Fluidic devices with bead well geometries with spatially separated bead retention and signal detection segments and related methods

Abstract

A fluidic device includes a plurality of reaction wells, typically in a dense array, with at least one bead retention segment in fluid communication with and spatially separated from at least one signal detection segment. A respective bead retention segment can be configured to hold a single bead, which can have a reagent attached thereto.

That which is claimed is: 
     
         1 . An analysis system comprising:
 a controller;   a detector in communication with the controller; and   an image processor with a module configured to identify signal present in signal detection segments of reaction wells of a device holding the reaction wells, wherein the reaction wells having at least one bead retention segment and at least one separate signal detection segment that extends a distance away from the at least one bead retention segment and is in fluid communication with the at least one bead retention segment,   wherein the module is configured to identify a positive assay signal associated with a signal detection segment that extends a distance away from the at least one bead retention segment.   
     
     
         2 . The system of  claim 1 , wherein the identification is carried out after a reaction without requiring a baseline readout from the detector before the reaction. 
     
     
         3 . The system of  claim 1 , wherein the module is configured to carry out bead decoding based on identified positive assay signals or before or during when an assay is carried out. 
     
     
         4 . The system of  claim 1 , wherein the module is configured to identify at least two beads held in first and second separate bead retention segments of a single reaction well, the well having at least one signal detection segment in fluid communication with one or both of the bead retention segments. 
     
     
         5 . The system of  claim 1 , wherein centerlines of bead retention segments of neighboring reaction wells are spaced apart a distance of between 1 μm and 1 mm, and wherein the at least one signal detection segment extends a distance L that is between 0.3× and 200× of a diameter of a target bead. 
     
     
         6 . The system of  claim 1 , wherein the distance L is in a range of 1-100 μm measured from a centerline of the at least one bead retention segment of a respective reaction well. 
     
     
         7 . The system of  claim 1 , wherein the reaction wells that are in fluid isolation from each other and sealed from one another by a sealing agent, and wherein the device comprises a plurality of magnetic beads, wherein one magnetic bead of the plurality of magnetic beads is physically retained in each bead retention segment of the plurality of reaction wells. 
     
     
         8 . The system of  claim 1 , wherein the at least one bead retention segment has a depth direction, wherein the at least one signal detection segment is defined by an elongate channel that extends away from the at least one bead retention segment in a length direction that is perpendicular to the depth direction, and wherein the at least one elongate channel has a length in the length direction that is greater than a width of the at least one bead retention segment. 
     
     
         9 . The system of  claim 1 , wherein the device is a microfluidic chip and the plurality of reaction wells are provided as an array of reaction wells, wherein the at least one bead retention segment and the at least one signal detection segment reside in a first planar substrate with the first planar substrate defining an open upper surface and sidewalls of the at least one bead retention segment and the at least one signal detection segment, and wherein the device further comprises a second planar substrate that couples to the first planar substrate and defines a closed outer surface with at least one fluid port. 
     
     
         10 . The system of  claim 1 , wherein each of the plurality of reaction wells has a volumetric capacity in a range of 1 aL to 1 μL, and wherein the device further comprises a sealing agent that seals the plurality of reaction wells from each other. 
     
     
         11 . The system of  claim 1 , wherein each bead retention segment of the plurality of reaction wells is sized and configured to hold only a respective single bead with a diameter in a range of about 10 nm to about 1 mm, and wherein at least one of the plurality of reaction wells has a single bead retention segment as the at least one bead retention segment that merges into a separate corresponding single elongate channel as the at least one signal detection segment, and wherein the separate corresponding single elongate channel has a width that is narrower than the width of the bead retention segment and has an end portion that resides a distance L in the length direction in a range of 1 μm to 1 mm from the single bead retention segment. 
     
     
         12 . The system of  claim 1 , wherein the reaction wells are provided in a density in a range of about 6,000 wells/cm 2  to about 2,000,000 wells/cm 2 . 
     
     
         13 . The system of  claim 1 , wherein reagents and/or analytes released from beads held in respective bead retention segments diffuse through a common solution volume of respective reaction wells, and wherein the detected signal is detected while the beads are held in the respective bead retention segments with the signal detection segment of the at least one signal detection segment generating an optical signal comprising a tail that is distinguishable from a background signal of a corresponding bead. 
     
     
         14 . The system of  claim 13 , wherein the detected signal comprises a fluorescence signal. 
     
     
         15 . The system of  claim 1 , wherein the module is configured to detect the signal for an array of the reaction wells in which one or more of the reaction wells comprise a different type of bead from one or more other ones of the reaction wells, wherein each type of bead is encoded with a unique signature and each type of bead is functionalized with a different reagent and the module is configured to detect different analytes or different chemical reactions or different analytes and different chemical reactions.