Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays

• US 20120129703A1
• Filed: 02/02/2011
• Published: 05/24/2012
• Est. Priority Date: 12/14/2006
• Status: Abandoned Application

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Rothberg, Jonathan M., Hinz, Wolfgang, Johnson, Kim L., Bustillo, James
• Application Number:
  US13/019,354
• Publication Number:
  US 20120129703A1
• Time in Patent Office: Days
• US Class Current: 506/2
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 27/4145 specially adapted for biomolecules, e.g. gate electrode with immobilised receptors
• CPC Class Codes: G01N 27/4148 Integrated circuits therefor, e.g. fabricated by CMOS processing CMOS processing per se H01L21/82
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: G01N 33/5438 Electrodes
• CPC Class Codes: H01L 27/088 the components being field-effect transistors with insulated gate
• CPC Class Codes: H01L 29/42324 Gate electrodes for transistors with a floating gate
• CPC Class Codes: H01L 29/78 with field effect produced by an insulated gate H01L29/7725, H01L29/775, H01L29/778 take precedence
• CPC Class Codes: H01L 2924/01006 Carbon [C]
• CPC Class Codes: H01L 2924/01013 Aluminum [Al]
• CPC Class Codes: H01L 2924/01015 Phosphorus [P]
• CPC Class Codes: H01L 2924/01073 Tantalum [Ta]
• CPC Class Codes: H01L 2924/14 Integrated circuits
• CPC Class Codes: H01L 2924/1433 Application-specific integrated circuit [ASIC]
• CPC Class Codes: Y10T 436/22 Hydrogen, per se

Abstract

Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.

Claims

1. An apparatus, comprising:

an array (100) of CMOS-fabricated sensors (105), each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) and occupying an area on a surface of the array of approximately ten micrometers by ten micrometers or less.

2. The apparatus of claim 1, wherein the area occupied by each sensor is approximately nine micrometers by nine micrometers or less.

3. The apparatus of claim 2, wherein the area occupied by each sensor is approximately five micrometers by five micrometers or less.

4. The apparatus of claim 3, wherein the area occupied by each sensor is approximately three micrometers by three micrometers or less.

5. The apparatus of any of claims 1 to 4, wherein the plurality of CMOS-fabricated sensors includes more than 256 sensors.

6. The apparatus of claim 5, wherein the array includes a two-dimensional array of at least 512 rows and at least 512 columns of the CMOS-fabricated sensors.

7. The apparatus of claim 6, wherein the two-dimensional array includes at least 2048 rows and at least 2048 columns of the CMOS-fabricated sensors.

8. The apparatus of claim 6, wherein the two-dimensional array includes at least 7400 rows and at least 7400 columns of the CMOS-fabricated sensors.

9. The apparatus of any of claims 5 to 8, wherein a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the apparatus further comprises control circuitry (110, 192, 194, 198) coupled to the array and configured to generate at least one array output signal (Vout) to provide multiple frames of data from the array at a frame rate of at least 10 frames per second.

10. The apparatus of claim 9, wherein the control circuitry is configured such that the frame rate is at least 20 frames per second.

11. The apparatus of claim 10, wherein the control circuitry is configured such that the frame rate is at least 30 frames per second.

12. The apparatus of claim 11, wherein the control circuitry is configured such that the frame rate is at least 40 frames per second.

13. The apparatus of any of claims 1 to 12, wherein the chemFET of each sensor comprises:

a floating gate structure (170); and

a source (156) and a drain (158) having a first semiconductor type and fabricated in a region (154) having a second semiconductor type, wherein there is no electrical conductor that electrically connects the region having the second semiconductor type to either the source or the drain.

14. The apparatus of claim 13, further comprising at least one first electrical conductor to electrically connect together all regions having the second semiconductor type of all chemFETs in the array.

15. The apparatus of any of claims 1 to 14, wherein each sensor comprises:

a plurality of field effect transistors (FETs), including the chemFET; and

a plurality of second electrical conductors electrically connected to the plurality of FETs,

wherein the plurality of FETs are arranged such that the plurality of second electrical conductors includes no more than four conductors traversing an area occupied by each sensor and interconnecting multiple sensors of the array.

