U.S. patent application number 13/790623 was filed with the patent office on 2013-10-17 for portable genetic detection and analysis system and method.
This patent application is currently assigned to ILLUMINA, INC.. The applicant listed for this patent is ILLUMINA, INC.. Invention is credited to Helmy A. Eltoukhy, Robert C. Kain, John A. Moon, Min-Jui Richard Shen.
Application Number | 20130274148 13/790623 |
Document ID | / |
Family ID | 49325620 |
Filed Date | 2013-10-17 |
United States Patent
Application |
20130274148 |
Kind Code |
A1 |
Kain; Robert C. ; et
al. |
October 17, 2013 |
PORTABLE GENETIC DETECTION AND ANALYSIS SYSTEM AND METHOD
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.
Inventors: |
Kain; Robert C.; (San Diego,
CA) ; Shen; Min-Jui Richard; (Poway, CA) ;
Moon; John A.; (San Diego, CA) ; Eltoukhy; Helmy
A.; (Woodside, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
ILLUMINA, INC. |
San Diego |
CA |
US |
|
|
Assignee: |
ILLUMINA, INC.
San Diego
CA
|
Family ID: |
49325620 |
Appl. No.: |
13/790623 |
Filed: |
March 8, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61622773 |
Apr 11, 2012 |
|
|
|
Current U.S.
Class: |
506/38 ;
435/287.2; 506/39 |
Current CPC
Class: |
B01L 2300/024 20130101;
B01L 2300/023 20130101; B01L 3/5027 20130101; G01N 33/48721
20130101; C12Q 1/6869 20130101; C12Q 1/6837 20130101; B01L 2200/10
20130101; B01L 2300/0636 20130101; G01N 33/4875 20130101; B01L
3/502715 20130101; G01N 2035/00881 20130101; B01L 2300/027
20130101; C12Q 1/68 20130101; G01N 33/48792 20130101 |
Class at
Publication: |
506/38 ;
435/287.2; 506/39 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A portable genetic detector comprising: a reading component
configured to detect nucleic acids of interest in a biological
sample introduced into the detector; a control system configured to
control operation of the reading component; and a communications
component configured to transmit data produced by the reading
component to a remote computer system for analysis.
2. The detector of claim 1, comprising a sample receiving component
configured to receive and prepare the biological sample on a
support for genetic analysis.
3. The detector of claim 2, wherein the sample receiving component
is controlled by the control system.
4. The detector of claim 1, wherein the detector has a form factor
suitable for hand-held operation.
5. The detector of claim 1, comprising memory circuitry for storing
at least some of the data produced by the reading component.
6. The detector of claim 1, comprising a processing system
configured to perform at least primary analysis of the data
produced by the reading component to create processed data.
7. The detector of claim 6, wherein the primary analysis comprises
eliminating image data not corresponding to locations on the
support having detectable nucleic acids.
8. The detector of claim 6, wherein at least one of the control
system and the processing system is configured to balance costs of
data acquisition, computation, storage and transmission of
data.
9. The detector of claim 6, wherein at least one of the control
system and the processing system is configured to determine a
quality of data acquired and/or processed.
10. The detector of claim 9, wherein at least one of the control
system and the processing system is configured to alter data
acquisition and/or data processing and/or data storage and/or data
transmission based upon the determined quality.
11. The detector of claim 1, wherein the reading component
comprises an optical imaging system.
12. The detector of claim 1, wherein the detector comprises a base
unit, and the sample receiving component comprises a cassette-like
system insertable into the base unit.
13. The detector of claim 1, wherein the detector comprises a base
unit in which the sample receiving component and the reading
component are disposed, and a separate processing unit in which the
processing system and communications component are disposed.
14. The detector of claim 1, comprising a locating component
configured to locate the portable detector as it is displaced to
sample locations.
15. The detector of claim 14, wherein the locating component
comprises a global positioning system locator.
16. The detector of claim 14, wherein the locating component
comprises a cellular network locator.
17. The detector of claim 1, wherein the communications component
is configured to transmit the data wirelessly to the remote
computer system.
18. A portable genetic detector comprising: a reading component
configured to detect nucleic acids of interest in a biological
sample; a control system configured to control operation of the
reading component; and a locating component configured to locate
the portable detector as it is displaced to sample locations.
19. The detector of claim 18, comprising a mapping component
configured to display a map for guidance of locations at which
samples should be taken or locations at which samples are
taken.
20. A portable genetic detector comprising: a reading component
configured to detect nucleic acids of interest in a biological
sample; a control system configured to control operation of the
reading component; and a memory circuit configured to store
signature data for target genetic sequence; wherein the processing
system is configured to compare data derived from the reading
component to the signature data.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] The present application claims priority to U.S. Provisional
Application No. 61/622,773, entitled "PORTABLE GENETIC DETECTION
AND ANALYSIS SYSTEM AND METHOD" and filed Apr. 11, 2012, the
disclosure of which is incorporated herein by reference for all
purposes.
BACKGROUND
[0002] The present disclosure relates generally to a field of
genetic analysis, such as for diagnostic sequencing and other
purposes. More specifically, the disclosure relates to a portable
analysis system that may be carried or transported to desired
locations to facilitate sample collection, sample analysis, and
further processing.
[0003] Genetic sequencing has become an increasingly important area
of genetic research, promising future uses in diagnostic and other
applications. In general, genetic sequencing involves determining
the order of nucleotides for a nucleic acid such as a fragment of
RNA or DNA. Relatively short sequences are typically analyzed, and
the resulting sequence information may be used in various
bioinformatics methods to logically fit fragments together to
reliably determine the sequence of much more extensive lengths of
genetic material from which the fragments were derived. Automated,
computer-based examinations of characteristic fragments have been
developed and have been used more recently in genome mapping,
identification of genes and their function, and so forth. However,
existing techniques are highly time-intensive, and resulting
genomic information is accordingly extremely costly to obtain.
[0004] A number of alternative sequencing techniques are presently
under investigation and development. In such techniques, typically
single nucleotides or strands of nucleotides (oligonucleotides) are
introduced and permitted or encouraged to bind to the template of
genetic material to be sequenced. Sequence information may then be
gathered by imaging the sites. In certain current techniques, for
example, each nucleotide type is tagged with a fluorescent tag or
dye that permits analysis of the nucleotide attached at a
particular site to be determined by analysis of image data.
Although such techniques show promise for significantly improving
throughput and reducing the cost of sequencing, further progress in
speed, reliability, and efficiency of data handling is needed.
