Apparatus for polynucleotide detection and quantitation

• US 20040014117A1
• Filed: 06/19/2003
• Published: 01/22/2004
• Est. Priority Date: 06/20/2002
• Status: Abandoned Application

• Current Assignee: PrimeraDx, Inc (Qiagen NV)
• Original Assignee: Sention
• Inventors: Slepnev, Vladimir I.
• Application Number:
  US10/464,941
• Publication Number:
  US 20040014117A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: G01N 35/0099 comprising robots or similar manipulators robots per se B25J

Abstract

An apparatus for expression profiling analysis, subjecting biological materials to polynucleotide extraction, amplification and analysis. The apparatus include an amplification device which permits the amplification of polynucleotides and an analysis device which quantifies the amount of the amplified polynucleotide products. The amplification device of the apparatus may further permit polynucleotide extraction to prepare the template for amplification, or sequence identification of a quantified polynucleotide product. A fraction collector may be included in the apparatus to collect a qualified polynucleotide product before its sequence is identified. The analysis device may further permit data generation, or alternatively, data can be generated by a separate data generation device provided with the apparatus. The devices within the apparatus are connected by connecting means which permit the transfer of a fluid or a signal for amplification and analysis.

Claims

1. An apparatus for expression profiling, comprising:

an amplification device which amplifies a polynucleotide in a reaction mixture to generate an amplified product; and

an analysis device connected to said amplification device by a first connecting means which permits an aliquot of said reaction mixture to transfer from said amplification device to said analysis device which detects and quantifies said amplified product, wherein said first connecting means is a robotic arm.

2. The apparatus in claim 1, further comprising a polynucleotide extraction device connected to said amplification device by a second connecting means which permits an extracted polynucleotide sample to transfer from said polynucleotide extraction device to said amplification device.

3. The apparatus in claim 1, further comprising a fraction collector device.

4. The apparatus in claim 3, wherein said fraction collector device is connected to said analysis device by a fourth connecting means which permits the collection of a quantified product.

5. The apparatus in claim 1, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said analysis device by a fifth connecting means which permits a quantified product to transfer from said analysis device to said sequence identifier.

6. The apparatus in claim 3, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said fraction collector device by a fifth connecting means which permits a collected product to transfer from said fraction collector device to said sequence identifier.

26. An apparatus in any one of the claims 1, 7, 12, 18, and 22, wherein said amplification device and said analysis device also permits sequence identification of a polynucleotide.

35. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein said amplification device is a polymerase chain reaction (PCR) amplification device.

36. The apparatus in claim 35, wherein said first connecting means permits an aliquot of said reaction mixture to transfer from said amplification device to said analysis device at the end of each PCR cycle.

37. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein said amplification device permits reverse transcription to generate cDNAs.

38. The apparatus in claim 37, wherein one or more primers used for reverse transcription are chemically linked to an inner wall of a reaction tube or a well of a microtiter plate.

39. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein said apparatus permits the detection and quantification of a signal generated by one or more fluorescent labels.

40. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein said first, second, fourth, or fifth connecting means is a robotic arm.

41. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein said first, second, third, fourth, or fifth connecting means is a tube or a channel.

42. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein said first, second, fourth, and fifth connecting means is a single connecting means.

43. The apparatus in any one of claims 1, 7, 12, 18, 22, and 27, wherein an electric current is applied to said first, second, fourth, or fifth connecting means to permit transfer.

44. The apparatus in any one of claims 1, 7, 12, 18, and 22, wherein said analysis device is a capillary electrophoresis device.

7. An apparatus for expression profiling, comprising:

an amplification device which amplifies a polynucleotide in a reaction mixture to generate an amplified product;

an analysis device connected to said amplification device by a first connecting means which permits an aliquot of said reaction mixture to transfer from said amplification device to said analysis device which detects and quantifies said amplified product; and

a polynucleotide extraction device connected to said amplification device by a second connecting means which permits an extracted polynucleotide sample to transfer from said polynucleotide extraction device to said amplification device.

8. The apparatus in claim 7, further comprising a fraction collector device.

9. The apparatus in claim 8, wherein said fraction collector is connected to said analysis device by a fourth connecting means which permits the collection of a quantified product.

10. The apparatus in claim 7, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said analysis device by a fifth connecting means which permits a quantified product to transfer from said capillary electrophoresis device to said sequence identifier.

11. The apparatus in claim 8, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said fraction collector device by a fifth connecting means which permits a collected product to transfer from said fraction collector device to said sequence identifier.