16. The apparatus of any of claims 1 to 15, wherein each sensor comprises three or fewer field effect transistors (FETs), including the chemFET.

17. The apparatus of any of claim 15 or 16, wherein all of the FETs in each sensor are of a same channel type and implemented in the region having the second semiconductor type.

18. The apparatus of any of claims 1 to 17, wherein the chemFET of each sensor is an ion-sensitive field effect transistor (ISFET).

19. The apparatus of any of claims 1 to 17, wherein:

at least one first sensor of the array includes a first chemFET configured to be chemically sensitive to at least one first analyte; and

at least one second sensor of the array includes a second chemFET configured to be chemically sensitive to at least one second analyte different from the at least one first analyte.

20. The apparatus of claim 19, wherein the at least one first analyte represents at least one first binding event associated with a nucleic acid sequencing process, and wherein the at least one second analyte represents at least one second binding event associated with the nucleic acid sequencing process.

21. A sensor array (100), comprising:

a two-dimensional array of electronic sensors (105) including at least 512 rows and at least 512 columns of the electronic sensors, each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) configured to provide at least one output signal representing a presence and/or concentration of an analyte proximate to a surface of the two-dimensional array.

22. The array of claim 21, wherein the array is fabricated on a semiconductor die having dimensions of approximately seven millimeters by seven millimeters.

23. The array of claim 21, wherein the array includes at least 2048 rows and at least 2048 columns of the electronic sensors.

24. The array of claim 23, wherein the array is fabricated on a semiconductor die having dimensions of approximately twenty millimeters by twenty millimeters.

25. The array of claim 21, wherein the array includes at least 7400 rows and at least 7400 columns of the electronic sensors.

26. The array of claim 25, wherein the array is fabricated on a semiconductor die having dimensions of approximately twenty millimeters by twenty millimeters.

27. The array of any of claims 21 to 26, wherein the array is configured as an application specific integrated circuit (ASIC), and wherein for each column of the plurality of columns, the ASIC comprises:

column circuitry (110) configured to provide a constant drain current and a constant drain-to-source voltage to respective chemFETs in the column.

28. The array of claim 27, wherein the column circuitry includes two operational amplifiers (107A,B) and a diode-connected FET arranged in a Kelvin bridge configuration with the respective chemFETs to provide the constant drain-to-source voltage.

29. The array of claim 27 or 28, wherein the ASIC further comprises:

at least one row select shift register (192) to enable respective rows of the plurality of rows; and

at least one column select shift register (194) to acquire chemFET output signals from respective columns of the plurality of columns.

30. The array of claim 29, wherein the at least one column select shift register includes a plurality of column select shift registers (194₁, 194₂) to simultaneously acquire chemFET output signals from multiple columns of the plurality of columns.

31. The array of claim 29 or 30, wherein the at least one row select shift register includes a plurality of row select shift registers to simultaneously enable multiple rows of the plurality of rows.

32. The array of any of claims 27 to 31, wherein the ASIC further comprises at least one output driver (198), the at least one output driver comprising:

at least one buffer amplifier (199); and

at least one switch (191) to couple at least some columns of the plurality of columns to the at least one buffer amplifier so as to provide at least one array output signal (Vout) based on multiple chemFET output signals.

33. The array of claim 32, wherein a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the at least one row select shift register, the at least one column select shift register, and/or the at least one output driver is/are configured to generate the at least one array output signal so as to provide multiple frames of data from the array at a frame rate of at least 10 frames per second.

34. The array of claim 33, wherein the frame rate is at least 20 frames per second.

35. The array of claim 34, wherein the frame rate is at least 30 frames per second.

36. The array of claim 35, wherein the frame rate is at least 40 frames per second.

37. The apparatus of any of claims 32 to 36, wherein the at least one switch includes at least one asymmetric switch comprising a CMOS-pair transmission gate having differently-sized FETs.

38. The array of any of claims 21 to 37, wherein the chemFET of each sensor is an ion-sensitive field effect transistor (ISFET).

39. The array of any of claims 21 to 37, wherein:

at least one first sensor of the array includes a first chemFET configured to be chemically sensitive to at least one first analyte; and

at least one second sensor of the array includes a second chemFET configured to be chemically sensitive to at least one second analyte different from the at least one first analyte.

