System and method for conducting an assay

Abstract

An automated method for analyzing a plurality of samples within a housing of a self-contained system. The system is loaded with a plurality of samples, after which a first assay is performed on a first sample subset and a second assay performed on a second sample subset. The two assays include exposing the samples to a target capture reagent having a solid support for directly or indirectly immobilizing a target nucleic acid that may be present in one or more of the samples. The two assays may be performed with the same or different target capture reagents and target nucleic acids, but the receptacles for performing the exposing step have substantially identical geometries. Following the exposing step, an amplification reaction for amplifying a region of the target nucleic acid is performed with each sample. The amplification reactions of the two assays are performed in receptacles having different geometries.

1 . A system for performing a nucleic acid amplification assay, the system comprising:
 one or more receptacle holders, each receptacle holder being formed from a thermally-conductive material and comprising one or more receptacle wells, wherein each receptacle well conforms to a lower portion of a vial, and wherein each receptacle holder includes a through-hole extending from a bottom-center of an inner surface of each well to a bottom outer surface of the receptacle holder;   one or more thermal elements positioned proximal to each receptacle holder for altering a temperature or temperatures of the one or more receptacle holders; and   a signal detection module in optical communication with each of the one or more receptacle wells via the through-hole of each receptacle well, wherein the signal detection module is configured to detect an optical emission signal emitted from a fluid contained in a vial supported by any of the receptacle wells, and wherein the signal detection module is configured to generate an excitation signal that is directed through the through-hole of a receptacle well and to detect an optical emission from a content of the vial contained in the respective receptacle well and through the through-hole of the respective receptacle well,   wherein at least one the receptacle wells supports a capped vial, the capped vial comprising a vial containing a fluid and an opaque cap in sealing engagement with an open end of the vial, wherein the fluid contains reagents for performing a nucleic acid amplification assay,   wherein the lower portion of the vial is contained within the at least one receptacle well, and   
       wherein the cap is situated above a top surface of the corresponding receptacle holder. 
     
     
         2 . The system of  claim 1 , wherein each capped vial comprises one of the caps engaged with the respective vial in a frictional fit. 
     
     
         3 . The system of  claim 2 , wherein an outer surface of a lower portion of the cap of each capped vial is in sealing engagement with an inner surface of an upper portion of the respective vial. 
     
     
         4 . The system of  claim 1 , wherein each cap is configured for inter-locking engagement with the respective vial. 
     
     
         5 . The system of  claim 4 , wherein each vial comprises a lip circumscribing the open end, wherein each cap comprises one or more locking arms extending toward a lower portion of cap, and wherein the one or more locking arms are configured for inter-locking engagement with the lip of a respective vial. 
     
     
         6 . The system of  claim 1 , wherein one of the one or more thermal elements are positioned proximal to a side surface of a respective receptacle holder, and wherein the thermal element provides thermal energy through the respective receptacle holder to each of the receptacle wells of the respective receptacle holder. 
     
     
         7 . The system of  claim 1 , wherein the one or more thermal elements are configured and controlled to cyclically vary the temperature of the one or more receptacle holders. 
     
     
         8 . The system of  claim 1 , wherein the signal detection module comprises an excitation signal source and an emission signal detector, and the system further comprises a plurality of optical fibers, each optical fiber comprising a first end and a second end, wherein the first end is in optical communication with one of the receptacle wells through the through-hole of the well, and wherein the second end is in optical communication with at least one of the excitation signal source and the emission signal detector. 
     
     
         9 . The system of  claim 8 , wherein the excitation signal source is configured to generate an excitation signal by generating a light at a predetermined wavelength. 
     
     
         10 . The system of  claim 9 , wherein the emission signal detector is configured to detect the optical emission signal by receiving an optical emission from the fluid contained in the respective vial and generating a voltage signal corresponding to an intensity of the received optical emission. 
     
     
         11 . The system of  claim 8 , wherein the second end of each optical fiber is in optical communication with the excitation signal source and the emission signal detector. 
     
