSPO2, RSPO3, SMO, and TP53. 
     
     
         34 . The method of  claim 31 , wherein the target genes comprise AKT1, AKT2, AKT3, ALK, AR, ARAF, BRAF, CDK4, CD274, CDKN2A, CHEK2, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MET, MTOR, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PIK3CA, PTEN, RAF1, RET, ROS1, RSPO2, RSPO3, SMO, and TP53. 
     
     
         35 . The method of  claim 31 , wherein the plurality of target sequences comprise one or more of the amplicon sequences detected by the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         36 . The method of  claim 31 , wherein the plurality of target sequences comprise each of the amplicon sequences detected by the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         37 . The method of  claim 31 , wherein the plurality of sets of primer pair reagents comprise the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         38 . The method of  claim 31 , wherein the plurality of sets of primer pair reagents consist of each of the primers of SEQ ID NO: 1-SEQ ID NO: 1563. 
     
     
         39 . The method of  claim 31 , wherein the biological sample comprises a tumor and/or tissue surrounding a tumor. 
     
     
         40 . The method of  claim 31 , wherein the biological sample and the control sample are from the same individual.