[0005] For example, in certain sequencing approaches that use image
data to evaluate individual sites, large volumes of image data may
be produced during sequential cycles of sequencing. In systems
relying upon sequencing by synthesis (SBS), for example, dozens of
cycles may be employed for sequentially attaching nucleotides to
individual sites. Images formed at each step result in a vast
quantity of digital data representative of pixels in
high-resolution images. These images are analyzed to determine what
nucleotides have been added to each site at each cycle of the
process. Other images may be employed to verify de-blocking and
similar steps in the operations.
[0006] Genetic analyses of the types described above are presently
performed in stationary, and even quite specialized equipment in
laboratory, medical facility, research and similar environments.
There is a growing need, however, for more flexible systems that
can be taken to the field for performing at least some sample
collection and analysis. The art has yet to respond to these needs,
owing in part to the designs of sample preparation equipment,
imaging components, processing needs, and so forth.
BRIEF DESCRIPTION
[0007] The present disclosure provides novel approaches to genetic
analysis designed to respond to such needs. The techniques are
based upon the design of a portable system, such as a hand-held
device, that may receive samples, perform nucleic acid detection,
such as reading of particular genes or genetic sequences, and at
least partial processing of the resulting data. In certain
embodiments described, the data may be only partially processed
on-board, and data may be transferred to other systems for further
processing. Various topologies for the device are envisaged,
including fully equipped devices that are able to perform
substantial processing, devices that are tethered or communicate
wirelessly with other local portable devices, and devices that can
do little or no processing, but transfer data to more
processing-capable systems for processing. Various usage scenarios
are also envisaged that go hand-in-hand with the portable nature of
the device. These may greatly simplify the data collection and
processing services carried out on the device, limit the degree of
analysis necessary depending on the application, and so forth.
[0008] In accordance with a first aspect of the disclosure,
portable genetic detector may comprise a reading component
configured to detect nucleic acids of interest in a biological
sample introduced into the detector. A control system is configured
to control operation of the reading component. A communications
component configured to transmit data produced by the reading
component to a remote computer system for analysis.
[0009] According to other aspects, portable genetic detector
comprises a reading component configured to detect nucleic acids of
interest in a biological sample, and a control system configured to
control operation of the reading component. A locating component is
configured to locate the portable detector as it is displaced to
sample locations.
[0010] In accordance with further aspects, a portable genetic
detector comprises a reading component configured to detect nucleic
acids of interest in a biological sample, and a control system
configured to control operation of the reading component. A memory
circuit is configured to store signature data for target genetic
sequence. The processing system is configured to compare data
derived from the reading component to the signature data.
[0011] The invention offers a number of other variants and
innovations, both in terms of a portable detector device, systems
in which the detector may be utilized, and method for performing
detection and analysis utilizing the advantages and unique benefits
of the portable detector.
DRAWINGS
[0012] These and other features, aspects, and advantages of the
present invention will become better understood when the following
detailed description is read with reference to the accompanying
drawings in which like characters represent like parts throughout
the drawings, wherein:
[0013] FIG. 1 is a diagrammatical overview of a portable genetic
analysis system in accordance with certain aspects of the present
techniques;
[0014] FIG. 2 is a diagrammatical view of a variant of the topology
shown in FIG. 1 designed to communicate with a portable support
unit;
[0015] FIG. 3 is a diagrammatical representation of further
topology in which a memory support may be used in conjunction with
the portable device;
[0016] FIG. 4 illustrates a further topology in which the portable
device receives a cartridge, such as for sample preparation or
management;
[0017] FIG. 5 is still a further topology in which the portable
analysis system receives a removable interface, such as a
smartphone;
[0018] FIG. 6 is a diagrammatical representation of certain of the
functional components that may be included in the portable analysis
system;
[0019] FIG. 7 is a diagrammatical representation of a portable
analysis system that incorporates means for locating the system and
places where samples are taken for analysis;
[0020] FIG. 8 is a diagrammatical representation of an exemplary
use case in which signatures are stored on the portable analysis
system for identifying matches in the field;
[0021] FIG. 9 is a process flow diagram illustrating the various
stages of sample and data processing that may be carried out in the
portable analysis system;
[0022] FIG. 10 is a flow chart illustrating exemplary steps in
primary and secondary processing of data for analysis; and
[0023] FIG. 11 is a flow chart illustrating a truncated or
"process-to-match" technique further facilitating processing within
the portable analysis system.
DETAILED DESCRIPTION
[0024] FIG. 1 illustrates a portable analysis system 10 that is
designed to provide ready and easy mobility between locations where
samples may be taken and at least partially processed. The system,
at its core, comprises a portable detector 12 that is packaged in a
housing 14 that have a form factor sized to be hand-held, carried
by a user, and used without the assistance of any special transport
equipment. That is, the detector itself is sufficiently light to be
easily carried and the housing may be configured in any suitable
manner to be comfortable and attractive for use. It is contemplated
that many different applications and uses may be envisaged for the
detector that are opened by virtue of its size and portability. For
example, the detector may be used in field applications, such as
for environmental pollutant analysis, animal and/or plant and/or
microbe detection and population mapping, conflict zone, triage,
disaster response, and similar applications, animal and livestock
management, to mention only a few. The detector may also find use
in medical environments, such as hospitals and clinics.
[0025] The portable analysis systems set forth herein are
particularly well suited for nucleic acid detection and analysis.
As such various embodiments of the system, its components and its
uses will be illustrated in the context of nucleic acid detection
procedures such as nucleic acid sequencing procedures. It will
however be understood that the portable analysis systems can be
used to detect other analytes including, but not limited to
proteins, small molecules, cells, viruses and other biologically
active molecules and particles. In some cases, non-nucleic acid
analytes can be detected based on detection of a nucleic acid tag
that is generated from an assay using those analytes or that is
selected in such an assay. Indeed a portable analysis system of the
present disclosure can be used for any of a variety of multi-step
chemical detection procedures that involve multiple cycles of
chemical processing before a conclusion is reached. The detector
can transmit data to remote processing system to store information
in time and then process the entire set before a conclusion is
reached. In the illustrated embodiment, the detector 12 is designed
to receive and prepare samples for analysis. A sample introduction
port 16 is thus provided through which a sample 18 may be
introduced. The sample itself may consist of genetic material,
biological fluids such as blood, biological tissues or cells,
crushed or partially prepared samples, environmental samples such
as water or other fluid-borne samples, and so forth. As described
below, in certain contexts, the sample preparation may be
off-loaded from the basic device, although the device could be
designed to both prepare samples for analytical detection and
perform the analytical detection, or more generally, sample
preparation, and detection on-board.