     
         12 . The system of  claim 8 , wherein the excitation signal source is configured to generate an excitation signal by generating a light at a predetermined wavelength, and wherein the emission signal detector is configured to detect the optical emission signal by receiving an optical emission from the fluid contained in the respective vial and generating a voltage signal corresponding to an intensity of the received optical emission. 
     
     
         13 . The system of  claim 1 , wherein the opaque cap has low to no autofluorescence. 
     
     
         14 . The system of  claim 1 , wherein the system does not include a cover configured to extend over the one or more receptacle holders. 
     
     
         15 . The system of  claim 14 , wherein the system is contained within a housing of an instrument. 
     
     
         16 . The system of  claim 1  further comprising a cover corresponding to each receptacle holder, wherein the cover is configured to move between an open position and a closed position relative to a respective receptacle holder. 
     
     
         17 . The system of  claim 16 , wherein the cover comprises a rigid element and one or more flexible extensions attached to, and extending laterally away from, the rigid element, wherein each flexible extension is associated with a respective receptacle well and is configured to apply a force to a respective capped vial when the cover is in the closed position, thereby securing the respective capped vial within the respective well. 
     
     
         18 . The system of  claim 1  further comprising a primary cover fixedly positioned over a respective receptacle holder, wherein the primary cover comprises one or more securing arms, each securing arm being configured for securable attachment to at least a portion of a respective cap, and a secondary cover fixedly positioned over the primary cover, wherein the secondary cover comprises one or more releasing arms in alignment with and in sliding contact with the securing arms of the primary cover. 
     
     
         19 . The apparatus of  claim 1  further comprising a cover configured to move relative to the receptacle holder between an open position and a closed position, wherein in the open position, the cover does not obstruct access to the receptacle wells, and wherein in the closed position, the cover blocks access to the receptacle wells of the receptacle holder. 
     
     
         20 . The apparatus of  claim 19 , wherein in the closed position, the cover does not exert force on the capped vial disposed in a receptacle well of the receptacle holder. 
     
     
         21 . The system of  claim 1  further comprising:
 a robotic pipettor having a probe, wherein the cap of each capped vial comprises an upper portion configured for removable engagement with the probe of the robotic pipettor; and 
 a centrifuge configured to receive the capped vial, wherein the robotic pipettor is configured to transfer the capped vial to a first location of the centrifuge. 
 
     
     
         22 . The system of  claim 21  further comprising a vial transfer arm configured for removable engagement with the upper portion of the cap, and wherein the vial transfer arm is further configured to transfer the capped vial from a second location of the centrifuge to one of the receptacle wells of the receptacle holder, the first and second locations of the centrifuge being different locations. 
     
     
         23 . The system of  claim 1 , wherein the nucleic acid amplification assay is a real-time amplification assay, and wherein the reagents are for performing the real-time amplification assay. 
     
     
         24 . A method for a nucleic acid amplification assay, the method comprising the steps of:
 (A) with a robotic pipettor, dispensing a fluid into a vial, the fluid containing reagents for performing a nucleic acid amplification assay;   (B) engaging an opaque cap with a probe of the robotic pipettor for removably securing the cap to the probe;   (C) with the robotic pipettor, moving the cap secured to the probe into an open end of a vial and securing the cap to the vial to form a capped vial;   (D) moving the capped vial into a receptacle well of a receptacle holder, wherein a lower portion of the vial is contained within the receptacle well, and wherein the cap is situated above a top surface of the receptacle holder;   (E) while the capped vial is in the receptacle holder, subjecting the fluid to temperature conditions for performing the nucleic acid amplification assay; and   (F) while the capped vial is in the receptacle holder, detecting an optical emission signal from the fluid through a through-hole extending from a bottom-center of an inner surface of the well beneath the vial to a bottom outer surface of the receptacle holder, the intensity of the optical emission being indicative of the presence or amount of an analyte in the fluid.