Sample preparation, processing and analysis systems

Abstract

This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.

1 . A cassette, comprising:
 (a) a container comprising a plurality of closed and fluidically isolated chambers, wherein each of the plurality of chambers comprises a friable seal; and   (b) a microfluidic device comprising a plurality of puncturing elements and a microfluidic channel, wherein multiple puncturing elements are disposed opposite each of said plurality of chambers,   wherein, upon engaging the microfluidic device with the container, said puncturing elements puncture the friable seal of each of the plurality of chambers, thereby creating a fluid flow path between said fluidically isolated chambers through said microfluidic channel; or   (b) a microfluidic device comprising a first channel and a second channel, each of which channels terminates at a port, and puncturing elements adjacent to said chamber,   wherein, upon engaging the microfluidic device with the container, said puncturing elements puncture the friable seal, thereby creating a fluid flow path comprising said first channel, chamber and second channel.   
     
     
         2 - 23 . (canceled) 
     
     
         24 . A cartridge module, comprising:
 a receptacle for accepting a cartridge that has a sample and one or more reagents for processing said sample, said cartridge having one or more chambers for sample processing and one or more valves for facilitating fluid flow to said one or more chambers;   a first assembly having a first pressure manifold that engages a first side of said cartridge and brings said one or more chambers in fluid communication with a pressure source;   a second assembly having a second pressure manifold that engages a second side of said cartridge and brings said one or more valves in fluid communication with a pressure source for pneumatic actuation; and   an elongation or moving member that moves one or both of said first pressure manifold and said second pressure manifold towards said cartridge.   
     
     
         25 - 35 . (canceled) 
     
     
         36 . A system for detecting an article, comprising:
 a cartridge engaged with a cartridge module, wherein the cartridge comprises a sample receptacle configured to receive an article that optionally comprises a sample; and   a detection assembly configured to detect the presence or absence of an article in the sample receptacle.   
     
     
         37 . A system for controlling custody of a sample, comprising:
 (a) a cartridge comprising a sample receptacle configured to receive an article (e.g., a swab) that optionally comprises a sample;   (b) a cartridge module having a cartridge receptacle configured to receive the cartridge;   (c) a housing that encloses the cartridge module and the cartridge, wherein the housing comprises a closable door;   (d) at least one sensor that produces a signal indicating:
 (1) insertion or removal of an article into or from the sample receptacle; 
 (2) whether the cartridge is inserted into the cartridge receptacle; or 
 (3) whether the door is open or closed; and 
   (e) a computer programmed to record a signal from the at least one sensor for a recording period of time and to display a signal history to a user.   
     
     
         38 - 41 . (canceled) 
     
     
         42 . A method of positioning a sample/analyte for injection into a separation channel, comprising:
 (i) providing an electrophoresis assembly comprising:
 (a) a fluidic conduit (e.g., a sample/analyte channel) having a channel inlet and a channel outlet; 
 (b) a separation channel (e.g., an electrophoresis capillary) having a separation channel inlet and a separation channel outlet, 
 wherein the separation channel comprises an electrically conductive separation medium (e.g., polymer or gel), and 
 wherein the separation channel inlet is in fluidic communication and electrical communication with the fluidic conduit at a point of connection; 
 (c) an anode and a cathode defining an electrical path and configured to apply a voltage across the separation channel inlet and the separation channel outlet, 
 wherein the anode or the cathode (e.g., the cathode when the sample/analyte is a nucleic acid) is in or adjacent to the fluidic conduit at or adjacent to the point of connection; 
 (d) a meter configured to measure current through the separation channel or voltage across the separation channel; 
   (ii) positioning a bolus of a material (e.g., air) downstream of a sample/analyte in the fluidic conduit, wherein the material has an electrical conductivity that differs from the electrical conductivity of an electrophoresis buffer or the sample/analyte;   (iii) moving the bolus of material and the sample/analyte in the fluidic conduit in the direction of the separation channel while measuring current or voltage with the meter;   (iv) detecting with the meter a change in current or voltage that corresponds to movement of the bolus of material into the electrical path; and   (v) based on the detecting, moving the sample/analyte into the electrical path.   
     
     
         43 . An article, comprising:
 a body containing a passage between openings;   a first movable stopper and a second movable stopper positioned in the passage so as to define a compartment between them; and   a fluid in the compartment, said fluid comprising an amplification premix,   wherein external pressure exerted against the first movable stopper is transmitted to the second movable stopper to move the second movable stopper toward an opening.   
     
     
         44 - 45 . (canceled)