U.S. patent application number 11/412030 was filed with the patent office on 2007-02-01 for system for genetic surveillance and analysis.
This patent application is currently assigned to Applera Corporation. Invention is credited to Hans Fuernkranz, Chirag J. Patel.
Application Number | 20070026426 11/412030 |
Document ID | / |
Family ID | 37215439 |
Filed Date | 2007-02-01 |
United States Patent
Application |
20070026426 |
Kind Code |
A1 |
Fuernkranz; Hans ; et
al. |
February 1, 2007 |
System for genetic surveillance and analysis
Abstract
A genetic surveillance system comprises a communications network
and at least one reader-analyzer instrument. The reader-analyzer
instrument has a communication interface to communicate over the
network. The reader-analyzer instrument is adapted to perform
genetic assay analysis of a sample obtained from a member of a
population and to generate detection-related data based upon the
analysis. The reader-analyzer instrument is adapted to associate
qualifying information with the detection-related data and to
communicate the associated qualifying information and
detection-related data over the network.
Inventors: |
Fuernkranz; Hans; (Saratoga,
CA) ; Patel; Chirag J.; (Foster City, CA) |
Correspondence
Address: |
HARNESS, DICKEY & PIERCE, P.L.C.
P.O. BOX 828
BLOOMFIELD HILLS
MI
48303
US
|
Assignee: |
Applera Corporation
Foster City
CA
|
Family ID: |
37215439 |
Appl. No.: |
11/412030 |
Filed: |
April 26, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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60674750 |
Apr 26, 2005 |
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60699950 |
Jul 15, 2005 |
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60749003 |
Dec 9, 2005 |
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60674876 |
Apr 26, 2005 |
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60696157 |
Jun 30, 2005 |
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Current U.S.
Class: |
435/5 ; 435/6.13;
702/20 |
Current CPC
Class: |
G06F 19/00 20130101;
G16B 30/00 20190201; Y02A 90/22 20180101; G16H 50/80 20180101; Y02A
90/24 20180101; G16B 50/00 20190201; Y02A 90/26 20180101; G16H
10/40 20180101; G16B 25/00 20190201; Y02A 90/10 20180101 |
Class at
Publication: |
435/006 ;
702/020 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; G06F 19/00 20060101 G06F019/00 |
Claims
1. An genetic surveillance information system, comprising: a
communications network; at least one reader-analyzer instrument
having communication interface to communicate over said network;
said reader-analyzer instrument being adapted to perform genetic
assay analysis of a sample obtained from an individual member of a
population and to generate genetic surveillance-related data based
on said analysis; said reader-analyzer instrument being adapted to
associate spatial information and temporal information with said
genetic surveillance-related data and to communicate said spatial
information and temporal information associated with said genetic
surveillance-related data over said network.
2. The system of claim 1 further comprising a database system
communicating with said network and configured to store said
spatial information and temporal information with associated said
genetic surveillance-related data as information reflecting the
status of said population.
3. A system to provide data to a laboratory response network
according to claim 1 further comprising a software system that
provides an interface between said laboratory response network and
said network whereby said spatial information and temporal
information with associated said genetic surveillance-related data
is made available to said laboratory response network.
4. A system to provide data to a laboratory response network
according to claim 2 further comprising a software system that
provides an interface between said laboratory response network and
said database whereby said spatial information and temporal
information with associated said genetic surveillance-related data
is made available to said laboratory response network.
5. The system of claim 1 wherein said reader-analyzer is a portable
instrument.
6. The system of claim 1 wherein said reader-analyzer is adapted to
process samples carried on a card having genetic assay materials
carried thereon and adapted to be inserted into said
reader-analyzer.
7. The system of claim 1 wherein said reader-analyzer instrument
performs PCR analysis.
8. The system of claim 1 wherein said reader-analyzer instrument
includes at least one hybridization array.
9. The system of claim 1 wherein said reader-analyzer instrument is
adapted for bidirectional communication.
10. The system of claim 1 further comprising a plurality of said
reader-analyzer instruments adapted for peer-to-peer communication
with one another.
11. The system of claim 1 wherein said reader-analyzer instrument
is adapted to receive control instructions via said network.
12. The system of claim 1 wherein said reader-analyzer instrument
is adapted to alter the manner in which said genetic
surveillance-related data are generated based on information
received by said reader-analyzer over said network.
