Apparatus for amplification of nucleic acids

Abstract

Described herein is a chip-based apparatus for amplifying nucleic acids, a cartridge housing the apparatus, and methods of using the apparatus for amplification of nucleic acids. More specifically, this invention provides integrated semiconductor chip, manufactured with standard semiconductor manufacturing process, with on-chip circuitry to perform thermal management and optical sensing necessary for amplification of nucleic acids. The apparatus and methods embodied in this invention makes it possible to build a disease diagnosis and prognosis tool that is easy to use, portable and disposable.

What is claimed is: 
     
         1 - 58 . (canceled) 
     
     
         59 . A cartridge apparatus for analyzing a biological sample, the cartridge apparatus comprising:
 (a) a first chamber,
 wherein the first chamber comprises a plurality of surfaces, and 
 wherein the plurality of surfaces of the first chamber comprise a first surface, said first surface comprising a first portion of a semiconductor chip; and 
   (b) the semiconductor chip comprising:
 (i) a semiconductor substrate comprising an integrated circuitry,
 wherein the integrated circuitry on the semiconductor substrate comprises:
 a temperature sensor; and 
 a first light sensor; and 
 
 
 (ii) a biocompatible coating over the semiconductor substrate,
 wherein the biocompatible coating is positioned to allow the biological sample to be in proximity to the integrated circuitry. 
 
   
     
     
         60 . The cartridge apparatus of  claim 59 , wherein the location of the first chamber is configured for analyzing the biological sample using the first light sensor. 
     
     
         61 . The cartridge apparatus of  claim 59 , wherein at least one of the plurality of surfaces of the first chamber is sufficiently transparent to allow excitation light into the first chamber. 
     
     
         62 . The cartridge apparatus of  claim 59 , wherein the first chamber has a sample capacity, as measured by the amount of the biological sample, of between 0.1 μL and 200 μL. 
     
     
         63 . The cartridge apparatus of  claim 59 , wherein the first chamber further comprises one or more chamber openings. 
     
     
         64 . The cartridge apparatus of  claim 63 , wherein the one or more chamber openings comprises:
 a first chamber opening,
 wherein the first chamber opening is a sample loading opening, 
 wherein the first chamber opening is configured for introduction of the biological sample to the first chamber; and 
   a second chamber opening,
 wherein the second chamber opening is a vent. 
   
     
     
         65 . The cartridge apparatus of  claim 64 , further comprising:
 a first seal,
 wherein the first seal is configured to seal the first chamber opening; and 
   a second seal,
 wherein the second seal is configured to seal the second chamber opening. 
   
     
     
         66 . The cartridge apparatus of  claim 59 , wherein the biocompatible coating is deposited on the semiconductor substrate. 
     
     
         67 . The cartridge apparatus of  claim 66 , wherein the biocompatible coating is hydrophilic. 
     
     
         68 . The cartridge apparatus of  claim 66 , wherein the biocompatible coating is a light wavelength filter. 
     
     
         69 . The cartridge apparatus of  claim 68 , wherein the biocompatible coating comprises a member selected from the group consisting of zinc sulfide, Cryolite, glass, quartz, and a transparent polymer. 
     
     
         70 . The cartridge apparatus of  claim 69 , wherein the biocompatible coating is a laminate placed over the semiconductor substrate. 
     
     
         71 . The cartridge apparatus of  claim 59 , wherein the biological coating of the first portion of the semiconductor chip further comprises a plurality of molecular probes, and wherein the plurality of molecular probes is attached to the surface of biocompatible coating. 
     
     
         72 . The cartridge apparatus of  claim 71 , wherein the location of the plurality of molecular probes is configured for analyzing the biological sample using the first light sensor. 
     
     
         73 . The cartridge apparatus of  claim 71 , wherein the plurality of molecular probes comprises a nucleic acid amplification reagent. 
     
     
         74 . The cartridge apparatus of  claim 59 , wherein the biological coating of the first portion of the semiconductor chip further comprises a nucleic acid amplification reagent deposited thereon, wherein the nucleic acid amplification reagent is one or more magnetic beads, and wherein the one or more magnetic beads comprises one or more nucleic acid probes covalently attached thereon. 
     
     
         75 . The cartridge of  claim 59 , wherein the integrated circuitry is configured to be in communication, via a communication interface, with:
 (i) one or more processors; and   (ii) memory storing one or more programs, the one or more programs configured to be executed by the one or more processors, the one or more programs including instructions for:
 detecting a first light input measurement from the first light sensor at a first time prior to triggering a light signal from the biological sample; 
 detecting a second light input measurement from the first light sensor at a second time after triggering the light signal from the biological sample; 
 detecting a plurality of temperature input measurements from the temperature sensor,
 wherein the plurality of temperature input measurements comprises:
 a first temperature input measurement detected at the first time; and 
 a second temperature input measurement detected at the second time; 
 
 
 using the first light measurement to estimate noise signal; and 
 using the plurality of temperature input measurements to further estimate noise signal and improve noise suppression, thereby determining the light signal from the biological sample. 
   
     
     
         76 . The cartridge apparatus of  claim 75 , wherein the integrated circuitry on the semiconductor substrate further comprises a first portion of the communication interface, and wherein a second portion of the communication interface is coupled to the one or more processors. 
     
     
         77 . The cartridge apparatus of  claim 76 , wherein the communication interface is a digital communication interface or a serial communication interface. 
     
     
         78 . The cartridge apparatus of  claim 59 , wherein the temperature sensor is a junction temperature sensor. 
     
     
         79 . The cartridge apparatus of  claim 75 , wherein the integrated circuitry on the semiconductor substrate further comprises a heating element. 
     
