System and method for processing paraffin embedded samples

Abstract

Method and apparatus for processing paraffin embedded samples, e.g., to disassociate paraffin from tissue components and/or other biomolecules from the paraffin. The sample may be exposed to focused acoustic energy while held in a vessel containing a non-solvent, aqueous solution. Disassociated paraffin may be emulsified into the liquid or otherwise separated from the sample.

What is claimed is:  
     
         1 . An acoustic treatment device, comprising:
 a vessel arranged to hold a sample, the vessel holding a formalin fixed, paraffin embedded tissue sample and a non-solvent, aqueous solution;   an acoustic energy source for providing acoustic energy to the sample while the sample is in the vessel and separated from the acoustic energy source, the acoustic energy having a focal zone;   a vessel holder arranged to support the vessel, the vessel holder adapted to position the vessel at a location at least partially in the focal zone of the acoustic energy; and   a system control circuit arranged to control the acoustic energy source to expose the sample to focused acoustic energy suitable to disassociate paraffin from the sample to allow recovery of biomolecules of the sample.   
     
     
         2 . The device of  claim 1 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample to focused acoustic energy for a time sufficient to disassociate enough paraffin from the sample to allow recovery of nucleic and/or proteomic material from the sample. 
     
     
         3 . The device of  claim 1 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample to focused acoustic energy to disassociate more than 90% of paraffin attached to the sample. 
     
     
         4 . The device of  claim 1 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample to focused acoustic energy to disassociate more than 98% of paraffin attached to the sample. 
     
     
         5 . The device of  claim 1 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample to focused acoustic energy to rehydrate the sample while exposing the sample to focused acoustic energy. 
     
     
         6 . The device of  claim 1 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample to focused acoustic energy while the vessel is located in a bath of liquid at a temperature of about 30-60 degrees C. 
     
     
         7 . The device of  claim 6 , wherein the bath is at a temperature of about 40 degrees C. 
     
     
         8 . The device of  claim 1 , wherein the system control circuit is arranged to maintain a temperature of the sample below about 60 degrees C. 
     
     
         9 . The device of  claim 1 , wherein the sample has a thickness of 5 to 25 microns and a length of less than 25 mm. 
     
     
         10 . The device of  claim 1 , wherein the non-solvent solution includes protease. 
     
     
         11 . The device of  claim 10 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample and the protease-containing solution to focused acoustic energy to mix the protease-containing solution with the sample. 
     
     
         12 . The device of  claim 11 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample and the protease-containing solution to focused acoustic energy suitable to fragment nucleic acid material from the sample into smaller fragments. 
     
     
         13 . The device of  claim 12 , wherein the system control circuit is arranged to control the acoustic energy source to expose the sample and the protease-containing solution to focused acoustic energy to cause a majority of the fragments of nucleic acid material to have a size of 50 to 1000 bp. 
     
     
         14 . The device of  claim 12 , wherein the vessel contains paraffin disassociated from the sample. 
     
     
         15 . The device of  claim 13 , further comprising a pipet for removing the sample, disassociated paraffin and non-solvent solution of nucleic acid and/or proteome material from the vessel. 
     
     
         16 . The device of  claim 10 , further comprising an incubator configured to incubate the sample in the vessel with the protease-containing solution at a temperature to reverse formaldehyde crosslinks in the sample. 
     
     
         17 . The device of  claim 10 , wherein the incubator is configured to incubate the sample in the vessel with the protease-containing solution at a temperature of 50-60 degrees C. to digest the tissue in the sample. 
     
     
         18 . The device of  claim 1 , further comprising a centrifuge configured to centrifuge the vessel containing the sample, disassociated paraffin and non-solvent solution of nucleic acid and/or proteome material to transfer the contents from the vessel to a second container. 
     
     
         19 . The device of  claim 1 , wherein the acoustic energy source is configured to produce acoustic energy having a frequency of between about 100 kilohertz and about 100 megahertz and has a focal zone with a width of less than about 2 centimeters, and the acoustic energy source is spaced from and exterior to the vessel, wherein at least a portion of the acoustic energy propagates exterior to the vessel. 
     
     
         20 . The device of  claim 20 , wherein the vessel and the solution provide a headspace such that an upper level of the solution is within 2 mm of a cap placed on the vessel.