[0026] In the illustrated embodiment, the portable detector 12
includes a display 20 on which instructions, feedback, operator
selections and options, and so forth may be displayed. An operator
interface 22 is provided through which the operator may make
selections and input instructions. In certain embodiments, however,
these functions could be united, such as in a touch display. Those
skilled in the art will also recognize that various functions of
the device could be controlled by other interface components, such
as buttons, slides, voice recognition systems and the like. The
portable detector is designed to communicate with other devices for
various purposes. For example, the detector may receive programming
and instructions from various data sources as indicated by
reference numeral 26. These could be data sources remote or local
to the device, at least in a part of the device's life and use.
That is, the portable detector may be programmed by a wired or
wireless connection to a programming station, charging station or
the like when in the vicinity of such equipment. Alternatively,
certain of the data needed for operation of the portable detector
may be received remotely, such as by wireless networks, based upon
any suitable technology and protocol. Moreover, the device is
designed to communicate data to one or more remote processing
systems, also represented by numeral 26 in FIG. 1.
[0027] As described more fully below, the detector will typically
perform at least very basic analysis on-board, and may communicate
certain results of the analysis to more capable processing systems
for further processing. This is particularly the case where the
detector will be limited in its own processing capabilities either
by the particular processing circuitry utilized, the amount of
memory provided, the sophistication of the analyses required, and
so forth. Off-loading certain of these capabilities, in certain
presently contemplated embodiments, will render the device even
more portable and light-weight, while not surrendering capabilities
of the overall system that would then include the off-board
processing capabilities. Finally, in the illustration of FIG. 1,
the remote data resource and processing system may be coupled to
network or cloud-based resources. It should be noted, however, that
the detector 12 could also be coupled to such resources directly.
In general, such resources may provide some or all of the more
demanding processing requirements, may be used as a resource for
obtaining desired programming, bio-signatures (as discussed below),
and so forth.
[0028] Where used with cloud-based resources, the portable detector
may be considered part of a cloud computing environment for
biological data. As used herein, the term "cloud" or "cloud
computing environment" may refer to various evolving arrangements,
infrastructure, networks, and the like that will typically be based
upon the Internet. The term may refer to any type of cloud,
including client clouds, application clouds, platform clouds,
infrastructure clouds, server clouds, and so forth. As will be
appreciated by those skilled in the art, such arrangements will
generally allow for use by owners or users of sequencing or
detection devices, provide software as a service (SaaS), provide
various aspects of computing platforms as a service (PaaS), provide
various network infrastructures as a service (IaaS) and so forth.
Moreover, included in this term should be various types and
business arrangements for these products and services, including
public clouds, community clouds, hybrid clouds, and private clouds.
Any or all of these may be serviced by third party entities.
However, in certain embodiments, private clouds or hybrid clouds
may allow for sharing of sequence data and services among
authorized users.
[0029] Such cloud computing environments may include a plurality of
distributed nodes. The computing resources of the nodes may be
pooled to serve multiple consumers, with different physical and
virtual resources dynamically assigned and reassigned according to
consumer demand. Examples of resources include storage, processing,
memory, network bandwidth, and virtual machines. The nodes may
communicate with one another to distribute resources, and such
communication and management of distribution of resources may be
controlled by a cloud management module, residing one or more
nodes. The nodes may communicate via any suitable arrangement and
protocol. Further, the nodes may include servers associated with
one or more providers. For example, certain programs or software
platforms may be accessed via a set of nodes provided by the owner
of the programs while other nodes are provided by data storage
companies. Certain nodes may also be overflow nodes that are used
during higher load times.
[0030] Several alternative topologies are presently envisaged for
the portable detector. In particular, FIG. 2 illustrates a detector
12 that is coupled to a support pack or processing unit 30. The
detector 12, in this case, may be thought of as an analytic
detection or data acquisition unit, while the support pack may be
thought of as a data analysis or processing unit. The support pack
may provide various resources that allow the portable detector to
be reduced in size and weight, while providing the desired
functionality. For example, the support pack could be tethered to
the portable detector as indicated generally by reference numeral
32. In addition, or alternatively, these could communicate with one
another wirelessly as indicated by reference numeral 24.
[0031] In the illustrated embodiment, the support pack 30 comprises
a power supply 34, processing circuitry 36 and communications
circuitry 38. In this embodiment, at least some of the power for
operation of the portable detector 12 can be provided by the power
supply 34. The power supply also affords power for operation of the
support pack. Alternatively or additionally, the portable detector
12 can include an on-board power supply. The processing circuitry
36 may supplement processing circuitry contained in the portable
detector, or in some cases all or virtually all of the processing
required by the detector may be provided by the processing
circuitry 36 of the support pack. Finally, communications circuitry
36 may be off-loaded from the portable detector and provided in the
support pack. Such communications circuitry will allow the system
to communicate with local or remote devices, either wirelessly or
when physically connected (via a wired connection), as discussed in
greater detail below. It should be noted, however, that the support
pack need not provide all of these services for the portable
detector, and those skilled in the art may recognize other
components or services that may be off-loaded from the portable
detector to the support pack. In a presently contemplated usage,
the portable detector may be hand-held, and the support pack could
be carried, such as either on the belt or back of the user.
[0032] FIG. 3 illustrates a further topology in which the portable
detector 12 receives one or more memory devices 40 for storage and
communication of raw, partially processed or fully processed and
analyzed data. Any convenient memory device may be utilized, such
as conventional memory chips, USB flash memories, and so forth. In
a field application, the memory device may be utilized with the
portable detector to capture certain data, and a user may insert
further memory devices when the memory device is full, or to
distinguish between different samples, collection points, and so
forth. In the embodiment illustrated in FIG. 3, then, the memory
device may be inserted into a support pack 30 of the type described
with reference to FIG. 2. Alternatively, such memory devices may
simply be transported back to a base location where the data may be
re-accessed for processing.
[0033] FIG. 4 illustrates a further topology in which a removable
sample preparation/reading cassette 42 is insertable into the
portable detector. The portable detector may contain control and
processing circuitry that is designed to interface with the
cassette 42. A port 44 is provided in the detector to receive the
cassette which is then automatically interfaced with any electrical
or electronic traces, pins, pads, and so forth for operation of the
detector based upon a sample stored in the cassette. In certain
presently contemplated embodiments, for example, the cassette may
include both a sample support and certain reagent flow control
devices. The cassette may also include reagents for use in nucleic
acid detection or sequencing procedures. Still further, where
desired, one or more imaging heads or components may be provided in
the cassette to allow for the detection of individual nucleotides
on a support.
