Variable valve apparatus and methods

Abstract

Sample processing devices with variable valve structures and methods of using the same are disclosed. The valve structures allow for removal of selected portions of the sample material located within the process chamber. Removal of the selected portions is achieved by forming an opening in a valve septum at a desired location. The valve septums may be large enough to allow for adjustment of the location of the opening based on the characteristics of the sample material in the process chamber. If the sample processing device is rotated after the opening is formed, the selected portion of the material located closer to the axis of rotation exits the process chamber through the opening. The remainder of the sample material cannot exit through the opening because it is located farther from the axis of rotation than the opening.

1 . A valved process chamber on a sample processing device, the valved process chamber comprising: 
 a process chamber comprising a process chamber volume located between opposing first and second major sides of the sample processing device, wherein the process chamber occupies a process chamber area on the sample processing device, and wherein the process chamber area comprises a length and a width transverse to the length, and further wherein the length is greater than the width;    a valve chamber located within the process chamber area, the valve chamber located between the process chamber volume and the second major side of the sample processing device, wherein the valve chamber is isolated from the process chamber by a valve septum separating the valve chamber and the process chamber, and wherein a portion of the process chamber volume lies between the valve septum and a first major side of the sample processing device; and    a detection window located within the process chamber area, wherein the detection window is transmissive to selected electromagnetic energy directed into and/or out of the process chamber volume.    
     
     
         2 . A valved process chamber according to  claim 1 , wherein the detection window is coextensive along the length of the process chamber with the valve septum.  
     
     
         3 . A valved process chamber according to  claim 1 , wherein the detection window is formed through the first major side of the sample processing device.  
     
     
         4 . A valved process chamber according to  claim 1 , wherein the detection window is formed through the second major side of the sample processing device.  
     
     
         5 . A valved process chamber according to  claim 1 , wherein the valve chamber and the detection window occupy mutually exclusive portions of the process chamber area.  
     
     
         6 . A valved process chamber according to  claim 1 , wherein the detection window is formed through the second major side of the sample processing device, and wherein the valve chamber and the detection window occupy mutually exclusive portions of the process chamber area.  
     
     
         7 . A valved process chamber according to  claim 1 , wherein the valve septum extends along the length of the process chamber area for 30% or more of a maximum length of the process chamber area.  
     
     
         8 . A valved process chamber according to  claim 1 , wherein the valve septum extends for a length of 1 millimeter or more along the length of the process chamber.  
     
     
         9 . A valved process chamber according to  claim 1 , wherein the sample processing device is opaque between the process chamber volume and the first major side of the sample processing device.  
     
     
         10 . A valved process chamber according to  claim 1 , wherein at least a portion of the valve chamber is located within a valve lip extending into the process chamber area, and wherein the valve septum is formed in the valve lip.  
     
     
         11 . A valved process chamber according to  claim 10 , wherein the valve lip occupies only a portion of the width of the process chamber area.  
     
     
         12 . A valved process chamber according to  claim 11 , wherein the detection window occupies at least a portion of the width of the process chamber area that is not occupied by the valve lip.  
     
     
         13 . A valved process chamber on a sample processing device, the valved process chamber comprising: 
 a process chamber comprising a process chamber volume located between opposing first and second major sides of the sample processing device, wherein the process chamber occupies a process chamber area on the sample processing device, and wherein the process chamber area comprises a length and a width transverse to the length, and further wherein the length is greater than the width;    a valve chamber located within the process chamber area, the valve chamber located between the process chamber volume and the second major side of the sample processing device, wherein the valve chamber is isolated from the process chamber by a valve septum separating the valve chamber and the process chamber, and wherein a portion of the process chamber volume lies between the valve septum and a first major side of the sample processing device, and further wherein the valve chamber and the detection window occupy mutually exclusive portions of the process chamber area, and still further wherein at least a portion of the valve chamber is located within a valve lip extending into the process chamber area, and wherein the valve septum is formed in the valve lip; and    a detection window located within the process chamber area, wherein the detection window is transmissive to selected electromagnetic energy directed into and/or out of the process chamber volume.    
     