13. The system of claim 1 further comprising integrated sample
preparation module to process said sample prior to analysis by said
reader-analyzer instrument.
14. The system of claim 13 wherein said integrated sample
preparation module has a communication interface to communicate
over said network.
15. The system of claim 13 wherein said integrated sample
preparation module is adapted to receive control instructions via
said network.
16. The system of claim 13 wherein said integrated sample
preparation module is adapted to alter the manner in which said
sample is processed based on information received by said sample
preparation module over said network.
17. The system of claim 13 wherein said integrated sample
preparation module manipulates at least one assay.
18. The system of claim 13 wherein said integrated sample
preparation module manipulates at least one assay, and wherein said
integrated sample preparation module is adapted to alter the manner
in which said assay manipulation is performed based on information
received by said sample preparation module over said network.
19. The system of claim 1 further comprising data identifying a
presence or absence of at least one pathogenic organism.
20. The system of claim 19 wherein said data is collected from
analysis of at least one target sequence related to the at least
one pathogenic organism.
21. The system of claim 1 further comprising obtaining demographic
information from said individual member of a population.
22. The system of claim 21 wherein said demographic information is
associated with said spatial information, said temporal information
and said genetic surveillance-related data.
23. The system of claim 1 further comprising a database on
electronic media operable for storing and analyzing said spatial
information and temporal information with associated said genetic
surveillance-related data retrieve from said network.
24. The system of claim 1 further comprising an algorithm for
predicting potential danger to the population based on said spatial
information and temporal information with associated said genetic
surveillance-related data.
25. The system of claim 1 further comprising a learning algorithm
for determining validity of new data based on lessons learn from
said spatial information and temporal information with associated
said genetic surveillance-related data.
26. A method of performing genetic surveillance, comprising: using
at least one reader-analyzer instrument to perform genetic assay
analysis of a sample obtained from an individual member of a
population and to generate genetic surveillance-related data based
on said analysis; associating spatial information and temporal
information with said genetic surveillance-related data; and
communicating said spatial information and temporal information
associated with said genetic surveillance-related data over a
network using said reader-analyzer instrument to effect said
communication.
27. The method of claim 26 further comprising storing said spatial
information and temporal information with associated said genetic
surveillance-related data in a database as information reflecting
the status of said population.
28. The method of claim 26 further comprising communicating said
spatial information and temporal information associated with said
genetic surveillance-related data to a laboratory response
network.
29. The method of claim 26 further comprising using at least one
portable reader-analyzer instrument to perform genetic assay
analysis of said sample.
30. The method of claim 26 further comprising communicating said
spatial information and temporal information associated with said
genetic surveillance-related data from a first reader-analyzer
instrument to a second reader-analyzer instrument.
31. The method of claim 30 wherein said communication from a first
reader-analyzer instrument to a second reader-analyzer instrument
is effected peer-to-peer.
32. The method of claim 26 further comprising sending control
instructions to said at least one reader-analyzer instrument via
said network.
33. The method of claim 26 further comprising altering the manner
in which said genetic surveillance-related data are generated based
on information received by said reader-analyzer over said
network.
34. The method of claim 26 further comprising performing sample
preparation steps on said sample based on information received over
said network.
35. The method of claim 34 wherein said sample preparation steps
include manipulation of at least one assay.
36. The method of claim 34 wherein said sample preparation steps
include manipulation of at least one assay and wherein said assay
manipulation is performed based on information received over said
network.
37. The method of claim 26 further comprising generating said
surveillance-related data by collecting data identifying a presence
or absence of at least one pathogenic organism.
38. The method of claim 27 wherein said collecting data step is
performed by analyzing at least one target sequence related to the
at least one pathogenic organism.
39. The method of claim 26 further comprising collecting
demographic information from said individual member of a
population.
40. The method of claim 39 wherein said demographic information is
associated with said spatial information, said temporal information
and said genetic surveillance-related data.
41. The method of claim 26 further comprising using said spatial
information, said temporal information and said genetic
surveillance-related data to predict potential danger to the
population.
42. The method of claim 26 further comprising applying a learning
algorithm to said spatial information, said temporal information
and said genetic surveillance-related data to validate data
acquired subsequent to said generation of surveillance-related
data.