[0034] A portable detector can be configured for use with several
different types of sample preparation/reading cassettes. For
example, different cassettes can be configured to detect different
types of analytes. In particular embodiments, one type of cassette
can be configured to genomic DNA, a second type of cassette can be
configured to detect mRNA and a third type of cassette can be
configured to detect proteins. Alternatively or additionally, a
sample preparation/reading cassette can include machine readable
code(s) (or other indicia), such as one or more RFID tags, barcodes
or the like, that direct the portable detector to run a particular
process or protocol on the cassette. Taking for example a cassette
that is configured to detect genomic DNA, one or more codes can
direct the portable detector and, in turn the analysis system, to
run a whole genome sequencing or exome sequencing protocol, for
example, to identify allelic variants at particular genetic loci.
As another example, a cassette that is configured for detection of
mRNA can include code(s) that instruct the portable detector and
related analysis system to determine expression levels for one or
more RNA species, for example, in a digital gene expression
analysis. In the example of a cassette that is configured for
protein detection, code(s) can instruct the portable detector to
determine the presence or absence of one or more proteins of
interest, for example, based on detection of nucleic acid tags
obtained from a protein binding assay.
[0035] Finally, FIG. 5 illustrates further topology in which the
portable detector 12 is capable of receiving a removable
interface/processing device 46. It is contemplated that such
devices may be specially designed for use with the portable
detector, although commercially available devices may be adapted
for this purpose. Thus, the device 46 could comprise a smartphone,
personal digital assistant, or any suitable device capable of
offering an interface in providing at least some processing and/or
control capabilities.
[0036] FIG. 6 illustrates certain of the physical and functional
components of an exemplary portable detector 12. The detector is
designed to operate on a support 48 that holds samples of genetic
material, such as material collected by displacement of the
portable detector to one or more collection locations. The support
48 may be contained in a flow cell 50 that allows for reagents,
flushing fluids, deblocking chemistry, and so forth to be moved
over the support to facilitate imaging and analysis. The support
48, in the illustrated embodiment, comprises a plurality of sites
52 disposed as an array on a surface of the support. Each site in
the array may, once the sample is prepared for reading, comprise a
single nucleic acid molecule or a population comprising several
copies of a nucleic acid molecule (i.e. several species having the
same nucleic acid sequence). The sample preparation may consist of
cleaving or separating genetic material and disposing the genetic
material at such sites. The sample preparation can further include
amplification of the genetic material before or after the genetic
material is disposed at the sites. Examples of supports, flow
cells, and technologies for sample preparation are described, for
example, in US 2010/0111768 A1 and U.S. Ser. No. 13/273,666, which
are hereby incorporated by reference.
[0037] For ease of explanation, the systems, devices, and methods
of the present disclosure are exemplified herein with regard to
optically-based SBS procedures. For example, flow cell supports
useful for optical detection of nucleic acid colonies in SBS
procedures are set forth above. In SBS, extension of a nucleic acid
primer along a nucleic acid template is monitored to determine the
sequence of nucleotides in the template. The underlying chemical
process can be polymerization (e.g. as catalyzed by a polymerase
enzyme). In a particular polymerase-based SBS embodiment,
fluorescently labeled nucleotides are added to a primer (thereby
extending the primer) in a template dependent fashion such that
detection of the order and type of nucleotides added to the primer
can be used to determine the sequence of the template. A plurality
of different templates can be subjected to an SBS technique on a
surface under conditions where events occurring for different
templates can be distinguished. For example, the templates can be
present on the surface of an array such that the different
templates are spatially distinguishable from each other. Typically
the templates occur at features each having multiple copies of the
same template (sometimes called "clusters" or "colonies"). However,
it is also possible to perform SBS on arrays where each feature has
a single template molecule present, such that single template
molecules are resolvable one from the other (sometimes called
"single molecule arrays").
[0038] Flow cells provide a convenient substrate for housing an
array of nucleic acids. Flow cells are convenient for sequencing
techniques because the techniques typically involve repeated
delivery of reagents in cycles. For example, to initiate a first
SBS cycle, one or more labeled nucleotides, DNA polymerase, etc.,
can be flowed into/through a flow cell that houses an array of
nucleic acid templates. Those features where primer extension
causes a labeled nucleotide to be incorporated can be detected, for
example, using methods or apparatus set forth herein. Optionally,
the nucleotides can further include a reversible termination
property that terminates further primer extension once a nucleotide
has been added to a primer. For example, a nucleotide analog having
a reversible terminator moiety can be added to a primer such that
subsequent extension cannot occur until a deblocking agent is
delivered to remove the moiety. Thus, for embodiments that use
reversible termination a deblocking reagent can be delivered to the
flow cell (before or after detection occurs). Washes can be carried
out between the various delivery steps. The cycle can then be
repeated n times to extend the primer by n nucleotides, thereby
detecting a sequence of length n. Exemplary SBS procedures, fluidic
systems and detection platforms that can be readily adapted for use
in a portable detector of the present disclosure are described, for
example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497;
U.S. Pat. No. 7,057,026; WO 91/06678; WO 07/123,744; U.S. Pat. No.
7,329,492; U.S. Pat. No. 7,211,414; U.S. Pat. No. 7,315,019; U.S.
Pat. No. 7,405,281, and US 2008/0108082, each of which is
incorporated herein by reference.
[0039] It should be noted that other types of supports and genetic
material reading technologies besides the SBS procedures
exemplified above may be utilized in a portable detector or
portable genetic analysis system. Other sequencing procedures that
use cyclic reactions can be used, such as those wherein each cycle
can include steps of delivering one or more reagents to nucleic
acids. A particularly useful sequencing procedure is
pyrosequencing. Pyrosequencing detects the release of inorganic
pyrophosphate (PPi) as particular nucleotides are incorporated into
a nascent nucleic acid strand (Ronaghi, et al., Analytical
Biochemistry 242(1), 84-9 (1996); Ronaghi, Genome Res. 11(1), 3-11
(2001); Ronaghi et al. Science 281(5375), 363 (1998); U.S. Pat. No.
6,210,891; U.S. Pat. No. 6,258,568 and U.S. Pat. No. 6,274,320, the
disclosures of which are incorporated herein by reference in their
entireties). In pyrosequencing, released PPi can be detected by
being immediately converted to adenosine triphosphate (ATP) by ATP
sulfurylase, and the level of ATP generated is detected via
luciferase-produced photons. Thus, the sequencing reaction can be
monitored via a luminescence detection system. Excitation radiation
sources used for fluorescence based detection systems are not
necessary for pyrosequencing procedures. Useful fluidic systems,
detectors and procedures that can be used for application of
pyrosequencing to a portable detector of the present disclosure are
described, for example, in WIPO Pat. App. Ser. No. PCT/US11/57111,
US 2005/0191698, U.S. Pat. No. 7,595,883, and U.S. Pat. No.
7,244,559, each of which is incorporated herein by reference.