12. An apparatus for expression profiling, comprising:

an amplification device which amplifies a polynucleotide in a reaction mixture to generate an amplified product;

an analysis device connected to said amplification device by a first connecting means which permits an aliquot of said reaction mixture to transfer from said amplification device to said analysis device which detects and quantifies said amplified product; and

a data generating device connected to said analysis device by a third connecting means which permits a signal to transfer from said analysis device to said data generating device.

13. The apparatus in claim 12, further comprising a polynucleotide extraction device connected to said amplification device by a second connecting means which permits an extracted polynucleotide sample to transfer from said polynucleotide extraction device to said amplification device.

14. The apparatus in claim 12, further comprising a fraction collector device.

15. The apparatus in claim 14, wherein said fraction collector device is connected to said analysis device by a fourth connecting means which permits the collection of a quantified product.

16. The apparatus in claim 12, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said analysis device by a fifth connecting means which permits a quantified product to transfer from said analysis device to said sequence identifier.

17. The apparatus in claim 12, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said fraction collector device by a fifth connecting means which permits a collected product to transfer from said fraction collector device to said sequence identifier.

45. The apparatus in any one of claims 2, 7, 12, 20, 23, and 28, wherein said polynucleotide extraction device permits isolating total RNAs or mRNAs from one or more biological materials.

18. An apparatus for expression profiling, comprising:

an amplification device which amplifies a polynucleotide in a reaction mixture to generate an amplified product;

an analysis device connected to said amplification device by a first connecting means which permits an aliquot of said reaction mixture to transfer from said amplification device to said analysis device which detects and quantifies said amplified product; and

a fraction collector device which permits the collection of a quantified product.

19. The apparatus in claim 18, wherein said fraction collector device is connected to said analysis device by a fourth connecting means which permits the collection of a quantified product.

20. The apparatus in claim 18, further comprising a polynucleotide extraction device connected to said amplification device by a second connecting means which permits an extracted polynucleotide sample to transfer from said polynucleotide extraction device to said amplification device.

21. The apparatus in claim 18, further comprising a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said fraction collector by a fifth connecting means which permits a collected product to transfer from said fraction collector device to said sequence identifier.

22. An apparatus for expression profiling, comprising:

an amplification device which amplifies a polynucleotide in a reaction mixture to generate an amplified product;

an analysis device connected to said amplification device by a first connecting means which permits an aliquot of said reaction mixture to transfer from said amplification device to said analysis device which detects and quantifies said amplified product; and

a sequence identifier which identifies a sequence of a quantified product, wherein said sequence identifier is connected to said analysis device by a fifth connecting means which permits a quantified product to transfer from said analysis device to said sequence identifier.

23. The apparatus in claim 22, further comprising a polynucleotide extraction device connected to said amplification device by a second connecting means which permits an extracted polynucleotide sample to transfer from said polynucleotide extraction device to said amplification device.

24. The apparatus in claim 22, further comprising a fraction collector device.

25. The apparatus in claim 24, wherein said fraction collector device is connected to said analysis device by a fourth connecting means which permits the collection of a quantified product, and wherein said fraction collector device is also connected to said sequence identifier by another fifth connecting means which permits a collected product to transfer from said fraction collector to said sequence identifier.

27. An apparatus for expression profiling, comprising:

an amplification device which amplifies a polynucleotide in a reaction mixture to generate an amplified product; and

a capillary electrophoresis device which detects and quantifies said amplified product, wherein a capillary of said capillary electrophoresis device is immersed in said reaction mixture to transfer an aliquot of said reaction mixture from said amplification device to said capillary electrophoresis device.

28. The apparatus in claim 27, further comprising a polynucleotide extraction device connected to said amplification device by a second connecting means which permits an extracted polynucleotide sample to transfer from said polynucleotide extraction device to said amplification device.

29. The apparatus in claim 27, further comprising a fraction collector device.

30. The apparatus in claim 27, wherein said fraction collector device is connected to said capillary electrophoresis device by a fourth connecting means which permits the collection of a quantified product.

31. The apparatus in claim 27, further comprising a sequence identifier which identifies the sequence of a quantified product, wherein said sequence identifier is connected to said capillary electrophoresis device by a fifth connecting means which permits a quantified product to transfer from said capillary electrophoresis device to said sequence identifier.

32. The apparatus in claim 27, wherein an electric current is applied to electrodes of the capillary electrophoresis device so that the capillary of said capillary electrophoresis device immersed in said reaction mixture transfers an aliquot of said reaction mixture from said amplification device to said capillary electrophoresis device.

33. The apparatus in claim 27, wherein said amplification device and said capillary electrophoresis also permits sequence identification of a polynucleotide.

34. The apparatus in claim 29, further comprising a sequence identifier which identifies the sequence of a quantified product, wherein said sequence identifier is connected to said fraction collector device by a fifth connecting means which permits a collected product to transfer from said fraction collector device to said sequence identifier.