43. The method of claim 26 wherein said reader-analyzer instrument
is associated with an automatic sensing device and the sample
obtaining step is performed automatically by said automatic sensing
device.
44. The method of claim 26 wherein said sample obtaining step is
performed by the user of said reader-analyzer instrument.
45. A computer program product for enabling a networked computer
system to perform genetic surveillance, comprising: at least one
computer readable medium bearing software instructions for enabling
predetermined operations, the predetermined operations including:
using at least one reader-analyzer instrument to perform genetic
assay analysis of a sample obtained from an individual member of a
population and to generate genetic surveillance-related data based
on said analysis; associating spatial information and temporal
information with said genetic surveillance-related data; and
communicating said spatial information and temporal information
associated with said genetic surveillance-related data over a
network using said reader-analyzer instrument to effect said
communication.
46. The computer program product of claim 45 wherein at least one
computer readable medium is associated with said reader-analyzer
instrument.
47. The computer program product of claim 45 further comprising
plural computer readable media bearing software instructions for
enabling said predetermined operations, where said plural computer
readable media are associated with plural reader-analyzer
instruments.
48. The computer program product of claim 45 wherein said
communicating said spatial information and temporal information
associated with said genetic surveillance-related data over a
network is effected peer-to-peer.
49. The computer program product of claim 45 wherein said software
instructions further implement a learning algorithm that uses said
spatial information, said temporal information and said genetic
surveillance-related data to validate data acquired subsequent to
said generation of surveillance-related data.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Application No. 60/674,750, filed Apr. 26, 2005; U.S. Provisional
Application No. 60/699,950, filed Jul. 7, 2005; U.S. Provisional
Application No. 60/749,003, filed Dec. 9, 2005; U.S. Provisional
Application No. 60/674,876, filed Apr. 26, 2005; and U.S.
Provisional Application No. 60/696,157, filed Jun. 30, 2005. The
disclosures of the above applications are incorporated herein by
reference.
[0002] All literature and similar materials cited in this
application, including, but not limited to, patents, patent
applications, articles, books, treatises, and internet web pages,
regardless of the format of such literature and similar materials,
are expressly incorporated by reference in their entirety for any
purpose. In the event that one or more of the incorporated
literature and similar materials differs from or contradicts this
application, including but not limited to defined terms, term
usage, described techniques, or the like, this application
controls.
INTRODUCTION
[0003] Currently, improved emergency preparedness and response to
bioterrorism, pathogenic epidemics, and other such public health
emergencies have become of great concern to governments, public
health organizations, and the public at large. Governments, public
health institutions, and other such laboratories are in need of
tools to aid in building networks for determining threats to the
public. Such entities are also in need of rapid, automated and
bidirectional communications and analysis methods to identify
threats and their spatial and temporal patterns for timely
efficient response and preventative measures.
DRAWINGS
[0004] The skilled artisan will understand that the drawings,
described below, are for illustration purposes only. The drawings
are not intended to limit the scope of the present teachings in any
way.
[0005] FIG. 1 is a high level system diagram illustrating a genetic
surveillance and analysis system working in conjunction with a
laboratory response network;
[0006] FIG. 2 is a data flow diagram useful in understanding some
of the principles of the genetic surveillance and analysis
system;
[0007] FIG. 3 is a high level process flow diagram illustrating
components of an a genetic surveillance and analysis system;
[0008] FIG. 4 is an information system that employs a plurality of
reader-analyzer instruments;
[0009] FIG. 5 is a more detailed view further illustrating how an
EpiMonitor software platform may be distributed;
[0010] FIG. 6 illustrates one possible parallel processing timing
diagram implementation for sample preparation;
[0011] FIG. 7 illustrates another possible parallel processing
timing diagram implementation for sample preparation;
[0012] FIG. 8 illustrates an example of an integrated sample and
assay preparation device;
[0013] FIG. 9 is an exploded view of an assay card assembly;
[0014] FIG. 10 is an exploded view of a thermal transfer plate;
[0015] FIG. 11 is a top view of the assay card assembly of FIG.
