Method and apparatus for reading reporter labeled beads

A flow imaging system for sequentially imaging and decoding a plurality or encoded beads entrained in a fluid, said encoded beads comprising one or more compounds from among a plurality of different compounds, and one or more reporters from among a plurality of different reporters, each different compound being uniquely identified by at least one reporter, said flow imaging system comprising:

• (a) at least one light source for illuminating an encoded bead within a flow of fluid passing through the flow imaging system;
• (b) a collection lens disposed so that light traveling from an encoded bead passes through the collection lens and travels along a collection path;
• (c) a dispersing component that receives the light from the collection lens and disperses the light into a plurality of light beams, as a function of a plurality of different discriminable characteristics of the light, said plurality of different discriminable characteristics being indicative of the plurality of different reporters;
• (d) at least one pixilated detector;
• (e) an imaging lens that focuses each of the plurality of light beams on said at least one pixilated detector, producing a respective image corresponding to each of the plurality of light beams, said at least one pixilated detector providing an output signal for each respective image, each output signal identifying those reporters present on the encoded bead;
• and
• (f) a signal processor coupled to receive the output signals from said at least one pixilated detector, said signal processor processing the output signals to decode those compounds present on the encoded bead, based on the identity of those reporters present on the encoded bead.

A flow imaging system for sequentially imaging and decoding a plurality of encoded beads entrained in a fluid, said encoded beads comprising one or more compounds from among a plurality of different compounds, and one or more reporters from among a plurality of different reporters, each compound being uniquely identified by at least one reporter, said flow imaging system comprising:

• (a) a collection lens disposed so that light traveling from an encoded bead passes through the collection lens and travels along a collection path;
• (b) a plurality of light reflecting elements disposed in the collection path, each light reflecting element reflecting light of a different predefined characteristic, and passing light that does not have that predefined characteristic, the reporters on an encoded bead determining the characteristics of light traveling along the collection path, each light reflecting element being positioned at a different location with respect to the collection path to reflect light of a specific predefined characteristic in a direction different from that of other light reflecting elements, each light reflecting element being positioned along an axis of said collection path, such that passing light not reflected by a preceding light reflecting element reaches a last light reflecting element;
• (c) at least one pixilated detector disposed to receive light that has been reflected by each of the light reflecting elements, said at least one pixilated detector comprising a plurality of pixilated regions, each pixilated region producing an output signal that is indicative of at least one characteristic of the encoded beads and thus indicative of the reporters;
• and
• (d) a signal processor coupled to receive the output signals from said the plurality of regions, said signal processor processing the output signals to decode an identity of the compounds as a function of the reporters present on the encoded bead.

A flow imaging system for sequentially imaging and decoding a plurality of encoded beads entrained in a fluid, said encoded beads comprising one or more compounds from among a plurality of different compounds, and one or more reporters from among a plurality of different reporters, each compound being uniquely identified by at least one reporter, said flow imaging system comprising:

• (a) a collection lens disposed so that light traveling from an encoded bead object passes through the collection lens and travels along a collection path;
• (b) a dispersing component that receives the light from the collection lens and disperses the light into a plurality of light beams, as a function of a plurality of different discriminable characteristics of the light, said plurality of different discriminable characteristics being indicative of the plurality of different reporters;
• (c) a plurality of light sensitive regions disposed on at least one detector;
• (d) an imaging lens that focuses each of the plurality of light beams on said plurality of light sensitive regions, producing a respective image corresponding to each of the plurality of light beams, said plurality of light sensitive regions providing an output signal for each respective image, each output signal indicating those reporters present on the encoded bead;
• and
• (e) means for processing the output signals to decode a sequence of the plurality of components.

A flow imaging system for sequentially imaging and decoding a plurality of encoded beads entrained in a fluid, said encoded beads being associated with one or more compounds from among a plurality of different compounds, and with one or more reporters from among a plurality of different reporters, each compound being uniquely identified by at least one reporter, said flow imaging system comprising:

• (a) a fluid system comprising an unanalyzed encoded bead supply, a detection volume, and an analyzed encoded bead reservoir, said fluid system being specifically adapted to hydrodynamically focus fluid moving from said unanalyzed encoded bead supply into said detection volume, such that encoded beads pass through said detection volume one at a time and into the encoded bead reservoir;
• (b) means for collecting image data from each encoded bead passing though said detection volume, said image data being indicative of at least one characteristic of the encoded bead passing through the detection volume that is determinative of the reporters associated with the encoded bead;
• and
• (c) a signal processor capable of decoding a plurality of encoded beads based on said at least one characteristic of the encoded beads collected by said means, to determine the compounds associated with each encoded bead that has been analyzed.

A method of employing an oligo library encoded on beads for at least one of a DNA sequencing, a polymorphism analysis, and an expression analysis, said method comprising the steps of:

• (a) providing an imaging system capable of decoding a sequence of encoded beads conveyed in a flow of fluid;
• (b) generating a complete encoded bead library of N-mer oligos;
• (c) selectively performing one of said DNA sequencing, said polymorphism analysis, and said expression analysis based on imaging data produced by imaging the encoded beads with the imaging system;
• (d) when the DNA sequencing is selected, amplifying genomic DNA using primers for extended sequences of interest;
• (e) when the polymorphism analysis is selected, amplifying genomic DNA using primers for polymorphic regions of interest;
• (f) when the expression analysis is selected, amplifying RNA using primers for genes of interest;
• (g) hybridizing an amplified component produced by any of steps (d)-(f) in relationship to said encoded bead library;
• (h) analyzing the encoded beads using the imaging data to identify oligo sequences of encoded beads hybridized in step (g);
• and
• (i) constructing sequence contigs from the oligo sequences identified in step (h) to identify one of a genomic DNA sequence, a polymorphic allele, and an expressed gene.