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EP-4735869-A1 - FAST MICROARRAY SCANNING USING MULTIBAND FILTERS

EP4735869A1EP 4735869 A1EP4735869 A1EP 4735869A1EP-4735869-A1

Abstract

A system for sample holder scanning is provided. The system includes a light source, a multiband excitation filter configured to select at least two excitation bands of light for fluorescent dyes used in the sample holder. The system further includes a multiband dichroic filter configured to reflect the at least two excitation bands of light, a multiband emission filter configured to transmit at least two bands of fluorescent emission light from each reaction site of the sample holder. The multiband dichroic filter is further configured to transmit the at least two bands of fluorescent emission light. The system also includes an optical sensor configured to detect the at least two bands of fluorescent emission light to generate an image of a sample holder.

Inventors

  • HILLENDAHL, JAMES
  • YANG, Chunxin
  • NGUYEN, DEVIN

Assignees

  • Affymetrix, Inc.
  • Life Technologies Corporation

Dates

Publication Date
20260506
Application Date
20240617

Claims (20)

  1. 1. A system for sample holder scanning, the system comprising: a light source; a multiband excitation filter configured to select at least two excitation bands of light, wherein each of the at least two excitation bands of light is an excitation band of light for a fluorescent dye used in the sample holder; a multiband dichroic filter configured to reflect the at least two excitation bands of light; a lens configured to direct the at least two excitation bands of light toward a sample holder; a multiband emission filter configured to transmit at least two bands of fluorescent emission light from each reaction site of the sample holder, wherein the multiband dichroic filter is further configured to transmit the at least two bands of fluorescent emission light; and an optical sensor configured to detect the at least two bands of fluorescent emission light from the multiband emission filter to generate an image of a sample holder.
  2. 2. The system of claim 1, further comprising: a mechanical apparatus configured to move the sample holder in a x and a y direction such that the optical sensor raster scans each reaction site in the sample holder.
  3. 3. The system of any of the claims 1 to 2, wherein the mechanical apparatus moves the sample holder such that the optical sensor detects emission light from a plurality of areas of each reaction site in the sample holder.
  4. 4. The system of claim 3, wherein the plurality of areas is 9-36 areas.
  5. 5. The system of any of the claims 1 to 4, wherein the optical sensor is selected from the group consisting of: a CCD sensor, CMOS sensor, and a sCMOS sensor.
  6. 6. The system of any of the claims 1 to 5, wherein the light source is a xenon lamp.
  7. 7. The system of any of the claims 1 to 6, further comprising: a light control apparatus configured to: restrict the output of the light source to a narrow wavelength band selected based on a desired band of light to pass through the multiband excitation filter, and switch the light off and on for a predetermined time period to set an exposure time for the optical sensor.
  8. 8. The system of any of the claims 1 to 7, wherein the light control apparatus includes an optical filter.
  9. 9. The system of any of the claims 1 to 7, wherein the light control apparatus includes a mechanical shutter.
  10. 10. The system of any of the claims 1 to 5, wherein the light source is a white LED.
  11. 11. The system of claim 10, further comprising: at least two bandpass filters.
  12. 12. The system of any of the claims 1 to 5, wherein the light source comprises at least two LED sources, wherein each of the two at least LED sources is matched to one of the at least two expected excitation bands of dyes selected for use in the sample holder, wherein the at least two LED sources have minimal spectral overlap.
  13. 13. The system of claim 12, wherein the light source comprises at least one a laser pumped phosphor device which is configured to match one of the at least two expected excitation bands of dyes selected for use in the sample holder.
  14. 14. A method for sample holder scanning, the method comprising: generating light from a light source; selecting, by a multiband excitation filter configured to transmit at least two excitation bands of light, a first excitation band of light, wherein each of the at least two excitation bands of light is an excitation band of light for a fluorescent dye used in the sample holder; reflecting, by a multiband dichroic filter configured to reflect the at least two excitation bands of light, the first excitation band of light; directing, by a lens, the first excitation band of light toward a sample holder; transmitting, by a multiband emission filter configured to transmit at least two fluorescent emission bands of light, the first band of fluorescent emission light from each reaction site of the sample holder; and detecting, by an optical sensor, the first band of fluorescent emission light from the multiband emission filter to generate an image of a sample holder.
  15. 15. The method of claim 14, further comprising moving, by a mechanical apparatus, the sample holder in a x and a y direction such that the optical sensor raster scans each reaction site in the sample holder.
  16. 16. The method of claim 15, wherein moving the sample holder includes moving the sample holder so that the optical sensor detects emission light from a plurality of areas of each reaction site in the sample holder.
  17. 17. The method of any of the claim 14 to 16, wherein the plurality of areas is 9-36 areas.
  18. 18. The method of any of the claims 14 to 17, further comprising: detecting the at least two bands of fluorescent emission light from the plurality of areas of each reaction site in the sample holder to generate the image of the sample holder.
  19. 19. The method of any of the claims 14 to 18, further comprising: designing the multiband excitation filter, multiband dichroic filter, and multiband emission filter to minimize crosstalk between fluorescent dyes used in the sample holder.
  20. 20. The method of any of the claims 1 to 19, wherein the optical sensor is selected from the group consisting of: a CCD sensor, CMOS sensor, and a sCMOS sensor.