9;
[0016] FIG. 12 is a perspective view of the thermal transfer plate
of FIG. 10;
[0017] FIG. 13 is a perspective view of a 384-well assay card;
[0018] FIG. 14 illustrates a multiple cartridge portable medical
device;
[0019] FIG. 15 is a perspective view of the cartridge usable by the
portable medical device of FIG. 14;
[0020] FIG. 16 is a perspective view of a handheld reader-analyzer
instrument;
[0021] FIG. 17 is an exploded view of a handheld reader-analyzer
instrument;
[0022] FIG. 18 illustrates an activation of a handheld
reader-analyzer instrument for an analysis;
[0023] FIG. 19 is a perspective view of the inside of an activation
slider of a handheld reader-analyzer instrument;
[0024] FIG. 20 is a flowchart illustrating a triple delta
calculation;
[0025] FIG. 21 is a flowchart illustrating a triple delta
calculation using PCR and microarray generated data sets;
[0026] FIG. 22 is a graphical depiction of an example of a
plurality of classes of information acquired and transmitted to the
EpiMonitor platform;
[0027] FIG. 23 illustrates a data structure and interaction of an
exemplary database;
[0028] FIG. 24 is a functional flow diagram of an exemplary
communication strategy between an EpiMonitor server and an
EpiMonitor client; and
[0029] FIG. 25 is a functional block diagram of EpiMonitor client
and EpiMonitor server components for a genetic surveillance and
analysis system.
DESCRIPTION OF VARIOUS EMBODIMENTS
[0030] While the present teachings are described in conjunction
with various embodiments, it is not intended that the present
teachings be limited to such embodiments. On the contrary, the
present teachings encompass various alternatives, modifications,
and equivalents, as will be appreciated by those of skill in the
art. In the event that one or more of the incorporated references
differs from or contradicts this application, including, but not
limited to, defined terms, term usage, described techniques, or the
like, this application controls.
[0031] In various embodiments, a genetic surveillance and analysis
system 10 shown in FIG. 1 illustrates the system 10 working in
conjunction with a laboratory response network 50. The laboratory
response network 50 has been illustrated as a three-tiered,
pyramidal, hierarchical arrangement of laboratories. However, the
genetic surveillance and analysis system 10 is not limited to
operating only with networks configured in this fashion. The
hierarchical pyramid relationship is illustrated to provide a
better understanding of how a genetic surveillance and analysis
system 10, according to the present teachings, might be integrated
with a contemporary laboratory response network 50, such as that
promulgated by the U.S. Department of Health and Human Services'
(HHS) Centers for Disease Control and Prevention (CDC).
[0032] For example, in 1999, the CDC established a Laboratory
Response Network (LRN) 50. The LRN's purpose is to coordinate a
network of laboratories that can respond to biological and chemical
terrorism. The LRN 50 has grown since it was first established, and
now includes a wide variety of different types of laboratories,
such as state and local public health laboratories, veterinary
laboratories, military laboratories, and international
laboratories.
[0033] The participating laboratories are designated as either
national, reference, or sentinel, depending on each individual
laboratory's function within the LRN 50. Sentinel labs, at the
broad base of the pyramid, represent the thousands of hospital- and
clinic-based labs that have direct contact with patients. In an
unannounced or covert terrorist attack, specimens provided by
patients during routine care might indicate the onset of a
bioterrorist attack. Similarly, specimens from patients visiting
hospitals and clinics may signal the spread of a disease. Sentinel
labs are thus often the first facility to spot a suspicious
specimen. The sentinel lab's responsibility is to refer that
specimen to the proper reference lab.
[0034] Reference labs, also referred to as confirmatory reference
labs, are equipped to perform tests to detect and confirm the
presence of a threat agent (including those related to bioterrorism
and epidemics). These labs ensure a timely local response in the
event of a terrorist incident or epidemic. Rather than having to
rely on confirmation from national labs at the CDC, reference labs
are capable of producing conclusive results upon which public
health authorities are able to act. In some cases, unique abilities
may be required, such as handling a highly infectious agent or
identifying and analyzing specific agent strains. This is the
function of the national laboratories, which are positioned at the
narrow top of the pyramid.
[0035] The named laboratory response network 50 might suggest that
an integrated computer network joins the participating
laboratories. Although computer networks and telecommunication
networks, such as the Internet and the public telephone
infrastructure, are utilized, there is currently no unified,
dedicated computer network for the collection and analysis of
aggregated genetic data. The genetic surveillance and analysis
system 10 can serve this function, linking together participating
members of the LRN and may also link other public health, safety,
and military organizations, which may have their own separate
computer networks.
