ENSEMBLE-DECISION ALIQUOT RANKING

• US 20120129190A1
• Filed: 04/13/2010
• Published: 05/24/2012
• Est. Priority Date: 04/13/2009
• Status: Abandoned Application

• Current Assignee: University of Washington
• Original Assignee: University of Washington
• Inventors: Chiu, Daniel T., Kuo, Jason S., Schiro, Perry G.
• Application Number:
  US13/257,571
• Publication Number:
  US 20120129190A1
• Time in Patent Office: Days
• US Class Current: 435/7.23
• CPC Class Codes: G01N 15/1433 using image recognition
• CPC Class Codes: G01N 21/25 Colour; Spectral properties, i.e. comparison of effect of material on the light at two or more different wavelengths or wavelength bands
• CPC Class Codes: G01N 21/64 Fluorescence; Phosphorescence
• CPC Class Codes: G01N 22/00 Investigating or analysing materials by the use of microwaves or radio waves, i.e. electromagnetic waves with a wavelength of one millimetre or more G01N3/00 - G01N17/00, G01N24/00 take precedence
• CPC Class Codes: G01N 33/5302 Apparatus specially adapted for immunological test procedures
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• CPC Class Codes: G01N 33/57407 Specifically defined cancers
• CPC Class Codes: G01N 33/582 with fluorescent label
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

Provided herein, among other aspects, are methods and apparatuses for ranking aliquots from a suspension containing bioparticles. In certain embodiments, the bioparticles may be cells, organelles, proteins, DNAs, debris of biological origin, microbeads coated with biological compounds, or viral particles. As such, the methods and apparatuses provided herein may be used to quantify rare cells such as circulating cancer cells, fetal cells and other rare cells present in bodily fluids for disease diagnosis, prognosis, or treatment.

Claims

1. A method for detecting a rare particle in a fluid sample, the method comprising the steps of:

(a) detecting the presence or absence of a rare particle in an aliquot of the fluid sample;

(b) assigning a value to the aliquot based on the presence or absence of the rare particle; and

(c) directing the flow or collection of the aliquot based on the assigned value.

2. The method of claim 1, wherein the step of detecting the presence of the rare particle comprises the sub-steps of:

(i) contacting the fluid sample with a detection reagent under conditions suitable to transform the detection reagent into a complex comprising said detection reagent and a rare particle; and

(ii) detecting the presence or absence of a complex formed in step (i) in an aliquot of the fluid sample.

3. The method of claim 1, wherein the step of detecting the presence of the rare particle comprises the sub-steps of:

(i) interrogating the aliquot with an external source of electromagnetic radiation; and

(ii) detecting fluorescence of the rare particle.

4. The method of claim 1, wherein the step of detecting the presence of a rare particle comprises detecting bioluminescence or chemiluminescence of the rare particle.

6. The method of claim 1, wherein the aliquot contains more than one rare particle.

7. The method of claim 1, wherein the fluid sample is a biological fluid.

8. The method of claim 1, wherein the fluid sample is simultaneously contacted with a plurality of differentiable detection reagents each having a different specificity under conditions sufficient to transform the plurality of detection reagents into a plurality of complexes comprising the detection reagents and a plurality of rare particles.

9. The method of claim 8, wherein the plurality of complexes are detected simultaneously.

10. The method of claim 8, wherein the detection reagents are differentiable by fluorescence at different wavelengths.

11. The method of claim 1, wherein the aliquot is assigned either a first value if the aliquot contains a rare particle or a second value if the aliquot does not contain a rare particle.

12. The method of claim 1, wherein said first value depends on either the identity of the rare particle or the concentration of the rare particle in the aliquot.

13. The method of claim 1, wherein multiple aliquots having the same assigned value are pooled together.

14. The method of claim 1, wherein the detection step is performed during continuous flow of the biological sample through a flow channel.

15. The method of claim 1, wherein a plurality of aliquots of the fluid sample are physically separated prior to the detection step.

16. The method of claim 15, wherein the aliquots are partitioned into separate flow channels or chambers prior to the detection step.

5. The method of 1, wherein the rare particle is a rare cell.

17. A method for providing a subject a diagnosis or prognosis for a condition associated with the presence of a rare particle in a biological fluid, the method comprising the steps of:

(a) contacting a biological fluid from the subject with a detection reagent under conditions suitable to transform the detection reagent into a complex comprising said detection reagent and a rare particle;

(b) detecting the presence or absence of a complex formed in step (a) in an aliquot of the biological fluid;

(c) assigning a value to the aliquot based on the presence or absence of a complex formed in step (a); and

(d) providing a diagnosis or prognosis to the subject based on the assigned value.

18. An apparatus for detecting a rare particle in a fluid sample, the device comprising:

(a) at least a first input channel;

(b) at least two exit channels;

(c) at least one detector capable of detecting one or more rare particles in an aliquot of the fluid sample;

(d) a mechanism for directing the flow of the aliquot; and

(e) a computer capable of assigning a value to the aliquot based on the presence, absence, identity, composition, or quantity of the rare particles in the aliquot, wherein the computer is in communication with the detector and the mechanism for directing the flow of the aliquot.

19. The apparatus of claim 18, wherein said mechanism directs the flow of the aliquot into either a first exit channel if the aliquot contains a rare particle or a second exit channel if the aliquot does not contain a rare particle.

20. The apparatus of claim 18, wherein said mechanism directs the flow of an aliquot containing a rare particle into one of a plurality of exit channels depending on the identity, composition, or quantity of the rare particle.

21. The apparatus of claim 18, wherein the mechanism for directing the flow of the aliquot comprises an electrode, a magnetic element, an acoustic element, or an electro-actuated element.

22. The apparatus of claim 18, wherein the mechanism for directing the flow of the aliquot comprises one or more electro-actuated valves or pistons, wherein the valves or pistons control the flow of a liquid in at least a first directional flow channel that intersects with the first input channel and the two exit channels at a first junction.

23. The apparatus of claim 18, wherein the detector is selected from the group consisting of a camera, an electron multiplier, a charge-coupled device (CCD) image sensor, a photomultiplier tube (PMT), an avalanche photodiode (APD), a single-photon avalanche diode (SPAD), and a complementary metal oxide semiconductor (CMOS) image sensor.

24. The apparatus of claim 18, wherein the apparatus further comprises an electromagnetic radiation source for interrogation of the aliquot.