40. The array of claim 39, wherein the at least one first analyte represents at least one first binding event associated with a nucleic acid sequencing process, and wherein the at least one second analyte represents at least one second binding event associated with the nucleic acid sequencing process.

41. An apparatus, comprising:

an array (100) of CMOS-fabricated sensors (105), each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150),

wherein the array of CMOS-fabricated sensors includes more than 256 sensors, wherein a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the apparatus further comprises;

control circuitry (110, 192, 194, 198) coupled to the array and configured to generate at least one array output signal (Vout) to provide multiple frames of data from the array at a frame rate of at least 1 frame per second.

42. The apparatus of claim 41, wherein the control circuitry is configured such that the frame rate is at least 10 frames per second.

43. The apparatus of claim 42, wherein the control circuitry is configured such that the frame rate is at least 20 frames per second.

44. The apparatus of claim 43, wherein the control circuitry is configured such that the frame rate is at least 30 frames per second.

45. The apparatus of claim 44, wherein the control circuitry is configured such that the frame rate is at least 40 frames per second.

46. The apparatus of claim 45, wherein the control circuitry is configured such that the frame rate is at least 50 frames per second.

47. The apparatus of claim 46, wherein the control circuitry is configured such that the frame rate is at least 100 frames per second.

48. The apparatus of any of claims 41 to 47, wherein the array includes a two-dimensional array of at least 512 rows and at least 512 columns of the CMOS-fabricated sensors.

49. The apparatus of claim 48, wherein the two-dimensional array includes at least 2048 rows and at least 2048 columns of the CMOS-fabricated sensors.

50. The apparatus of claim 49, wherein the two-dimensional array includes at least 7400 rows and at least 7400 columns of the CMOS-fabricated sensors.

51. An apparatus, comprising:

an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150), the chemFET comprising;

a floating gate structure (170); and

a source (156) and a drain (158) having a first semiconductor type and fabricated in a region (154) having a second semiconductor type, wherein there is no electrical conductor that electrically connects the region having the second semiconductor type to either the source or the drain.

52. The apparatus of claim 51, further comprising at least one first electrical conductor to electrically connect together all regions having the second semiconductor type of all chemFETs in the array.

53. The apparatus of claim 51 or 52, wherein the chemFET is a p-channel chemFET, and wherein the region having the second semiconductor type is formed as an n-type well in a p-type substrate (152) for the array.

54. The apparatus of any of claims 51 to 53, wherein each sensor comprises:

a plurality of field effect transistors (FETs), including the chemFET; and

a plurality of second electrical conductors electrically connected to the plurality of FETs,

wherein the plurality of FETs are arranged such that the plurality of second electrical conductors includes no more than four conductors traversing an area occupied by each sensor and interconnecting multiple sensors of the array.

55. The apparatus of any of claims 51 to 54, wherein each sensor comprises three or fewer field effect transistors (FETs), including the chemFET.

56. The apparatus of claim 55, wherein each sensor consists of three FETs, including the chemFET.

57. The apparatus of any of claims 54 to 56, wherein all of the FETs in each sensor are of a same channel type and implemented in the region having the second semiconductor type.

58. The apparatus of claim 57, wherein all of the FETs in each sensor are p-channel FETs, and wherein the region having the second semiconductor type is formed as an n-type well (154) in a p-type substrate (152) for the array.

59. The apparatus of any of claims 51 to 58, wherein each sensor occupies an area on a surface of the array of ten micrometers by ten micrometers or less.

60. The apparatus of claim 59, wherein the area occupied by each sensor is approximately five micrometers by five micrometers or less.

61. The apparatus of claim 60, wherein the area occupied by each sensor is approximately three micrometers by three micrometers or less.

62. The apparatus of any of claims 51 to 61, wherein the array includes a two-dimensional array of the CMOS-fabricated sensors arranged in a plurality of rows and a plurality of columns.

63. The apparatus of claim 62, wherein the array includes at least 512 rows and at least 512 columns of the CMOS-fabricated sensors.