     
         14 . A method of selectively removing sample material from a process chamber, the method comprising: 
 providing a sample processing device comprising: 
 a process chamber comprising a process chamber volume, wherein the process chamber occupies a process chamber area on the sample processing device, and wherein the process chamber area comprises a length and a width transverse to the length, and further wherein the length is greater than the width;  
 a valve chamber located within the process chamber area, wherein the valve chamber is isolated from the process chamber by a valve septum located between the valve chamber and the process chamber; and  
 a detection window located within the process chamber area, wherein the detection window is transmissive for selected electromagnetic energy;  
   providing sample material in the process chamber;    detecting a characteristic of the sample material in the process chamber through the detection window;    forming an opening in the valve septum at a selected location along the length of the process chamber, wherein the selected location is correlated to the detected characteristic of the sample material; and    moving only a portion of the sample material from the process chamber into the valve chamber through the opening formed in the valve septum.    
     
     
         15 . A method according to  claim 14 , wherein moving only a portion of the sample material from the process chamber into the valve chamber comprises rotating the sample processing device.  
     
     
         16 . A method according to  claim 14 , wherein the process chamber area comprises a length and a width transverse to the length, and further wherein the length is greater than the width.  
     
     
         17 . A method according to  claim 14 , wherein the detected characteristic comprises a free surface of the sample material, and wherein the portion of the sample material moved from the process chamber into the valve chamber comprises a selected volume of the sample material.  
     
     
         18 . A method according to  claim 14 , further comprising rotating the sample processing device to separate components of the sample material in the process chamber.  
     
     
         19 . A method according to  claim 18 , wherein the detected characteristic of the sample material comprises a boundary between the separated components of the sample material, and wherein the portion of the sample material moved from the process chamber into the valve chamber comprises a portion of a selected component of the sample material.  
     
     
         20 . A method according to  claim 14 , wherein moving only a portion of the sample material from the process chamber into the valve chamber comprises moving a selected volume of the sample material from the process chamber into the valve chamber.  
     
     
         21 . A method according to  claim 14 , wherein the sample material comprises blood.  
     
     
         22 . A method of selectively removing sample material from a process chamber, the method comprising: 
 providing a sample processing device comprising: 
 a process chamber comprising a process chamber volume, wherein the process chamber occupies a process chamber area on the sample processing device, and wherein the process chamber area comprises a length and a width transverse to the length, and further wherein the length is greater than the width;  
 a valve chamber located within the process chamber area, wherein the valve chamber is isolated from the process chamber by a valve septum located between the valve chamber and the process chamber; and  
 a detection window located within the process chamber area, wherein the detection window is transmissive for selected electromagnetic energy;  
   providing sample material in the process chamber;    detecting a characteristic of the sample material in the process chamber through the detection window;    forming an opening in the valve septum at a selected location within the process chamber area, wherein the selected location is correlated to the detected characteristic of the sample material; and    moving only a portion of the sample material from the process chamber into the valve chamber through the opening formed in the valve septum by rotating the sample processing device.    
     
     
         23 . A method of isolating nucleic acid from whole blood, the method comprising: 
 providing a device comprising a loading chamber and a variable valved process chamber;    placing whole blood in the loading chamber;    transferring the whole blood to a valved process chamber;    centrifuging the whole blood in the valved process chamber to form a plasma layer, a red blood cell layer, and an interfacial layer comprising white blood cells;    removing at least a portion of the interfacial layer comprising white blood cells; and    lysing the white blood cells in the separated interfacial layer and optionally lysing the nuclei therein to release inhibitors and/or nucleic acid.    
     
     
         24 . The method of  claim 23  wherein prior to lysing the white blood cells, the method includes diluting the separated interfacial layer of the sample with water or buffer, optionally further concentrating the diluted layer to increase the concentration of nucleic acid material, optionally separating the further concentrated region, and optionally repeating this process of dilution followed by concentration and separation to reduce the inhibitor concentration to that which would not interfere with an amplification method.  
     
