Integrated Analysis System

Patent metadata

Field	Value
Publication number	US-2016016140-A1
Application number	US-201514804675-A
Country	US
Kind code	A1
Filing date	Jul 21, 2015
Priority date	Aug 20, 2010
Publication date	Jan 21, 2016
Grant date	—

Abstract

The invention provides systems, devices, methods, and kits for performing an integrated analysis. The integrated analysis can include sample processing, library construction, amplification, and sequencing. The integrated analysis can be performed within one or more modules that are fluidically connected to each other. The one or more modules can be controlled and/or automated by a computer. The integrated analysis can be performed on a tissue sample, a clinical sample, or an environmental sample. The integrated analysis system can have a compact format and return results within a designated period of time.

First claim

1 . A device comprising:
(a) a valve array comprising a series of valves connected through fluidic connections, the array comprising, in order, a first terminal valve, at least three intermediate valves and a second terminal valve; (b) at least one first port, each fluidically connected through a separate control valve to the first terminal valve; and (c) at least one second port, each fluidically connected through a separate control valve to the second terminal valve.

2 . The device of claim 1 wherein the fluidic connections are unbranched.

3 . The device of claim 1 wherein the at least one first port is a plurality of first ports fluidically connected to the first terminal valve through a common rail.

4 . (canceled)

5 . The device of claim 3 wherein the at least one second port is a plurality of second ports fluidically connected to the second terminal valve through a common rail.

6 - 32 . (canceled)

33 . A microfluidic apparatus comprising:
at least one microfluidic channel, said channel comprising N chambers in series, where N is at least two; and at least N+1 reservoirs fluidically connected to said channel, wherein said reservoirs comprise at least two reagents; wherein said chambers and said reservoirs are arranged to allow sequential addition and mixing of reagents from each of said reservoirs.

34 .- 35 . (canceled)

36 . The microfluidic apparatus of claim 33 , wherein said channel is unbranched.

37 . The microfluidic apparatus of claim 33 , wherein said channel comprises a first end and a second end, further comprising
at least a second and third channel, wherein said second channel is fluidically connected to said first end and said third channel is fluidically connected to said second end.

38 .- 41 . (canceled)

42 . The microfluidic apparatus of claim 33 , wherein each of said chambers comprises a valve.

43 .- 102 . (canceled)

103 . A method comprising:
providing a reaction mixture comprising a nucleic acid substrate and a labeled enzyme in free solution, wherein said labeled enzyme comprises an affinity tag; performing an enzymatic reaction in free solution using said labeled enzyme acrd said nucleic acid substrate to produce a product nucleic acid in said reaction mixture; providing a solid substrate comprising a binding moiety for said affinity tag; binding said labeled enzyme to said solid substrate; and separating said reaction mixture from said bound labeled enzyme to generate a product mixture substantially depleted of the labeled enzyme.

104 . (canceled)

105 . The method of claim 103 , wherein said solid substrate comprises a particle.

106 .- 107 . (canceled)

108 . The method of claim 103 , further comprising performing the following steps at least once: performing an additional reaction on said product nucleic acid without separating said product nucleic acid from said product mixture, wherein said additional reaction is optionally performed in free solution with an additional labeled enzyme;
and optionally separating said product mixture from said additional labeled enzyme.

109 . The method of claim 103 , wherein said nucleic acid substrate is a nucleic acid polymer, said labeled enzyme is a first labeled polymerase, wherein said reaction mixture further comprises free nucleotides and other reagents necessary for nucleic acid polymerization, and wherein said enzymatic reaction is synthesizing a first DNA strand complementary to the nucleic acid polymer;
further comprising performing one or more of the following steps: i) providing a second labeled polymerase to the product mixture, wherein said second labeled polymerizing enzyme comprises a second affinity tag, ii) synthesizing a second DNA strand complementary to said first DNA strand to form a product DNA molecule in said product mixture, iii) providing a second solid substrate comprising a binding moiety for said second affinity tag, iv) binding said second labeled polymerase to said second solid substrate, and v) separating the product mixture from the bound second labeled polymerase; vi) providing an additional enzyme and processing said product DNA molecule using said additional enzyme; further providing an adapter nucleic acid and a ligase; ligating the adapter nucleic acid to said product DNA molecule to produce a ligated DNA molecule; and purifying said ligated DNA molecule.

110 .- 113 . (canceled)

114 . An automated system comprising:
a first module configured to receive a sample comprising a target polynucleotide and modify said target polynucleotide; a second module fluidically connected to the first module configured to receive said modified polynucleotide and perform a sequencing reaction on said modified polynucleotide; and computer logic for controlling the first module and the second module.

115 . The system of claim 114 , wherein the first module comprises a microfluidic channel with pneumatically actuated valves leading to a chamber comprising beads.

116 . The system of claim 114 , wherein the first module comprises a sample processing module configured to modify the target polynucleotide by purifying and fragmenting DNA.

117 .- 136 . (canceled)

137 . The system of claim 114 , wherein the system provides sequence information on said target polynucleotide in less than about 22 hours.

138 .- 149 . (canceled)

150 . A method for performing sequencing comprising:
isolating a target polynucleotide from a sample; modifying the target polynucleotide; transferring the modified polynucleotide to a sequencing module; and sequencing the modified polynucleotide in the sequencing module, wherein each step is automated by computer logic and occurs in a fluidically connected environment.

151 . The method of claim 150 , wherein greater than about 250 million, 10 billion, or 100 billion bases are sequenced in less than about 2.5, 4, 5.5, 6.5, 12, or 22 hours.

152 .- 155 . (canceled)

156 . The method of claim 150 , wherein the isolating step comprises binding the polynucleotide in the sample to magnetic beads.

157 .- 164 . (canceled)

165 . The method of claim 150 , wherein the sequencing step comprises a sequencing method selected from the group consisting of Sanger sequencing, sequencing by ligation, reversible dye-terminating sequencing, real-time sequencing, and pyrosequencing.

166 .- 247 . (canceled)

Assignees

• Jovanovich Stevan B
• Stern Seth
• Van Gelder Ezra
• Vangbo Mattias
• Integenx Inc

Inventors

• Jovanovich Stevan B
• Stern Seth
• Van Gelder Ezra
• Vangbo Mattias

Classifications

• B01L2200/0647

  Handling flowable solids, e.g. microscopic beads, cells, particles · CPC title

• B01L2200/10

  Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept · CPC title

• B01L3/502738

  characterised by integrated valves (throttle valves in microfluidic sample containers B01L3/502746) · CPC title

• B01J2219/00716

  Heat activated synthesis · CPC title

• B01L7/52

  with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples · CPC title