64. The apparatus of claim 62 or 63, wherein for each column of the plurality of columns, the array further comprises:

column circuitry (110) configured to provide a constant drain current and a constant drain-to-source voltage to respective chemFETs in the column.

65. The apparatus of claim 64, wherein the column circuitry includes two operational amplifiers (107A,B) and a diode-connected FET arranged in a Kelvin bridge configuration with the respective chemFETs to provide the constant drain-to-source voltage.

66. The apparatus of any of claims 62 to 65, wherein the array further comprises:

at least one row select shift register (192) to enable respective rows of the plurality of rows; and

at least one column select shift register (194) to acquire chemFET output signals from respective columns of the plurality of columns.

67. The apparatus of claim 66, wherein the at least one column select shift register includes a plurality of column select shift registers (194₁, 194₂) to simultaneously acquire chemFET output signals from multiple columns of the plurality of columns.

68. The array of claim 66 or 67, wherein the at least one row select shift register includes a plurality of row select shift registers to simultaneously enable multiple rows of the plurality of rows.

69. The apparatus of any of claims 62 to 68, further comprising at least one output driver (198), the at least one output driver comprising:

at least one buffer amplifier (199); and

at least one asymmetric switch (191) to couple at least some columns of the plurality of columns to the at least one buffer amplifier so as to provide at least one array output signal (Vout),

wherein the at least one asymmetric switch comprises a CMOS-pair transmission gate having differently-sized FETs.

70. The apparatus of claim 69, wherein a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the at least one row select shift register, the at least one column select shift register, and/or the at least one output driver is/are configured to generate the at least one array output signal so as to provide multiple frames of data from the array at a frame rate of at least 20 frames per second.

71. The apparatus of any of claims 51 to 70, wherein the chemFET of each sensor is an ion-sensitive field effect transistor (ISFET).

72. The apparatus of any of claims 51 to 70, wherein:

at least one first sensor of the array includes a first chemFET configured to be chemically sensitive to at least one first analyte; and

at least one second sensor of the array includes a second chemFET configured to be chemically sensitive to at least one second analyte different from the at least one first analyte.

73. The apparatus of claim 72, wherein the at least one first analyte represents at least one first binding event associated with a nucleic acid sequencing process, and wherein the at least one second analyte represents at least one second binding event associated with the nucleic acid sequencing process.

74. An apparatus, comprising:

an array (100) of electronic sensors (105), each sensor consisting of three field effect transistors (FETs) including one chemically-sensitive field effect transistor (chemFET) (150).

75. The apparatus of claim 74, wherein the chemFET comprises:

a floating gate structure (170); and

a source (156) and a drain (158) having a first semiconductor type and fabricated in a region (154) having a second semiconductor type, wherein there is no electrical conductor that electrically connects the region having the second semiconductor type to either the source or the drain.

76. An apparatus, comprising:

an array (100) of electronic sensors (105), each sensor comprising three or fewer field effect transistors (FETs), wherein the three or fewer FETs includes one chemically-sensitive field effect transistor (chemFET) (150).

77. An apparatus, comprising:

an array (100) of electronic sensors (105), each sensor comprising;

a plurality of field effect transistors (FETs) including one chemically-sensitive field effect transistor (chemFET) (150); and

a plurality of electrical conductors electrically connected to the plurality of FETs,

wherein the plurality of FETs are arranged such that the plurality of electrical conductors includes no more than four conductors traversing an area occupied by each sensor and interconnecting multiple sensors of the array.

78. An apparatus, comprising:

an array (100) of CMOS-fabricated sensors (105), each sensor comprising a plurality of field effect transistors (FETs) including one chemically-sensitive field effect transistor (chemFET) (150), wherein all of the FETs in each sensor are of a same channel type and implemented in a single semiconductor region of an array substrate.

79. The apparatus of claim 78, wherein all of the FETs in each sensor are p-channel FETs, wherein the array substrate is a p-type substrate (152), and wherein the single semiconductor region is formed as an n-type well (154) in the p-type substrate.

