Scanning system and method for imaging and sequencing
A scanning detection system is provided wherein emissions from locations in a flow cell are detected. In some embodiments, the system can comprise an excitation source, a photocleavage source, and modulating optics configured to cause an excitation beam generated by the excitation source to irradiate a first group of the fixed locations and to cause a photocleavage beam generated by the photocleavage source to irradiate a second group of the fixed locations, which is separate and apart from the first group of fixed locations. Methods of detecting sequencing reactions using such a system are also provided.
1. A system for detecting fluorescently labeled polynucleotides, comprising:
a substrate comprising a first end, and a second end, one or more channels formed therein, and a plurality of labeled polynucleotide beads immobilized in the one or more channels, each of the plurality of labeled polynucleotide beads at a respective fixed location of a plurality of fixed locations, each of the labeled polynucleotide beads having a diameter and being labeled with a respective marker that is responsive to radiation and that emits emission light indicative of the presence of at least one nucleotide;
at least one irradiation source for emitting radiation and disposed for irradiating the plurality of labeled polynucleotide beads to thereby excite the markers responsive to the radiation and to cause the markers to emit emission light, wherein the at least one irradiation source comprises at least one laser;
modulating optics comprising a set of prisms including a first prism, a second prism and a trombone prism configured to render intensity consistent across the plurality of fixed locations irritated by the at least one irradiation source;
a scanning detector array positioned with respect to the plurality of labeled polynucleotide beads, the scanning detector array configured to collect the emission light produced by the markers and to produce charges corresponding to the emission light, the detector array having an output; and
a time-delay integration (TDI) system that accumulates charges corresponding to the emission light, within the detector array, and reads accumulated charges at the output of the scanning detector array.
2. The system of claim 1 , further comprising second modulating optics disposed between the at least one irradiation source and the scanning detector array, the second modulating optics comprising at least one of a cylindrical lens, a trombone prism, and a holographic beam shaper.
3. The system of claim 1 , wherein the TDI system is configured to accumulate charge by moving, relative to one another, the at least one irradiation source and the plurality of labeled polynucleotide beads, without moving the at least one irradiation source and the scanning detector array relative to one another.
4. The system of claim 1 , wherein the one or more channels comprises from two to 10 channels, and the scanning detector array is configured to collect emission light produced by at least two channels sequentially.
5. The system of claim 1 , wherein the at least one irradiation source further comprises a holographic beam shaper.
6. The system of claim 1 , wherein at least some of the labeled polynucleotide beads are labeled with a respective marker that fluoresces when excited by radiation emitted from the at least one irradiation source.
7. The system of claim 1 , wherein the substrate comprises a flow cell.
8. The system of claim 7 , wherein the flow cell comprises 104 to 106 channels for containing the plurality of labeled polynucleotide beads.
9. The system of claim 1 , wherein the scanning detector array comprises a two dimensional charge-coupled device.
10. The system of claim 1 , further comprising a translational stage configured to move the at least one irradiation source and the scanning detector array together.