Description

FAST MICROARRAY SCANNING USING MULTIBAND FILTERS CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of priority of U.S. Provisional Patent Application No. 63/511,435, filed on June 30, 2023, which is incorporated herein in its entirety by reference. BACKGROUND [0002] Optical systems for biological and biochemical reactions have been used to monitor, measure, and/or analyze such reactions. Such systems are commonly used in sequencing, genotyping, polymerase chain reactions (PCR), and other biochemical reactions to monitor progress and provide quantitative data. [0003] For example, an optical system may be used in DNA-DNA hybridization arrays to illuminate fluorescent DNA-binding dyes or fluorescent probes to produce fluorescent signals indicative of the degree of similarity between sample and probe. In a hybridization analysis, arrays are set up with selected sets of DNA sequences of interest. If a sample has complementary sequences to the target DNA in the array, a fluorescent dye can be attached. When excitation light shines on the DNA array after hybridization, array spots fluoresce if a dye is attached. An optical system is needed to determine fluorescence emission. [0004] Previously, in these optical systems, fluorescent emission data is read by taking multiple images at each sub-array location to scan an entire sample holder. Further, for each sub-anay location, two or more matched filter sets are mechanically moved to take images of two or more fluorescent dye emissions from the sample holder adding to the time required to analyze the array. Each filter set includes excitation, dichroic, and emission filters matched to a fluorescent dye used in the array. As a result, scanning an entire array with more than one fluorescent dye is a lengthy process. [0005] Moreover, there are increasing demands to provide greater numbers of reactions per test or experiment, resulting in instruments that are able to conduct large numbers of reactions simultaneously. Increasing the number of reactions also increases the time the optical system takes to scan an entire sample holder. [0006] The combination of having large numbers of samples and the desire to perform experiments in a faster manner has created a need for optical systems that scan quickly and also provide high optical performance for observing, testing, and/or analyzing one or more biological samples. SUMMARY [0007] In one exemplary embodiment, a system for sample holder scanning is provided. The system includes a light source. The system further includes a multiband excitation filter configured to select at least two excitation bands of light. Each of the at least two excitation bands of light is an excitation band of light for a fluorescent dye used in the sample holder. The system further includes a multiband dichroic filter configured to reflect the at least two excitation bands of light, a lens configured to direct the at least two excitation bands of light toward a sample holder, and a multiband emission filter configured to transmit at least two bands of fluorescent emission light from each reaction site of the sample holder. The multiband dichroic filter is further configured to transmit the at least two bands of fluorescent emission light. The system also includes an optical sensor configured to detect the at least two bands of fluorescent emission light from the multiband emission filter to generate an image of a sample holder. [0008] In another exemplary embodiment, a method for sample holder scanning is provided. The method includes generating light from a light source, and selecting, by a multiband excitation filter configured to transmit at least two excitation bands of light, a first excitation band of light. Each of the at least two excitation bands of light is an excitation band of light for a fluorescent dye used in the sample holder. The method further includes reflecting, by a multiband dichroic filter configured to reflect the at least two excitation bands of light, the first excitation band of light, and directing, by a lens, the first excitation band of light toward a sample holder. The method includes transmitting, by a multiband emission filter configured to transmit at least two fluorescent emission bands of light, the first band of fluorescent emission light from each reaction site of the sample holder, and detecting, by an optical sensor, the first band of fluorescent emission light from the multiband emission filter to generate an image of a sample holder. DESCRIPTION OF THE FIGURES [0009] FIG. 1 illustrates a block diagram of a general fluorescent optical system configuration. [0010] FIG. 2A illustrates an exemplary fluorescent transmission and emission data plot. [0011] FIG. 2B illustrates an exemplary fluorescent transmission and emission data plot with single band excitation, dichroic, and emission optical filters. [0012] FIG. 3 illustrates a block diagram of an inverted general fluorescent