80. A sensor array (100), comprising:

a plurality of electronic sensors (105) arranged in a plurality of rows and a plurality of columns, each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) configured to provide at least one output signal representing a presence and/or a concentration of an analyte proximate to a surface of the array,

wherein for each column of the plurality of columns, the array further comprises;

column circuitry (110) configured to provide a constant drain current and a constant drain-to-source voltage to respective chemFETs in the column, the column circuitry including two operational amplifiers and a diode-connected FET arranged in a Kelvin bridge configuration with the respective chemFETs to provide the constant drain-to-source voltage.

81. A sensor array (100), comprising:

a plurality of electronic sensors (105) arranged in a plurality of rows and a plurality of columns, each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) configured to provide at least one output signal representing a concentration of ions in an analyte proximate to a surface of the array;

at least one row select shift register (192) to enable respective rows of the plurality of rows; and

at least one column select shift register (194) to acquire chemFET output signals from respective columns of the plurality of columns.

82. The array of claim 81, wherein the at least one column select shift register includes a plurality of column select shift registers to simultaneously acquire chemFET output signals from multiple columns of the plurality of columns.

83. The array of claim 81 or 82, wherein the at least one row select shift register includes a plurality of row select shift registers to simultaneously enable multiple rows of the plurality of rows.

84. The array of any of claims 81 to 83, further comprising at least one output driver (198), the at least one output driver comprising:

at least one buffer amplifier (199); and

at least one asymmetric switch (191) to couple at least some columns of the plurality of columns to the at least one buffer amplifier so as to provide at least one array output signal (Vout),

wherein the at least one asymmetric switch comprises a CMOS-pair transmission gate having differently-sized FETs.

85. The array of claim 84, wherein a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the at least one row select shift register, the at least one column select shift register, and/or the at least one output driver is/are configured to generate the at least one array output signal so as to provide multiple frames of data from the array at a frame rate of at least 20 frames per second.

86. An apparatus, comprising:

an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150), the chemFET comprising;

a floating gate structure (170); and

a source (156) and a drain (158) having a first semiconductor type and fabricated in a region (154) having a second semiconductor type, wherein there is no electrical conductor that electrically connects the region having the second semiconductor type to either the source or the drain,

wherein;

the array includes a two-dimensional array of at least 512 rows and at least 512 columns of the CMOS-fabricated sensors;

each sensor consists of three field effect transistors (FETs) including the chemFET;

each sensor includes a plurality of electrical conductors electrically connected to the three FETs;

the three FETs are arranged such that the plurality of electrical conductors includes no more than four conductors traversing an area occupied by each sensor and interconnecting multiple sensors of the array;

all of the FETs in each sensor are of a same channel type and implemented in a single semiconductor region of an array substrate; and

a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data,

and wherein the apparatus further comprises;

control circuitry (110, 192, 194, 198) coupled to the array and configured to generate at least one array output signal (Vout) to provide multiple frames of data from the array at a frame rate of at least 20 frames per second.

87. A method for processing an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150), the method comprising:

A) dicing a semiconductor wafer including the array to form at least one diced portion including the array; and

B) performing a forming gas anneal on the at least one diced portion.

88. The method of claim 87, wherein B) comprises:

C) heating the at least one diced portion in a hydrogen and nitrogen gas mixture.

89. The method of claim 88, wherein the gas mixture includes approximately 10 percent to 15 percent hydrogen.

90. The method of claim 88 or 89, wherein C) further comprises:

D) heating the at least one diced portion for approximately 30 to 60 minutes.

91. The method of any of claims 88 to 90, wherein C) further comprises:

heating the at least one diced portion at a temperature in a range of from approximately 400 degrees Celsius to approximately 425 degrees Celsius.

92. The method of claim 88, wherein the gas mixture includes 10 percent hydrogen, and wherein C) comprises:

heating the at least one diced portion for approximately 30 minutes at a temperature of approximately 425 degrees Celsius.

93. The method of claim 91 or 92, further comprising:

performing a prior forming gas anneal on the semiconductor wafer prior to A).

94. A method for processing an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150) having a chemically-sensitive passivation layer of silicon nitride and/or silicon oxynitride deposited via plasma enhanced chemical vapor deposition (PECVD), the method comprising:

A) depositing at least one additional passivation material on the chemically-sensitive passivation layer so as to reduce a porosity and/or increase a density of the passivation layer.