     
         25 . The method of  claim 23  wherein the device further comprises a separation chamber comprising a solid phase material.  
     
     
         26 . The method of  claim 25  wherein the solid phase material comprises capture sites, a coating reagent coated on the solid phase material, or both; wherein the coating reagent is selected from the group consisting of a surfactant, a strong base, a polyelectrolyte, a selectively permeable polymeric barrier, and combinations thereof.  
     
     
         27 . The method of  claim 25  further comprising contacting the lysed sample with the solid phase material in the separation chamber to preferentially adhere at least a portion of the inhibitors to the solid phase material; wherein lysing can occur before, simultaneous with, or after contacting the solid phase material.  
     
     
         28 . The method of  claim 25  further comprising separating at least a portion of the nuclei and/or nucleic acid from the solid phase material having at least a portion of the inhibitors adhered thereto.  
     
     
         29 . The method of  claim 23  wherein lysing comprises subjecting the white blood cells to a strong base with optional heating to release nucleic acid.  
     
     
         30 . The method of  claim 29  further comprising adjusting the pH of the sample comprising the released nucleic acid to be within a range of 7.5 to 9.  
     
     
         31 . The method of  claim 23  further comprising diluting the lysed sample with water to reduce the inhibitor concentration to that which would not interfere with an amplification method; optionally further lysing the nuclei to release nucleic acid; and optionally adjusting the pH of the sample comprising released nucleic acid.  
     
     
         32 . The method of  claim 31  wherein diluting the lysed sample comprises diluting with water to reduce the concentration of heme to less than 2 micromolar.  
     
     
         33 . The method of  claim 31  wherein diluting the lysed sample comprises diluting sufficiently with water to form a 20×-1000× dilution of the lysed sample.  
     
     
         34 . The method of  claim 31  wherein the water is RNAse-free sterile water.  
     
     
         35 . A method of isolating nucleic acid from whole blood, the method comprising: 
 providing a device comprising a loading chamber and a variable valved process chamber;    placing whole blood in the loading chamber;    transferring the whole blood to a valved process chamber;    contacting the whole blood with a density gradient material;    centrifuging the whole blood and density gradient material in the valved process chamber to form layers, at least one of which contains cells of interest;    removing at least a portion of the layer comprising the cells of interest; and    lysing the separated cells of interest to release nucleic acid.    
     
     
         36 . The method of  claim 35  wherein prior to lysing the separated cells of interest, the method includes diluting the separated cells of interest with water or buffer, optionally further concentrating the diluted layer to increase the concentration of cells of interest, optionally separating the further concentrated region, and optionally repeating this process of dilution followed by concentration and separation.  
     
     
         37 . The method of  claim 35  wherein prior to lysing the separated cells of interest, the method includes diluting the separated cells of interest with water.  
     
     
         38 . The method of  claim 37  wherein diluting the separated cells of interest comprises diluting sufficiently with water to form a 20×-1000× dilution.  
     
     
         39 . A method of isolating nucleic acid from whole blood comprising one or more pathogens, the method comprising: 
 providing a device comprising a loading chamber, a variable valved process chamber, and a separation chamber comprising pathogen capture material;    placing whole blood in the loading chamber;    transferring the whole blood to a valved process chamber;    centrifuging the whole blood in the valved process chamber to form a plasma layer comprising one or more pathogens, a red blood cell layer, and an interfacial layer comprising white blood cells;    transferring at least a portion of the plasma layer comprising one or more pathogens to the separation chamber comprising pathogen capture material;    separating at least a portion of the one or more pathogens from the pathogen capture material; and    lysing the one or more pathogens to release nucleic acid.    
     
     
         40 . A kit for isolating nucleic acid from a sample, the kit comprising: 
 a device comprising a loading chamber and a variable valved process chamber; and    instructions for centrifuging whole blood and removing a portion of the whole blood according to the method of  claim 23.