Biological analysis arrangement and approach therefor

• US 8,313,904 B2
• Filed: 11/26/2008
• Issued: 11/20/2012
• Est. Priority Date: 09/16/2002
• Status: Expired due to Fees

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: El Gamal, Abbas, Eltoukhy, Helmy, Salama, Khaled
• Primary Examiner(s): Kapushoc, Stephen
• Assistant Examiner(s): BHAT, NARAYAN KAMESHWAR
• Application Number:
  US12/323,645
• Publication Number:
  US 20090075838A1
• Time in Patent Office: 1,455 Days
• Field of Search: 435/6.1, 435/91.2, 435/283.1, 435/287.2, 536/23.1, 536/24.3, 422/82.01, 356/246, 356/440
• US Class Current: 435/6.1
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2300/0877 Flow chambers
• CPC Class Codes: B01L 2300/1822 using Peltier elements
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: C12Q 1/66 involving luciferase
• CPC Class Codes: G01N 21/253 for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• CPC Class Codes: G01N 21/6454 using an integrated detector array

Abstract

Characteristics of a chemical or biological sample are detected using an approach involving light detection. According to an example embodiment of the present invention, an assaying arrangement including a light detector is adapted to detect light from a sample, such as a biological material. A signal corresponding to the detected light is used to characterize the sample, for example, by detecting a light-related property thereof. In one implementation, the assaying arrangement includes integrated circuitry having a light detector and a programmable processor, with the light detector generating a signal corresponding to the light and sending the signal to the processor. The processor provides an output corresponding to the signal and indicative of a characteristic of the sample.

Claims

1. A method for determining a DNA sequence comprising:

delivering a dNTP to a substrate comprising;

(i) an integrated circuit chip integrated with

an array of optical sensors and circuitry for both analog and digital signal processing; and

an array of microwells, each microwell including a test site with a primed DNA template;

whereby the incorporation of a dNTP into the primed DNA template results in the release of pyrophosphate (PPi), and each microwell optically coupled to at least one optical sensor of the array of optical sensors and;

enzymatically generating light from the released PPi;

detecting the light at the array of optical sensors and producing analog signals representing the detected light; and

processing, for each optical sensor, the analog signals using the circuitry for analog and digital signal processing to determine the amount of dNTP incorporated at each test site.

2. The method of claim 1, wherein the integrated circuit chip generates a signal representing the light emitted from the microwells.

3. The method of claim 2, wherein the integrated circuit chip processes the signal to provide an indication of a nucleic acid sequence of the primed DNA template.

4. The method of claim 3, wherein the substrate comprises a processor that processes the signal to provide the indication of the nucleic acid sequence of the primed DNA template.

5. The method of claim 4, wherein the substrate comprises a data storage circuit, coupled to the processor and adapted to store data, wherein the processor retrieves data from the data storage circuit to process the signal and provide the indication of a nucleic acid sequence of the primed DNA template.

6. The method of claim 2, wherein the substrate comprises a control circuit that synchronizes detection of the light by the optical sensors with delivery of the dNTP.

7. The method of claim 2, wherein the substrate further comprises a memory arrangement that stores the signals for subsequent analysis.

8. The method of claim 2, wherein the substrate comprises noise reduction circuitry that reduces noise in the digital signal.

9. The method of claim 1, further comprising repeating the steps of delivering, generating and detecting for an additional dNTP.

10. The method of claim 1, further comprising mixing reagents using electrical methods.

11. A method for determining a DNA sequence comprising:

providing a substrate that includes a chip integrated with an array of sensors, a digital processing circuit, and an array of wells integral with the chip;

associating multiple nucleic acids of different sequences with the substrate such that multiple wells of the array of wells are each associated with a respective nucleic acid, wherein a nucleic acid in at least one well is of a different type of nucleic acid with respect to a type of nucleic acid in at least one other well;

delivering at least one nucleotide to the substrate such that incorporation of the at least one nucleotide into a strand complementary to a nucleic acid in a well of the array of wells, results in the release of pyrophosphate;

generating signals based on the release of pyrophosphate; and

detecting the signals to determine the incorporation of the at least one nucleotide at multiple individual wells of the array of wells.

12. The method of claim 11, wherein a circuit on the substrate generates an electrical signal indicative of the signals detected at the multiple individual wells and the circuit provides the electrical signal to a processing circuit separate from the substrate, the circuit on the substrate including the digital processing circuit.

13. The method of claim 11, further comprising processing second signals that are based on the detected signals with the digital processing circuit to provide data indicative of portions of nucleic acid sequences of the multiple nucleic acids of different sequences.

14. The method of claim 13, further comprising processing the second signals using a noise reduction circuit carried by the substrate.