95. The method of claim 94, wherein the at least one additional passivation material is selected from the group consisting of silicon nitride, silicon oxynitride, aluminum oxide, tantalum oxide, tin oxide and silicon dioxide.

96. The method of claim 94 or 95, wherein A) comprises RF sputtering, DC magnetron sputtering, thermal or e-beam evaporation, or ion-assisted deposition of the at least one additional passivation material.

97. The method of any of claims 94 to 96, wherein A) comprises depositing the at least one additional passivation material to a thickness of approximately 400 to 600 Angstroms.

98. A method for sequencing a nucleic acid comprising

disposing a plurality of template nucleic acids into a plurality of reaction chambers, wherein the plurality of reaction chambers is in contact with a chemical-sensitive field effect transistor (chemFET) array comprising at least one chemFET for each reaction chamber, and wherein each of the template nucleic acids is hybridized to a sequencing primer and is bound to a polymerase,

synthesizing a new nucleic acid strand by incorporating one or more known nucleotide triphosphates sequentially at the 3′

end of the sequencing primer,

detecting the incorporation of the one or more known nucleotide triphosphates by a change in current at the at least one chemFET within the array.

99. The method of claim 98, wherein the chemFET array comprises more than 256 sensors.

105. The fluidics assembly of claim 98 or 99 further including an electrode formed in or on the second member between said first and second ports so as to be in contact with said fluid along a ceiling of said flow chamber.

106. The fluidics assembly of claim 98 or 99 further including a reference electrode comprising a conductive capillary tube mounted into the second port to be in contact with fluid flowing through said port.

100. A method for sequencing a nucleic acid comprising

disposing a plurality of template nucleic acids into a plurality of reaction chambers, wherein the plurality of reaction chambers is in contact with an chemical-sensitive field effect transistor (chemFET) array comprising at least one chemFET for each reaction chamber, and wherein each of the template nucleic acids is hybridized to a sequencing primer and is bound to a polymerase,

synthesizing a new nucleic acid strand by incorporating one or more known nucleotide triphosphates sequentially at the 3′

end of the sequencing primer,

detecting the incorporation of the one or more known nucleotide triphosphates by the generation of sequencing reaction byproduct,

wherein a center-to-center distance between adjacent reaction chambers is 1-10 μ

m.

101. A method for sequencing a nucleic acid comprising

disposing a plurality of template nucleic acids into a plurality of reaction chambers, wherein the plurality of reaction chambers is in contact with an chemical-sensitive field effect transistor (chemFET) array comprising at least one chemFET for each reaction chamber, and wherein each of the template nucleic acids is hybridized to a sequencing primer and is bound to a polymerase,

synthesizing a new nucleic acid strand by incorporating one or more known nucleotide triphosphates sequentially at the 3′

end of the sequencing primer,

directly detecting release of inorganic pyrophosphate (PPi) as an indicator of incorporation of the one or more known nucleotide triphosphates.

102. An apparatus comprising

a chemical-sensitive field effect transistor (chemFET) having disposed on its surface a PPi receptor.

103. A fluidics assembly for use with an array of sensors on an active semiconductor device capped with a protective layer, comprising:

a first member having therein an aperture for mating to the sensor array; and

a second member fixed to the first member in a fluid-tight seal therebetween, and having first and second fluid ports for supporting fluid passage, the first and second members and the sensor array defining a fluid chamber,

whereby fluid introduced into one of said ports flows over the array before exiting via the other of said ports.

104. A fluidics assembly for use with an array of sensors on an active semiconductor device capped with a protective layer, comprising:

a microwell array configured and arranged to provide fluid access to said protective layer;

a first member having therein an aperture for mating to the sensor array around the microwell array; and

a second member fixed to the first member in a fluid-tight seal therebetween, and having first and second fluid ports for supporting fluid passage, the first and second members and the microwell array defining a fluid chamber over the protective layer of the semiconductor device when mated to the sensor array,

whereby fluid introduced into one of said ports flows over the microwell array before exiting via the other of said ports and the active semiconductor device senses chemical activity in at least some of the microwells in the microwell array.