[0040] Sequencing-by-ligation reactions are also useful including,
for example, those described in Shendure et al. Science
309:1728-1732 (2005); U.S. Pat. No. 5,599,675; and U.S. Pat. No.
5,750,341, each of which is incorporated herein by reference in its
entirety. Some embodiments can include sequencing-by-hybridization
procedures as described, for example, in Bains et al., Journal of
Theoretical Biology 135(3), 303-7 (1988); Drmanac et al., Nature
Biotechnology 16, 54-58 (1998); Fodor et al., Science 251(4995),
767-773 (1995); and WO 1989/10977, each of which is incorporated
herein by reference. In both Sequencing-by-ligation and
sequencing-by-hybridization procedures, target nucleic acids can be
immobilized on a solid support and cycles of oligonucleotide
delivery and detection can be repeated. Fluidic systems for SBS
methods as set forth herein or in references cited herein can be
readily adapted for delivery of reagents for sequencing-by-ligation
or sequencing-by-hybridization procedures. Typically, the
oligonucleotides are fluorescently labeled and can be detected
using fluorescence detectors similar to those described with regard
to SBS procedures herein or in references cited herein.
[0041] Some embodiments can utilize nanopore sequencing. In such
embodiments, target nucleic acid strands, or nucleotides
exonucleolytically removed from target nucleic acids, pass through
a nanopore. The nanopore can be a synthetic pore or biological
membrane protein, such as .alpha.-hemolysin (Deamer & Akeson
Trends Biotechnol. 18, 147-151 (2000), incorporated herein by
reference), Mycobacterium smegmatis porin A (MspA, WO 2010/034018
A2, incorporated herein by reference) or solid-state pores (U.S.
Pat. No. 6,627,067 or U.S. Pat. No. 6,413,792, each of which is
incorporated herein by reference). As the target nucleic acids or
nucleotides pass through the nanopore, each type of base can be
identified by measuring fluctuations in the electrical conductance
of the pore (U.S. Pat. No. 7,001,792; Soni & Meller, Clin.
Chem. 53, 1996-2001 (2007); Healy, Nanomed. 2, 459-481 (2007); and
Cockroft, et al. J. Am. Chem. Soc. 130, 818-820 (2008), the
disclosures of which are incorporated herein by reference in their
entireties). Thus, a device of the present disclosure can include a
detector of electrical properties of nucleic acids, nucleotides
and/or their environment.
[0042] Some embodiments can utilize methods involving the real-time
monitoring of DNA polymerase activity. Nucleotide incorporations
can be detected through fluorescence resonance energy transfer
(FRET) interactions between a fluorophore-bearing polymerase and
.gamma.-phosphate-labeled nucleotides, or with zeromode waveguides.
The illumination can be restricted to a zeptoliter-scale volume
around a surface-tethered polymerase such that incorporation of
fluorescently labeled nucleotides can be observed with low
background (Levene et al. Science 299, 682-686 (2003); Lundquist et
al. Opt. Lett. 33, 1026-1028 (2008); Korlach et al. Proc. Natl.
Acad. Sci. USA 105, 1176-1181 (2008), the disclosures of which are
incorporated herein by reference in their entireties).
[0043] Some SBS embodiments include detection of a proton released
upon incorporation of a nucleotide into an extension product. For
example, sequencing based on detection of released protons can use
an electrical detector and associated techniques that are
commercially available from Ion Torrent (Guilford, Conn., a Life
Technologies subsidiary) or sequencing methods and systems
described in US 2009/0026082 A1; US 2009/0127589 A1; US
2010/0137143 A1; or US 2010/0282617 A1, each of which is
incorporated herein by reference in its entirety.
[0044] Where desired, a portable detector may comprise a sample
preparation component 54 that is configured, for example, to
fragment, separate, distribute and/or amplify nucleic acid samples
for detection in a sequencing procedure such as one or more of
those set forth above. Nucleic acid samples can be fragmented, for
example, using sonication, passage through a nozzle that forms tiny
droplets (nebulisation), chemical cleavage, enzymatic cleavage,
heat and/or radiation. The fragmented nucleic acids can optionally
be purified or size selected prior to other sample preparation
steps or prior to detection steps. Useful procedures for size
selection include, but are not limited to, isotachophoresis (see,
for example, US 2002/0189946 A1, US 2010/0224494 A1, and US
2010/0294663 A1, each of which is incorporated herein by reference)
or droplet micro-actuation by electrowetting (see, for example,
U.S. Pat. No. 7,998,436, U.S. Pat. No. 7,815,871, U.S. Pat. No.
6,911,132, and US 2010/0048410 A1, each of which is incorporated
herein by reference). Hardware and/or processes described in the
aforementioned references can be used in a portable detector of the
present disclosure.
[0045] In some embodiments, sample preparation can include steps of
attaching nucleic acids to a surface and amplifying the nucleic
acids on the surface prior to or during sequencing. For example,
amplification can be carried out using bridge amplification to form
nucleic acid clusters on a surface. Useful bridge amplification
methods are described, for example, in U.S. Pat. No. 5,641,658; US
2002/0055100 A1; U.S. Pat. No. 7,115,400; US 2004/0096853 A1; US
2004/0002090 A1; US 2007/0128624 A1; or US 2008/0009420 A1, each of
which is incorporated herein by reference. Another useful method
for amplifying nucleic acids before or after attachment to a
surface is rolling circle amplification (RCA), for example, as
described in Lizardi et al., Nat. Genet. 19:225-232 (1998) and US
2007/0099208 A1, each of which is incorporated herein by reference.
Emulsion PCR on beads can also be used, for example as described in
Dressman et al., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003),
WO 05/010145, US 2005/0130173 A1 or US 2005/0064460, each of which
is incorporated herein by reference.
[0046] Various combinations of the above sample preparation process
steps can occur in a portable detector of the present disclosure.
Particularly useful arrangements for integrating sample preparation
with nucleic acid sequencing detection apparatus are provided in WO
2010/077859 A2, and U.S. Ser. No. 61/556,427, each of which is
incorporated herein by reference. It will be understood, that some
or all of the sample preparation process steps exemplified herein
or in the references cited herein can occur in a portable detector
of the present disclosure. Some steps however, can be carried out
prior to loading a sample (or sample-bearing substrate) into a
portable detector. For example, nucleic acid fragmentation, size
purification and amplification can be carried out to obtain
amplified nucleic acid fragments and the amplified nucleic acid
fragments can then be loaded as the `sample` into a portable
detector.