[0036] In various embodiments, the genetic surveillance and
analysis system 10 may be a population security and epidemiological
analysis system. In various embodiments, epidemiology can be the
study of the distribution and determinants of disease frequency in
human populations. This can include two main areas of
investigation, one, the study of distribution and disease and two,
the search for the determinants (causes of the disease and its
distribution). The first area can include describing the
distribution of health status in terms of age, gender, race,
geography, time, weather conditions, and other demographics. The
second area can involve an explanation of the patterns into the
disease distribution in the terms of causal factors.
[0037] Epidemiology can include the search for concordance between
known and suspected cause of a disease, and known patterns of
distribution of disease, or use of these patterns to postulate
elements of the environment that should be investigated for
possible causal roles. An excessive frequency, or even the mere
occurrence of biological contaminants in environmental or
biological samples, may be a feature of many infectious and
non-infectious diseases, as well as diseases known to be associated
with microorganisms or pathogens. Identifying the frequency of a
particular disease as being excessive may be developed by following
its frequency over time, by comparing its frequency in different
places, or by comparing its frequencies among subgroups in a single
population at a particular time. Such identification may include
identifying the excessive frequency that comes about in a short
period of time and in a narrowly defined geographic area. Other
terms that may relate to excessive frequency include epidemic,
pandemic, incidence, and prevalence. In addition to frequency, mere
occurrence of biological contaminants in environmental or
biological samples may also be of concern.
[0038] The genetic surveillance and analysis system 10 can utilize
genetic assay technology capable of detecting and analyzing a
variety of different strains of bacteria, viruses, and pathogens.
As will be more fully explained below, genetic assay technology can
be deployed using an assortment of different types of
reader-analyzer instruments 176 that can be adapted for
bidirectional communication through an integrating software
platform named EpiMonitor.
[0039] The system 10 supports a plurality of reader-analyzer
instruments 176 of different sizes and capabilities, including
those ranging from sophisticated laboratory instruments 52 to
portable multi-cartridge units (a portable instrument 54) to small,
shirt-pocket-sized units such as handheld instruments 56-1, 56-2,
and 56-3. The reader-analyzer instruments 176 analyze samples,
whether taken from a patient or from the environment, and have
varying processing ability to process the results. In various
embodiments, at least some of the reader-analyzer instruments 176
are capable of peer-to-peer (P2P) interaction with one another, as
illustrated diagrammatically at 58 between handheld instruments
56-2 and 56-3. In various embodiments, at the base of the pyramid,
sentinel laboratories may employ primarily handheld 56 and portable
instruments 54 and, as such, these instruments may be present in
numbers on the order of thousands to tens of thousands to
accommodate the large number of sentinel laboratories. In various
embodiments, the next layer of the pyramid, reference laboratories,
may employ portable instruments 54 and more powerful laboratory
instruments 52 and, as such, hundreds or thousands of these
instruments may be present. In various embodiments, national
laboratories may employ hundreds of laboratory instruments 52.
[0040] In various embodiments, the laboratory instrument 52 can be
implemented using any one of a variety of different reader-analyzer
instruments 176, such as genetic assay analysis platforms. Suitable
platforms include the model 7500 fast real-time PCR system and the
7900 HT fast real-time PCR system, both available from Applied
Biosystems, Foster City, Calif. Other genetic assay analysis
platforms can also be used such as, for example, PCR instruments
commercially available from Bio Rad, Strategene, Roche Applied
Science, Techne Quantica, and Cepheid, as well as, PCR instruments
that operate using isothermal methods. Still, examples of other
genetic analysis platforms that may be useful herein include
microarray technology such as those commercially available from
Applied Biosystems, Affymetrix, Agilent, Illumina, and Xeotron.
Typically, the laboratory instrument 52 would be deployed, for
example, in hospital laboratory, at a university, or in a
government public health laboratory, which may or may not be a
participating member of the laboratory response network.
[0041] In various embodiments, a reader-analyzer instrument 176 can
be portable instrument 54, which can be physically smaller than the
laboratory instrument 52 to make it suitable for deployment in a
doctor's office or small clinic. It can be connected to a computer,
eliminating the need for on-board processing. The portable
instrument 54 is generally capable of analyzing fewer samples for
fewer target sequences than the laboratory instrument 52.
