Portable genetic detection and analysis system and method

• US 10,428,367 B2
• Filed: 07/13/2016
• Issued: 10/01/2019
• Est. Priority Date: 04/11/2012
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kain, Robert C., Shen, Min-Jui Richard, Moon, John A., Eltoukhy, Helmy A.
• Primary Examiner(s): Merkling, Sally A
• Application Number:
  US15/209,351
• Publication Number:
  US 20160319327A1
• Time in Patent Office: Days
• CPC Class Codes: B01L 2200/10 Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
• CPC Class Codes: B01L 2300/023 Sending and receiving of information, e.g. using bluetooth
• CPC Class Codes: B01L 2300/024 Storing results with means integrated into the container
• CPC Class Codes: B01L 2300/027 Digital display, e.g. LCD, LED
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• 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 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 2035/00881 network configurations
• CPC Class Codes: G01N 33/48721 Investigating individual macromolecules, e.g. by translocation through nanopores Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68
• CPC Class Codes: G01N 33/4875 Details of handling test elements, e.g. dispensing or storage, not specific to a particular test method test-elements per se B01L, automatic analysers G01N35/00, in-vivo analysis on the human body for medical diagnosis A61B
• CPC Class Codes: G01N 33/48792 Data management, e.g. communication with processing unit for in vivo diagnostics A61B5/0002; transmission systems for measured values G08C

Abstract

A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed.

Claims

1. A portable genetic detector system comprising:

a plurality of portable detectors, wherein each portable detector comprises;

a housing;

an interface disposed on or in the housing and configured to receive input from an operator to control operation of the portable detector;

a sample receiving component disposed on or in the housing and configured to receive a biological sample wherein the biological samples are different from one another;

a reader disposed on or in the housing and configured to detect nucleic acids of interest in the biological sample to generate sample data;

a control system disposed on or in the housing and programmed to control the operation of the portable detector;

a locator configured to generate location information of the portable detector;

a transceiver disposed on or in the housing and configured to output the sample data generated by the reading component, wherein the sample data comprises data identifying nucleotides present in the biological sample; and

a display disposed on or in the housing and configured to display information related to the operation of the portable detector; and

a remote processing system in communication with each of the plurality of portable detectors and separate from the plurality of portable detectors, wherein the remote processing system comprises;

communications circuitry configured to receive the sample data and the location information from each of the plurality of portable detectors; and

a processor programmed to assemble a nucleic acid sequence of at least one biological sample based on the sample data;

determine a sequence coverage for one or more regions of a genome based on sequence; and

provide instructions to stop operation of the control system of each of the plurality of portable detectors when the sequence coverage has achieved a threshold and to provide new instructions to a subset of the plurality of portable detectors to analyze respective new biological samples, wherein the subset is selected based on the location information.

2. The portable genetic detector system of claim 1, wherein the instructions comprise instructions to stop operation of the reader for at least one of the portable detectors when the sequence represents the predetermined sequence coverage.

3. The portable genetic detector system of claim 2, wherein the instructions to stop operation of the reader for at least one of the portable detectors are provided before the reader has completed a sequencing run.

4. The portable genetic detector system of claim 2, wherein the instructions to stop operation of the reader for at least one of the portable detectors are provided before the at least one of the portable detectors has consumed available sequencing reagents.

5. The portable genetic detector system of claim 1, wherein the threshold is 10×

sequence coverage for the one or more regions of the genome.

6. The portable genetic detector system of claim 1, wherein the processor is programmed to provide instructions to the control system of each of the plurality of portable detectors when the sequence coverage has achieved a threshold and when the sample data is associated with a predetermined data quality score.