15. The method of claim 13, wherein the step of providing the substrate further includes providing a substrate that includes a processor configured to process the second signals to provide the data indicative of the portions of the nucleic acid sequences.

16. The method of claim 15, wherein the step of providing the substrate further includes providing a substrate that includes a data storage device coupled to the processor and configured to store data.

17. The method of claim 16, further comprising retrieving data from the data storage device to process the second signals.

18. The method of claim 11, further comprising synchronizing, using a control circuit, the step of detecting the signals with the step of delivering the at least one nucleotide.

19. The method of claim 11, further comprising storing data based on the detected signals in a memory element carried by the substrate, and providing the data stored in the memory element for analysis.

20. The method of claim 11, further comprising repeating the steps of delivering, generating, and detecting for additional nucleotides until a multiple base sequence of multiple nucleic acids is determined.

21. The method of claim 11, further comprising mixing reagents using an electrical method.

22. The method of claim 11, wherein the step of detecting the signals to determine the incorporation of the at least one nucleotide at multiple individual wells includes detecting the signals using multiple individual optical sensors of the array of sensors.

23. The method of claim 11, wherein the step of detecting the signals to determine the incorporation of the at least one nucleotide at multiple individual wells includes detecting the signals to determine how many of the at least one nucleotide are incorporated at the multiple individual wells.

24. The method of claim 11, wherein the array of sensors on the substrate comprise an array of complementary metal-oxide-semiconductor based sensors.

25. The method of claim 11, wherein the array of sensors on the substrate comprise an array of optical sensors.

26. A method for determining nucleic acid sequences comprising:

receiving a substrate at a sequencing system, the substrate including a chip integrated with an array of sensors, a processing circuit configured to process signals from one or more sensor elements of the array of sensors, and an array of wells integral with the chip, the chip comprising a complementary metal-oxide-semiconductor (CMOS) circuit, and the chip comprising wells for sequencing that do not include a lens for light detection;

receiving at the sequencing system a reagent container separate from the substrate, the reagent container configured to contain nucleotides for use in sequencing;

associating multiple nucleic acids of different sequences with the substrate such that multiple wells of the array of wells are associated with a nucleic acid to be sequenced;

delivering at least one nucleotide from the reagent container to the substrate such that incorporation of the at least one nucleotide into a strand complementary to the nucleic acid to be sequenced in a well of the array of wells results in an extended sequence complementary to the nucleic acid in that well;

generating signals based on the incorporation of the at least one nucleotide into the strand complementary to the nucleic acid at multiple individual wells of the array of wells; and

detecting the signals to determine the incorporation of the at least one nucleotide at multiple individual wells of the array of wells;

wherein delivering the at least one nucleotide comprises delivering, for multiple rounds, nucleotides that can be used to provide information to identify at least one base in the nucleic acid to be sequenced different than a base identifiable from information based on nucleotides delivered in an immediately previous round of delivering nucleotides;

wherein generating signals based on the incorporation comprises generating signals for each of the multiple rounds; and

wherein detecting the signals comprises detecting the signals for the multiple rounds.

27. The method of claim 26, wherein individual sensor elements of the array of sensors are associated with a pre-determined well of the array of wells.

28. The method of claim 27, wherein a single sensor element is associated with each well.

29. The method of claim 27, wherein a plurality of sensor elements are associated with each well.

30. The method of claim 26, further comprising receiving at the substrate, control information from an interface system that is separate from the substrate and connected to a man-machine interface, the control information used to control processing by the processing circuit;

and providing information from the processing circuit to the interface system.

31. The method of claim 26, further comprising receiving a plurality of reagent containers that contain different reagents of the sequencing system.

32. The method of claim 26, wherein the reagent container contains a plurality of different reagents, and delivering the at least one nucleotide from the container comprises delivering the at least one nucleotide from a channel specifically connected to a portion of the reagent container containing the at least one nucleotide.

33. The method of claim 26, wherein

delivering, for multiple rounds, nucleotides that can be used to provide information to identify at least one base in the nucleic acid to be sequenced different than a base identifiable based on nucleotides delivered in an immediately previous round,

delivering, for multiple consecutive rounds, nucleotides that can be used to provide information to identify at least one base in the nucleic acid to be sequenced different than a base identifiable based on nucleotides delivered in an immediately previous round, and

wherein nucleotides are delivered such that adenine, guanine, cytosine, and thymine or uracil bases in the nucleic acid to be sequenced are individually identifiable in separate rounds of the multiple rounds.

34. The method of claim 26, wherein the at least one nucleotide is delivered from the reagent container to the substrate such that nucleotides are provided in a manner such that more than one nucleotide can be incorporated in a round of addition of nucleotides when the added nucleotide complements multiple bases in the nucleic acid to be sequenced in a row.