[0047] The device may also support reagent delivery components 56
that allow for the control of flow of chemistry utilized in
performing the analysis of the sample. Reagents 58 may also be
carried on the device, or these could be provided separately (e.g.,
in one or more cartridges, capsules, vials, cassettes, and so
forth). For example, reagents can be provided to a portable
detector of the present disclosure in the form of a cartridge as
described in U.S. patent application Ser. No. 13/273,666, which is
incorporated herein by reference. The cartridge can contain
reservoirs for the reagents absent a flow cell or other fluidic
components. Alternatively, the cartridge can include fluidic
components such as one or more valves, pressure sources (e.g.
pumps), fluidic lines and other components used to actively
manipulate the fluids in the cartridge. The cartridge can also
include one or more integrated flow cells or other sample detection
chambers. Exemplary cartridges having fluidic components and
integrated flow cells that can be adapted for use with a portable
detector of the present disclosure are described in U.S. Pat. App.
Ser. No. 61/619,784, which is incorporated herein by reference.
Further examples of reagents and reagent delivery components that
can be readily adapted for use in a portable detector, especially
for nucleic acid sequencing embodiments, are described, for
example, in US 2010-0009871 A1; US 2010-0187115 A1; US 2010-0111768
A1; and US2011-0072914 A1, which are hereby incorporated by
reference.
[0048] In a presently contemplated embodiment, the detector further
comprises reading/imaging components 60. As will be appreciated by
those skilled in the art, the chemistry utilized for genotyping,
sequencing, and similar genetic processing may be based upon
compounds that fluoresce when illuminated by particular wavelengths
of light, such as from laser sources. The fluorescent light signals
given off by these compounds, once attached to the genetic material
at the sites, can be imaged by an optical imaging head or
circuitry, such as circuitry including charge coupled devices,
filters, and so forth. These imaging systems may be miniaturized to
facilitate their use in the portable detector. In certain
embodiments, the reading/imaging components may move with respect
to the support, or these may be stationary with respect to the
support, depending upon such factors as the size of the support,
the size of the reading/imaging component (e.g., a read head) the
resolution of the imaging components, the density of the sites on
the support, and so forth. Examples, of reading/imaging components
are described, for example, in US 2010-0111768 A1; U.S. Pat. No.
7,329,860, U.S. patent application Ser. No. 13/273,666 or U.S. Pat.
App. Ser. No. 61/619,784, which are hereby incorporated by
reference.
[0049] The reading/imaging components need not be capable of
optical detection for all embodiments of the invention. For
example, the reading/imaging component can be an electronic
detector used for detection of protons or pyrophosphate (see, for
example, US 2009/0026082 A1; US 2009/0127589 A1; US 2010/0137143
A1; or US 2010/0282617 A1, each of which is incorporated herein by
reference in its entirety) or as used in detection of nanopores
(U.S. Pat. No. 7,001,792; Soni & Meller, Clin. Chem. 53,
1996-2001 (2007); Healy, Nanomed. 2, 459-481 (2007); and Cockroft,
et al. J. Am. Chem. Soc. 130, 818-820 (2008), each of which is
incorporated herein by reference).
[0050] As further illustrated in FIG. 6, the portable detector will
have certain on-board circuitry, indicated collectively by
reference numeral 62. This circuitry may include, for example,
interface circuitry 64 designed to communicate with the
reading/imaging component 60 to receive raw signal data (e.g.
imaging data) for primary analysis, filtering, compression, and so
forth. Data processing circuitry 66 is provided, and may include
any suitable type of processor, such as microprocessors, field
programmable gate arrays, and so forth. As described more fully
below, the processing circuitry 66 may perform initial operations
on the raw data received from the reading/imaging component 60, and
may stop at the initial primary processing, or may carry on more
sophisticated processing designed to recognize particular markers,
genes, traits, individuals, and so forth. Memory circuitry 68
supports the processing circuitry 66 and may store programming
carried out by the processing circuitry 66. Moreover, the memory
circuitry may serve to store raw, processed or any other data
received or utilized by the interface circuitry 64 or processing
circuitry 66.
[0051] A display/operator interface 70 is provided as described
above. This may include a visual display and one or more buttons or
locations for touching by the user, touch screens, and so forth.
The display/operator interface 70 may also allow for certain
audible commands, warnings, and so forth to be received and/or
output by the device. Communications circuitry 72 allows the
detector to communicate with other devices, both local and remote
as described above. Such communications circuitry may be based upon
any suitable communications technology or protocol, such as
Internet protocols, cellular telephone protocols, wireless
protocols, wired data communication protocols, and so forth. A
power supply 74 is provided to power the various functions of the
device, particularly the data processing circuitry, display,
communication circuitry, and so forth. The power supply will
typically comprise one or more batteries, voltage regulators,
amplifiers, and so forth that allow for extended use of the
portable detector between battery changes or recharges. An arrow in
FIG. 6 indicates that the power supply 74 may be rechargeable.
Finally, control circuitry/routines 76 are provided for
coordinating the operation of the various components, particularly
the reading/imaging component, the processing components, the
communication components, the display, and so forth. Instructions
and routines for the control circuitry 76 may be stored in the
memory circuitry 68. Where provided, the control circuitry 76 may
also regulate operation of the reagent delivery component, any
sample preparation component, and so forth.
[0052] As summarized above, some or all of the circuitry may be
off-loaded from the portable detector. The circuitry may be
provided in a support pack of the type described above. This is
particularly the case for the power supply 74 illustrated in FIG.
6, certain of the processing circuitry 66, the communications
circuitry 72, even of certain of the control circuitry 76.
[0053] FIG. 7 illustrates a further embodiment of the portable
detector that includes circuitry for determining the location of
the detector, such as for tracking locations where samples are
procured or should be procured, or both. In this embodiment, the
detector includes a receiver/transmitter 78 as designed to exchange
signals with one or more locating device. For example, the
receiver/transmitter 78 may comprise a GPS receiver designed to
receive signals from geostationary satellites 80 in accordance with
existing technologies. Alternatively, the receiver/transmitter 78
may include cellular data exchange circuitry designed to exchange
signals with cellular transmitters/receivers 82. Where desired,
both of these technologies, as well as others, subsequently
developed may be provided in the device. The receiver/transmitter
is coupled to a locating component 84 which is capable of
triangulating or otherwise computing the location of the device
based upon the received signals. The locating component 84 is
coupled to the other circuitry 86 as described above, such as for
providing control and power to the locating component. A tagging
component 88 may be provided which may interface with data
processing circuitry to place a location tag on data acquired by
the reading/imaging component, or to data processed by the data
processing circuitry. Locations 90 of samples may be located on a
map 92 that may be displayed on the interface of the detector. As
will be appreciated by those skilled in the art, such locations may
indicate points where samples should be taken, points where samples
have been taken, or both. It is presently contemplated that such
functionality may be useful in certain applications, such as for
environmental testing, mapping of flora and fauna, persons,
animals, livestock, and so forth. As noted, the location
information may be stored in a file with any processed data to
indicated such factors as the time at which the sample was taken
and/or processed, the location at which the sample was taken and/or
processed, any other environmental or input information provided by
the user via the interface, the identification of the person or
persons who took the sample, the identification of the portable
detector, and so forth.
