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

Abstract

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

1 . (canceled) 
     
     
         2 . A method for analyzing a target nucleic acid from a cellular specimen, the method comprising:
 a) collecting the cellular specimen comprising at least a whole cell derived from a surface of a surgical specimen obtained from a subject of a procedure, wherein the cellular specimen comprises the target nucleic acid; and   b) detecting a presence of the target nucleic acid in the cellular specimen, wherein detecting the presence of the target nucleic acid comprises determining an expression level of the target nucleic acid corresponding to one or more genes or a portion thereof associated with the condition, wherein the one or more genes or a portion thereof comprise at least one of COL10A1 and MMP11, wherein the target nucleic acid expression level indicates a presence of the condition in the cellular specimen derived from the surface of the surgical specimen;   wherein the presence of the condition in the cellular specimen derived from the surface of the surgical specimen indicates completeness of removal of the condition from the subject of the procedure.   
     
     
         3 . The method of  claim 2 , further comprising determining a likelihood of success of the surgical procedure, wherein the completeness of removal of the condition of the subject determines the likelihood of success of the procedure for removing the condition from the subject. 
     
     
         4 . The method of  claim 2 , wherein the presence of the condition indicates incomplete removal of the condition from the subject. 
     
     
         5 . The method of  claim 2 , wherein the cellular specimen comprises at least 50% of the surface of the surgical specimen. 
     
     
         6 . The method of  claim 2 , wherein the method has a false negative rate of less than 20%. 
     
     
         7 . The method of  claim 2 , further comprising extracting the target nucleic acid from the cellular specimen, wherein the target nucleic acid is selected from the group consisting of genomic DNA, reverse-transcribed cDNA, RNA, mRNA, spliced RNA, and non-spliced RNA. 
     
     
         8 . The method of  claim 2 , wherein the surgical specimen is selected from the group consisting of a lumpectomy, a cancer, a solid tumor, a liquid tumor, a malignant tumor, a benign tumor, a primary tumor, a metastatic tumor, a polyp, a lymph node, an early stage tumor, a localized tumor, a non-metastatic tumor, and healthy tissue. 
     
     
         9 . The method of  claim 2 , wherein the condition is a presence of a cancer after a treatment, a risk of a cancer, or a risk of a cancer recurrence. 
     
     
         10 . The method of  claim 9 , wherein the cancer is selected from the group consisting of a breast cancer, a prostate cancer, a colon cancer, a lung cancer, a brain cancer, a skin cancer, a gastrointestinal cancer, a biliary tract cancer, a testicular cancer, a blood-derived cancer, an autoimmune disorder, a pancreatic cancer, an oral cancer, a cervical cancer, a uterine cancer, and an ovarian cancer. 
     
     
         11 . The method of  claim 9 , wherein the condition is invasive adenocarcinoma of the breast. 
     
     
         12 . The method of  claim 2 , wherein collecting the cellular specimen comprises contacting the surface of the surgical specimen with a sample collection unit, wherein the sample collection unit comprises information about a location from which the cellular specimen is derived from the surface of the surgical specimen. 
     
     
         13 . The method of  claim 2 , collecting the cellular specimen comprises a method selected from a touch prep method, a brush biopsy method, and a blotting method. 
     
     
         14 . The method of  claim 2 , wherein the one or more genetic loci comprises between 1 and 10 genetic loci. 
     
     
         15 . The method of  claim 2 , wherein the one or more genetic loci further comprises one or more genes or a portion thereof selected from the group consisting of ABCA10, ABCA9, ADAM33, ADAMTS5, ANGPT1, ANKRD29, ARHGAP20, ARMCX5, GPRASP2, 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, and ZWINT, and combinations thereof. 
     
     
         16 . The method of  claim 2 , wherein the one or more genes or a portion thereof is encoded by a cDNA fragment reverse-transcribed from an mRNA encoding a protein selected from ABCA10, ABCA9, ADAM33, ADAMTS5, ANGPT1, ANKRD29, ARHGAP20, ARMCX5-GPRASP2, ASB1, CA4, CACHD1, CAPN11, CAV2, CAV3, CBX7, CCNE2, CD300LG, CDC14B, CDC42SE1, CENPF, CEP68, CFL2, CHL1, CLIP4, CNTNAP3, COL10A1, COL11A1, CRIME BMP, CXCL3, DAB2IP, DMD, DPYSL2, DST, EEPD1, ENTPD7, ERCC6L, EZH1, F10, FAM126A, FBXO31, FGF1, FIGF, FMO2, FXYD1, GIPC2, GLYAT, GPR17, GPRASP1, GPRASP2, HAND2-AS1, HAGHL, HLF, HMMR, HOXA2, HOXA4, IGSF10, IL11RA, INHBA, ITM2A, JADE1, JUN, KIAA0101, KIF4A, KLHL29, LCAT, LG14, LIFR, LIMS2, LRIG3, LRRC2, LRRC3B, MAMDC2, MATN2, MICU3, MIR99AHG, MME, MMP11, NECAB1, NEK2, NKAPL, NPHP3, NR3C1, NR3C2, NUF2, PAFAH1B3, PAMR1, PAQR4, PARK2, PEAR1, PGM5, PLEKHM3, PLSCRR4, PKMYT1, POU6F1, PPAP2B, PPP1R2B, PRCD, PRX, PYCR1, RAPGEF3, RBMS2, SCN4B, SDPR, SH3BGRL2, SLC35A2, SPRY2, STAT5B, SYN2, TK1, TMEM220, TMEM255A, TMOD1, TPM3, TPX2, TSHZ2, TSLP, TSTA3, TTC28, USHBP1, USP44, WISP1, and ZWINT, and combinations thereof. 
     
     
         17 . The method of  claim 2 , wherein at least one step of the method is performed within a surgical suite, an operation room, a procedure room, an examination room, a hospital, a clinic, a pathology laboratory, a clinical laboratory improvement amendments (CLIA) laboratory, a non-CLIA laboratory, or an ambulatory surgical center. 
     
     
         18 . The method of  claim 2 , wherein the procedure is selected from a surgery, a lumpectomy, a biopsy, a core biopsy, and an aspiration. 
     
     
         19 . The method of  claim 2 , wherein the expression level of the target nucleic acid is a pre-determined threshold from a non-linear algorithm score. 
     
     
         20 . The method of  claim 2 , wherein collecting the cellular specimen comprises using a sample collection unit having a coating that promotes adhesion of the cellular specimen to the surface, wherein the coating comprises an agent selected from poly lysine, poly-ornithine, a collagen, a laminin, a fibronectin, a mucopolysacharride, heparin sulfate, hyaluronidate, chondroitin sulfate, and a hydrogel.