[0042] In various embodiments, a reader-analyzer instrument 176 can
be a handheld instrument 56 and may represent an economical end of
the instrument spectrum. In various embodiments, the handheld
instrument 56 may be of convenient, portable size (e.g.,
approximately the size of a deck of playing cards). It can be
configured to detect a specific disease such as multidrug-resistant
tuberculosis. The handheld instrument 56 can be capable of
analyzing samples obtained in a variety of different forms
including sputum samples, blood samples, and the like. The handheld
instrument 56 can be battery powered and can include an embedded
internal controller so that no external computer is required.
[0043] Reader-analyzer instruments 176 that may be used in the
system are not limited to such instruments that can perform PCR.
Any instrument that can provide data on the analysis of pathogens
such as identifying a strain of bacteria, fungi, virus, and the
like, may be integrated into the genetic surveillance and analysis
system 10. Examples of other such reader-analyzer instruments 176
include mass spectrometers, which may include the use of MADLI,
chromatography, pyrolization, and other such techniques for
introducing a sample, DNA micro arrays such as, for example, those
commercially available from Affymetrix, Agilent, Illumina, Xeotron,
and Applied Biosystems, as well as those systems that may be
developed in-house by a particular laboratory, and may also include
instruments capable of detection using an antibody such as ELISA,
and the like.
[0044] While the instruments described above are adapted for
processing a sample obtained from a human, plant or animal, the
genetic surveillance and analysis system 10 can be readily adapted
to utilize other types of input devices, such as environmental
sensors. Environmental sensors such as, for example, air samplers
60, water samplers 62 for bodies of water (e.g., reservoirs, tanks,
lakes, etc.), as well as other sampling configurations, can be
readily adapted for use with the present teachings. The
environmental samplers 60, 62 can be adapted to analyze samples
taken from strategic locations. The results obtained by analyzing
those samples can be integrated with the data being collected by
reader-analyzer instruments 176 via the EpiMonitor software
platform 100, described more fully below.
[0045] Referring now to FIG. 2, the genetic surveillance and
analysis system 10 utilizes an EpiMonitor software platform 100
that integrates various reader-analyzer instruments 176 within a
database system. The EpiMonitor software platform 100 organizes and
supports bidirectional communication among a collection 102 of
reader-analyzer instruments 176, each analyzing samples of genetic
data.
[0046] The collection 102 provides reaction data and contextual
data to a queue/security server 104 of the EpiMonitor software
platform 100. In various embodiments, the queue/security server 104
can establish secure connections with the collection 102 of
reader-analyzer instruments 176, verify that data has been received
uncorrupted, and queue received data for processing. The
queue/security server 104 can communicate with the collection 102
of reader-analyzer instruments 176 through a variety of
intermediaries, including the public Internet, Virtual Private
Networks, and private networks. The queue/security server 104 can
also communicate information, such as sample preparation
instructions, to the collection 102 of reader-analyzer instruments
176.
[0047] The queue/security server 104 provides data to an
observation/analytical server 106 of the EpiMonitor software
platform 100. In various embodiments, the observation/analytical
server 106 can pre-process data, perform rules-based analysis, and
discern data trends. Together, the servers 104 and 106 validate,
collect, and analyze data, as described in more detail below. The
servers 104 and 106 can be implemented as stand-alone servers, as a
single unified server, or as a distributed system of multiple
servers. In addition, various functions of the servers 104 and 106
can be distributed to the collection 102 of reader-analyzer
instruments 176 or to computers associated with any of the
collection 102 of reader-analyzer instruments 176.
[0048] The collection 102 of reader-analyzer instruments 176
depicted includes a portable instrument 54, a laboratory instrument
52, a handheld instrument 56-1, a handheld instrument 56-4, which
communicates with the queue/security server 104 via a stand-alone
computer 114, and environmental samplers 60, 62. The
observation/analytical server 106 can store reaction and contextual
data obtained from the collection 102 of reader-analyzer
instruments 176 into a suitable database. The
observation/analytical server 106 can provide access to this
database via an HTML (hypertext markup language) web interface to a
remote client 120-1. A web browser within the remote client 120-1
can display observations and analysis from the
observation/analytical server 106. Examples of web browser displays
include "Biomarker: ABC, Incidence during 1/2003-12/2004: XX,
Prevalence during 1/2003-12/2004: XY," and "Date/Time: Nov. 19,
2004, 8:00 AM, Region: Northern California, Biomarker: ABC, Current
Incidence: XX, Current Prevalence: XY." Access to the database can
also be provided programmatically via web services, such as to a
second remote client 120-2.