[0054] As noted above, a number of uses may be envisaged for the
portable detector. One family of uses presently contemplated
involves the identification of people, animals and stocks, plants,
microbes, pathogens, and so forth. Moreover, it is presently
contemplated that, as described more fully below, the reduction of
analysis to a particular candidate trait or traits, and/or to a
particular candidate individual or individuals, may greatly
facilitate the use of the portable detector, and assist in
reduction of the size and complexity of the detector by
facilitating processing. FIG. 8 illustrates an exemplary set of
scenarios of this type. As shown in FIG. 8, the portable analysis
system may be utilized to locate and/or identify sub-populations
94, 96, and/or 98, which correspond to human beings 100, animals or
stock 102, and one or more microbes 104. Each of these populations
may be associated with genetic material 106, 108, and 110,
respectively. Within this genetic material, then, particular
sequences or segments of material, each comprising a series of
nucleotides, may be identified as indicated by reference numerals
112, 114, and 116, respectively. Each of these segments may then be
characterized by the particular nucleotides and their unique order
to create signatures identified in FIG. 8 by reference numerals
118, 120, and 122.
[0055] It should be noted that in various use cases the segments of
interest and the consequent signatures may correspond to such
parameters as a population of individuals sharing a common trait or
gene, particular individuals separately identifiable by strings of
genetic material, particular plants or animals identifiable by such
strings, individual microbes similarly identifiable, including
strings of such microbes, and so forth. Similarly, the signatures
may encode particular traits of interest, such as physical traits
desirable or more generally of interest in managed stocks, animal,
and plant populations.
[0056] The signatures for the sub-population of interest may be
stored in a signature repository 124 which may be loaded onto the
portable detector or stored separately. In addition to the
signatures themselves, the repository may receive various mappings
of traits 126, individuals 128 and other mappings 130, such as for
species, group identifications, and so forth. These signatures may
be utilized, as discussed more fully below, in the analysis
performed by the portable detector. An advantage of using a
signature repository is that analysis, for example, in a
re-sequencing or sequence alignment protocol can occur more rapidly
and using fewer computational resources than would be necessary
when using standard databases having more comprehensive and larger
collections of reference sequences.
[0057] By way of example, the portable detector may be used in
conflict zones to identify individuals in the field, and in many
applications for disaster relief, humanitarian aid, and so forth.
In such situations, individuals may become separated from a family,
military unit or other group, individuals may be dispersed or
individuals may be in need of assistance. Where possible, the
portable detector may receive samples for individuals and determine
whether a match for a known signature for the individual can be
made. A signature repository used for determining such matches can
be custom tailored to the query at hand. For example, in a conflict
zone application, the signature repository can include only
sequences previously acquired for soldiers who were deployed to the
particular conflict field or theater of conflict being
investigated. Alternatively, a larger data repository can be used,
for example, including sequence data for an entire army, but
weighting factors can be used during the comparison analysis based
on information and belief as to likely candidates in a particular
scenario. Similar signature repositories can be made for other
subsets of individuals such as members of a particular family,
citizens of a particular country, state, city or other region,
individuals having a criminal record, individuals suspected of a
particular criminal activity or the like. In connection with
localization techniques described above, the individuals could be
tagged based upon their location, at least at the time of sampling
and/or processing. Similarly, in environmental and agricultural
applications, particular plant varieties, hybrids, genetically
modified plants, and the like may be tracked and located based upon
specific signatures for the target population of interest. Traits
of managed livestock may also be determined in a similar manner.
The system may thus afford selection of individuals for
reproduction or separating from groups, and so forth.
[0058] Thus, an individual whose genomic material is tested using a
portable detector can constitute a candidate for inclusion in a
group of individuals who share one or more of the genetic
characteristic that are detected by the portable detector. The
group against which an individual is compared can be a predefined
group such as a military unit suspected or believed to be
associated with a candidate human individual, a family suspected or
believed to be associated with a candidate human individual, a herd
of animals suspected or believed to be associated with a candidate
stock animal, a crop variety suspected or believed to be associated
with a candidate individual plant or the like.
[0059] FIG. 9 is an exemplary diagram illustrating a process flow
132 that may be carried out in the portable detector. In general,
the process begins with the sample 134 which is collected, such as
from one or more locations, individuals or any other desired
source. A sample preparation phase 136 will generally comprise one
or more of the steps set forth previously herein, optionally
including one or more of isolation of genetic material from the
sample, cleaving of the genetic material into smaller segments, and
attachment of the smaller segments to the sites on a support, where
such support processing is performed. The sample preparation phase
may also include amplification and other operations designed to
improve the reliability and signal-to-noise ratio in the acquired
data.
[0060] A resulting prepared sample 138 is then provided to a
reading component 140. In several, but not all, presently
contemplated embodiments the reading component allows for optical
imaging of the genetic material of the sample. The sample may be
further processed, particularly when sequencing is desired, to read
successive nucleotides in a string of nucleotides at the sites on
the sample support for sequencing analysis. The reading component
produces raw data 142, which will typically include image data
comprising pixilated values for the genetic materials at each of
the sites, as well as for spaces between these sites. This raw
image data may then be processed by the processing system 144, such
as to eliminate un-needed image data (e.g., corresponding spaces
between sites) and to determine the type of genetic material (e.g.,
nucleotides) at the sites. Exemplary methods for masking or
compressing image data and that can be used in accordance with the
systems, methods and devices herein are described in US
2008/0182757 A1 and US 2012/0020537 A1, each of which is
incorporated herein by reference.
[0061] The processed data 146 resulting from this primary analysis
may then be fed to analysis system 148. This analysis system may
determine, based upon the data drawn from the images, whether
certain genetic material of interest is present in the sample,
whether a match to a target is identified, and so forth. The
analysis system may also determine, where such programming is
provided, particular sequences of interest, and may assemble
sequences into longer sequences for identification of individuals,
traits, and so forth. As noted above, where desired, at any stage
in this process data may be off-loaded to associated components for
processing, or the data may simply be stored and transmitted to
other systems for more sophisticated processing. It is presently
contemplated that initial embodiment of the portable detector, such
off-loading may be very useful in reducing the processing needs,
programming requirements, power requirements of the device, and
allowing for quick and easy access to a certain level of useful
information. As more rapid and capable processing circuits become
available, then, these may be utilized in later versions of the
detector to enhance the turn-around on processing and analysis,
enable more sophisticated processing to take place, and so
forth.
