Methods, compositions, kits and devices for rapid analysis of biological markers

Abstract

Provided herein are kits, devices and methods for rapid analysis of biological samples. In particular, kits, devices and methods described herein can be applied to rapid nucleic acid analysis of solid tissue samples.

1 . (canceled) 
     
     
         2 . A method for determining success of a surgical procedure for removing a tumor from a subject, comprising:
 a) collecting a biological sample from said subject, wherein said biological sample is collected from the surface of a surgical specimen of said tumor; and   b) detecting a pattern of expression of at least one biomarker associated with a cancer in said biological sample for detecting a presence or absence of a positive surgical margin of said tumor; wherein said pattern of expression of said at least one biomarker determines a presence or absence of a positive surgical margin of said tumor, thereby determining a likelihood of success of said surgical procedure for removing said tumor.   
     
     
         3 . The method of  claim 2 , wherein said detecting a pattern of expression of at least one biomarker associated with a cancer in said biological sample is performed after said surgical procedure. 
     
     
         4 . The method of  claim 2 , wherein said detecting a pattern of expression of at least one biomarker associated with a cancer in said biological sample is performed during said surgical procedure. 
     
     
         5 . The method of  claim 2 , wherein said biological sample comprises at least 20% of the surface of said surgical specimen. 
     
     
         6 . The method of  claim 2 , further comprising extracting nucleic acid molecules from said biological sample. 
     
     
         7 . The method of  claim 3 , wherein said nucleic acid molecules comprise RNA, mRNA, spliced RNA, or non-spliced RNA. 
     
     
         8 . The method of  claim 6 , further comprising synthesizing cDNA from said biological sample. 
     
     
         9 . The method of  claim 2 , wherein said at least one biomarker is associated with a gene selected from the group consisting of ACTR3B, ALK, ANLN, AURKA, BAG1, BcI2, BCL2, BCR-Abl, BIRC5, BLVRA, BRAF, c-KIT Cathepsin L2, CCNB1, CCNE1, CD20 antigen, CD30, CD68, CDC20, CDC6, CDH3, CENPF, CEP55, CXXC5, Cyclin B1, EGFR, ER, ERBB2, ESR1, EXO1, FGFR4, FIP1L-PDGFRalpha, FOXA1, FOXC1, GPR160, GRB7, GSTM1, HOXB13, IL17BR, Ki-67, KIF2C, KRAS, KRT14, KRT17, KRT5, MAPT, MDM2, MELK, MIA, MKI67, MLPH, MMP11, MYBL2, MYC, NAT1, NDC80, NUF2, ORC6L, PDGFR, PGR, PHGDH, PML/RAR alpha, PR, PTTG1, RRM2, SCUBE2, SFRP1, SLC39A6, STK15, Stromelysin 3 (MMP11), Survivin, TMEM45B, TPMT, TYMS, UBE2C, UBE2T, UGT1A1, ABCA10, ABCA9, ADAM33, ADAMTS5,ANGPT1, ANKRD29, ARHGAP20, ARMCX5GPRASP2, ASB1, CA4, CACHD1, CAPN11, CAV1, CAV2, CAV3, CBX7, CCNE2, CD300LG, CDC14B, CDC42SE1, CENPF, CEP68, CFL2, CHL1, CLIP4, CNTNAP3, COL10A1, COL11A1, CRIM1, CXCL3, DAB2IP, DMD, DPYSL2, DST, EEPD1, ENTPD7, ERCC6L, EZH1, F10, FAM126A, FBXO31, FGF1, FIGF,FMO2, FXYD1,GIPC2, GLYAT, GPR17, GPRASP1, GPRASP2, HAGL, HAND2-AS1, HLF, HMMR, HOXA2, HOXA4, HOXA5, IGSF10, INHBA, IL11RA,ITM2A, JADE1, JUN, KIAA0101, KIF4A, KLHL29, LCAT, LGI4, LIFR, LIMS2, LRIG3,LRRC2, LRRC3B, MAMDC2, MATN2, MICU3, MIR99AHG, MME, MMP11, NECAB1, NEK2, NKAPL, NPHP3,NR3C1, NR3C2, NUF2, PAMR1, PAFAH1B3, PAQR4, PARK2, PEAR1, PGM5, PKMYT1, PLEKHM3, PLSCR4, POU6F1, PPAP2B, PPP1R12B, PRCD, PRX, PYCR1, RAPGEF3, RBMS2, SCN4B, SDPR, SLC35A2, SH3BGRL2, SPRY2, STAT5B, SYN2, TK1, TMEM220, TMEM255A, TMOD1, TPM3, TPX2, TSHZ2, TSLP, TSTA3, TTC28, WISP1, USHBP1, USP44, IBSP, CST1, ZWINT, and combinations thereof. 
     
     
         10 . The method of  claim 9 , wherein said at least one biomarker comprises at least three biomarkers. 
     
     
         11 . The method of  claim 9 , wherein said at least one biomarker associated with a gene are selected from biomarkers associated with COL10A1, MMP11, IBSP, CST1, and combinations thereof. 
     
     
         12 . The method of  claim 2 , wherein said tumor is associated with breast cancer, prostate cancer, colon cancer, lung cancer, liver cancer, brain cancer, skin cancer, testicular cancer, oral cancer, pancreatic cancer, stomach cancer, cervical cancer, uterine cancer, endometrial cancer, or ovarian cancer. 
     
     
         13 . The method of  claim 2 , wherein said tumor is associated with breast cancer. 
     
     
         14 . The method of  claim 2 , wherein detecting said pattern of expression comprises performing a polymerase chain reaction (PCR), quantitative PCR (QPCR), next generation sequencing, RNAseq, digital PCR (dPCR), digital droplet PCR (ddPCR), isothermal amplification, an endoribonucleotide strand displacement assay (ERiN SDA), or a microarray assay on said biological sample. 
     
     
         15 . The method of  claim 2 , wherein said detecting said pattern of expression comprises performing a QPCR assay. 
     
     
         16 . The method of  claim 2 , wherein a presence of said positive surgical margin in said biological sample indicates incomplete removal of said tumor from said subject. 
     
     
         17 . The method of  claim 2 , wherein said pattern of expression of said at least one biomarker has at least 60% sensitivity for determining success of said surgical procedure for removing said tumor. 
     
     
         18 . The method of  claim 2 , further comprising indicating chemotherapy, radiotherapy, trastuzumab, endocrine therapy, or combinations thereof based on said presence or absence of said positive surgical margin in said biological sample. 
     
     
         19 . The method of  claim 2 , wherein said tumor is a benign tumor, a pre-cancerous tumor, an early-stage tumor, a non-metatstatic tumor, or a metastatic tumor. 
     
     
         20 . The method of  claim 2 , wherein said tumor is a pre-cancerous or an early-stage tumor.