     
         80 . The cartridge apparatus of  claim 79 , wherein the heating element is a transistor or a resistor. 
     
     
         81 . The cartridge apparatus of  claim 79 , wherein the one or more programs further includes instructions for:
 heating the semiconductor substrate; or   cooling the semiconductor substrate.   
     
     
         82 . The cartridge apparatus of  claim 81 , the instructions for heating the semiconductor substrate comprise:
 detecting a first temperature control input measurements from the temperature sensor;   controlling the heating element, thereby obtaining a pre-determined temperature set point of the semiconductor substrate.   
     
     
         83 . The cartridge apparatus of  claim 75 , wherein the one or more programs further includes instructions for:
 detecting a temperature input measurement from the temperature sensor;   comparing the temperature input measurement to an actual temperature measurement; and   calibrating the temperature input measurement.   
     
     
         84 . The cartridge apparatus of  claim 83 , wherein calibrating the temperature input measurement comprises applying a correction factor between the actual temperature measurement and the temperature input measurement. 
     
     
         85 . The cartridge apparatus of  claim 75 , wherein the one or more programs further includes instructions for:
 applying a first excitation light from a first light source to trigger the light signal from the biological sample.   
     
     
         86 . The cartridge apparatus of  claim 85 , wherein the first light source is positioned to illuminate the biological sample. 
     
     
         87 . The cartridge apparatus of  claim 86 , wherein the first light source is a laser or LED. 
     
     
         88 . The cartridge apparatus of  claim 59 , wherein the integrated circuitry comprises complementary metal-oxide-semiconductor circuitry. 
     
     
         89 . The cartridge apparatus of  claim 59 , further comprising a second chamber, said second chamber comprising a plurality of surfaces,
 wherein a first surface of the plurality of surfaces of the second chamber comprises a second portion of the semiconductor chip, and   wherein the integrated circuitry of the semiconductor substrate further comprises a second light sensor, and.   
     
     
         90 . The cartridge apparatus of  claim 89 , wherein the location of the second chamber is configured for analyzing the biological sample using the second light sensor. 
     
     
         91 . The cartridge apparatus of  claim 89 , wherein at least one of the plurality of surfaces of the second chamber is optically transmissive. 
     
     
         92 . The cartridge apparatus of  claim 89 , wherein the second chamber has a sample capacity, as measured by the amount of the biological sample, of between 0.1 μL and 200 μL. 
     
     
         93 . The cartridge apparatus of  claim 89 , wherein the second chamber further comprises one or more chamber openings. 
     
     
         94 . The cartridge apparatus of  claim 89 , wherein the biological coating of the second portion of the semiconductor chip further comprises a second plurality of molecular probes, and wherein the second plurality of molecular probes are attached to the surface of biocompatible coating. 
     
     
         95 . The cartridge apparatus of  claim 94 , wherein the second plurality of molecular probes of the second portion of the semiconductor chip are the same as other molecular probes on the semiconductor chip. 
     
     
         96 . The cartridge apparatus of  claim 94 , wherein the second plurality of molecular probes of the second portion of the semiconductor chip are different from other molecular probes on the semiconductor chip. 
     
     
         97 . The cartridge apparatus of  claim 94 , wherein the location of the second plurality of molecular probes of the second portion of the semiconductor chip is configured for analyzing the biological sample using the second light sensor. 
     
     
         98 . The cartridge apparatus of  claim 89 , wherein the first chamber and the second chamber are not in fluidic communication. 
     
     
         99 . A system for analyzing a biological sample comprising:
 (a) a semiconductor substrate comprising an integrated circuitry,
 wherein the integrated circuitry on the semiconductor substrate comprises:
 a temperature sensor; 
 a first light sensor; and 
 a communication interface, and 
 
 wherein the integrated circuitry is configured to be in communication, via the communication interface, with:
 (i) one or more processors; 
 (ii) memory storing one or more programs, the one or more programs configured to be executed by the one or more processors, the one or more programs including instructions for:
 detecting a first light input measurement from the first light sensor at a first time prior to triggering a light signal from the biological sample; 
 detecting a second light input measurement from the first light sensor at a second time after triggering the light signal from the biological sample; 
 detecting a plurality of temperature input measurements from the temperature sensor, 
  wherein the plurality of temperature input measurements comprises: 
   a first temperature input measurement detected at the first time; and 
   a second temperature input measurement detected at the second time; 
 using the first light measurement to estimate noise signal; and 
 using the plurality of temperature input measurements to further estimate noise signal and improve noise suppression, thereby determining the light signal from the biological sample; and 
 
 
   (b) a biocompatible coating over the semiconductor substrate,
 wherein the biocompatible coating is positioned to allow the biological sample to be in proximity to the integrated circuitry. 
   
     
     
         100 . A method of determining the light signal from a biological sample, the method comprising:
 (a) depositing the biological sample on the biocompatible coating of the cartridge apparatus of  claim 59 ;   (b) forming a reaction mixture on the biocompatible coating, wherein the reaction mixture comprises the biological sample and a reagent;   (c) detecting a first light input measurement from the first light sensor at a first time prior to triggering a light signal from the biological sample;   (d) detecting a second light input measurement from the first light sensor at a second time after triggering the light signal from the biological sample;   (e) detecting a plurality of temperature input measurements from the temperature sensor, wherein the plurality of temperature input measurements comprises:
 a first temperature input measurement detected at the first time; and 
 a second temperature input measurement detected at the second time; 
   (f) using the first light measurement to estimate noise signal; and   (g) using the plurality of temperature input measurements to further estimate noise signal and improve noise suppression, thereby determining the light signal from the biological sample.