[0062] As described above, the portable detector and analysis
system may perform various types of analysis, extending from simple
raw image processing to primary analysis, to matching of individual
sample donors and populations, to more sophisticated sequencing
operations. Certain of the processes are illustrated
diagrammatically in FIG. 10. In general, FIG. 10 illustrates data
analysis 150 as divided between primary analysis 152 and secondary
analysis 154. Again, certain of the primary analysis 152 may be
off-loaded from the device, and some or all of the secondary
analysis 154 may off-loaded. However, the various phases of
analysis are described here to provide an indication of the type of
data processing and analysis that may be performed on the
device.
[0063] In the primary analysis 152, for example, the processing
circuitry may receive raw data as indicated at step 156. This raw
data may be stored as indicated at 158. However, in presently
contemplated embodiments not all of the raw data is permanently or
semi-permanently stored following primary analysis as indicated at
step 160. As discussed above, this primary analysis may consist of
eliminating certain of the image data not corresponding to sites of
interest. The primary analysis may also identify particular genetic
material (e.g., nucleotides) by virtue of particular wavelengths at
which attached material fluoresces under the influence of
stimulating light (e.g., from lasers included in the reading
component). The result of the primary analysis, as discussed above,
may be stored, or some of the data may be discarded as indicated at
step 162. The resulting stored data may comprise a data file which
identifies one or more nucleotides detected at individual sites on
a support along with addresses of these sites.
[0064] The secondary analysis 154 may then include assembly of
certain sequence data, and/or comparison to a known sequence,
and/or counting of particular sequences, etc. where sequencing is
performed. As will be appreciated by those skilled in the art, such
operations may include the assembly of a list of nucleotides
detected at individual sites through successive steps in reagent
application to the support, attachment of tags or markers to the
genetic materials at the individual sites, and so forth. The
resulting data may comprise relatively small lengths of sequences
of these nucleotides by individual sites. The processing at step
164 may further include analysis of the resulting small segments to
accumulate larger segments or sequences of nucleotides in the
sample.
[0065] Further, at step 166, these sequences may be compared to
certain known genes, traits, signatures for individuals, species,
and so forth. Finally, the processing may end with storage and
communication of the data as indicated at steps 168. Of course,
where a processing is terminated on the portable detector at an
earlier stage, such data communication may also occur then. Still
further, where raw or semi-processed data is produced by the
device, this may be stored on a memory support that is removable
from the device for conveyance to another storage and/or analysis
system as described above.
[0066] As noted above, certain types of processing may be performed
on the portable detector that may greatly assist in affording
usable results while reducing the processing demands on the
detector itself. The affect of relaxed processing demands may allow
for a lighter and faster device capable of providing useful output
in a range of applications. FIG. 11 illustrates exemplary
processing in a "process-to-match" approach. The processing,
designated generally by reference numeral 170, may begin with
receiving population data or signatures at step 172. As noted above
with reference to FIG. 8, such signatures may correspond to
individuals, groups of individuals, animal and plant populations,
microbes, or any features or traits of these. Preliminary
processing is then carried out as indicated by reference numeral
174 which may be similar to that summarized above with reference to
FIG. 10. This preliminary processing may be generally similar to
that described above during phase 152 illustrated in FIG. 10. At
step 176, then, limited secondary processing may be performed. In
the presently contemplated embodiment, this limited secondary
processing may consist of assembling of sequences of nucleotides
from the information collected from the individual sites on the
support. Longer sequences of these nucleotides may then be
assembled based upon generally known informatics techniques. At
step 178, then, based upon such sequences, the system may determine
whether a match to an individual, trait, species, or any
sub-population is possible. Because a limited number of signatures
may be of interest, this match may be performed relatively quickly
as compared to sequencing an entire genome. Once sufficient
sequencing and comparison has been made to confirm a positive
match, the processing may be stopped and the results stored and,
where desired, communicated to external devices, as represented at
step 180.
[0067] In accordance with the process exemplified in FIG. 11, once
a positive match has been confirmed, instructions can be
communicated to the portable detector (or to the user of the
portable detector) to stop the sequencing procedure. Thus,
unnecessary or unwanted consumption of sequencing reagents can be
avoided as can unnecessary waste of time. If desired, a new sample
can be loaded on the portable detector and sequenced. Furthermore
based on the information obtained from a first portable detector,
instructions can be communicated to one or more other portable
detectors or to the users of the other portable detector(s) to
modify schedules or planned procedures. For example, if sufficient
information has been obtained from the group of portable detectors
the current sequencing procedures can be halted for all of the
portable detectors. Alternatively or additionally, one or more of
the other portable detectors can be tasked with new instructions
regarding samples to evaluate or new priorities can be set with
regard to a group of samples that is in the queue for one or more
portable detectors, respectively. The group of portable detectors
(or their users) that receive such instructions can be determined
based on any number of criteria including, but not limited to,
proximity to a particular location where candidate individuals or
samples are located (for example, as determined from GPS
information transmitted from the portable detectors), predefined
instructions as to the samples to be evaluated, or optimization of
workload spread across a network of portable detectors (or their
users).
[0068] A decision process similar to that shown in FIG. 11 can be
based on balancing costs and benefits. For example, processing may
begin with receiving nucleic acid sequencing data from one or more
portable detectors. Primary processing can then carried out,
followed by secondary processing. However, during either or both
processing steps, the system can be evaluating factors such as
costs (in money or time) of data acquisition, data computation,
data storage and data transmission. Once costs and benefits are
determined to be balanced or to have reached an otherwise desired
level, the processing may be stopped and the results stored and,
where desired, instructions can be communicated to external
devices. For example, at a decision step, based upon the evaluation
of such factors, the system may determine whether to proceed with
sequencing at one or more of the portable detectors or not. An
instruction to halt or pause sequencing can be sent to one or more
of the portable detectors in response. Similar evaluation and
decision processes can be carried out based on achieving a desired
level of data quality or data quantity. For example, data
collection and analysis can be allowed to proceed until a desired
data quality score is achieved (for example, a Q score of 30)
and/or until a desired sequence coverage is achieved (for example,
10.times., 20.times. or 30.times. sequence coverage for one or more
regions of a genome of interest).
[0069] While only certain features of the invention have been
illustrated and described herein, many modifications and changes
will occur to those skilled in the art. It is, therefore, to be
understood that the appended claims are intended to cover all such
modifications and changes as fall within the true spirit of the
invention.
* * * * *