[0049] The observation/analytical server 106 can integrate data
from sources other than the collection 102 of reader-analyzer
instruments 176. To convert external data sources into a standard
form that the observation/analytical server 106 can process, the
EpiMonitor software platform 100 includes, in various embodiments,
a data integration server 108. The data integration server 108
communicates with contextual data stores 122. Contextual data
stores 122 can include medical records, such as an electronic
medical record server 124 located at hospital A. Contextual data
stores 122 can also include national retail information 126, a
demographic/census data store 128, such as provided by the U.S.
Census Bureau, and a data store 130 of the CDC Public Health
Information Network.
[0050] FIG. 3 illustrates a functional flow diagram for a simple
genetic surveillance and analysis system 10 implementation. One or
more samples 170 are taken from human, plant or animal subjects (or
from other sources such as environmental sampler units). The
samples 170 are processed, for example, using a stand-alone
Integrated Sample and Assay Preparation (ISAP) module 172. In this
regard, the user provides the sample 170 as an input to the ISAP
module 172, and the ISAP module 172 provides a standardized card,
such as a microfluidic card 174, as its output. If desired, the
ISAP module 172 can be integrated with the EpiMonitor software
platform 100 and thus provide communication capability. Such
communication capability and integration into the EpiMonitor
software platform 100 allows the operating parameters of the ISAP
module 172 to be updated or controlled remotely to conform its
operation to rapidly changing analysis parameters and assays.
[0051] Once the microfluidic card 174 has been filled with properly
prepared sample 170 and PCR reagents including at least one primer
probe set, the card 174 can be then inserted into a reader-analyzer
instrument 176. In some embodiments, reader-analyzer instrument 176
can be a genetic analysis platform such as, for example, a PCR
system. In various embodiments, reader-analyzer instrument 176 may
be any of those illustrated in FIG. 1 as instruments 52, 54, and
56. In various embodiments, the reader-analyzer instrument 176 may
be capable of performing reverse transcription PCR (RT-PCR),
further described below, either simultaneously with PCR or as a
separate step.
[0052] In various embodiments, the output of the reader-analyzer
instrument 176, either as raw data or processed data, can be
processed by EpiMonitor software 100 and information extracted from
this analysis can be stored in a suitable database 180. The
database 180 can be at a central location or it can be distributed
across multiple locations. In various embodiments, the EpiMonitor
software 100 can mediate bidirectional communication between the
components that make up the system such as, for example, the
reader-analyzer instrument 176 and database 180, in some
implementations also the ISAP module 172 and microfluidic card
174). Although a single data flow has been illustrated (from sample
170 to database 180), similar data flows can occur concurrently at
multiple locations distributed throughout the world. The EpiMonitor
software 100 coordinates this data gathering among a potentially
large number of instruments 176 and ensures that the information
extracted from a plurality of reader-analyzer instruments 176 can
be stored in the database 180 in a consistent manner that
facilitates further operations on the collected information such
as, for example, statistical analysis.
[0053] FIG. 4 illustrates a flowchart of a parallel workflow
implementation. In the workflow illustrated in FIG. 3, a single
ISAP module 172 supplied microfluidic cards 174 serially to one
reader-analyzer instrument 176. In FIG. 4, a single ISAP module 172
prepares a plurality of microfluidic cards 174 for a plurality of
reader-analyzer instruments 176-1, 176-2, and 176-3, operating in
parallel. This arrangement may be most useful when an analysis uses
a short sample and assay preparation time by the ISAP module 172 to
prepare a microfluidic card 174 as compared to the time required
for analyzing the microfluidic card 174 by one of the plurality of
reader-analyzer instrument 176. As such, a single ISAP module 172
can supply a plurality of reader-analyzer instruments 176 without
delays.
[0054] Referring to FIG. 5, each of the individual devices and
instruments (ISAP module 172, microfluidic card 174,
reader-analyzer instruments 176-1 and 176-2, and database 180) can
be embedded or associated components of the EpiMonitor software
platform 100. The reader-analyzer instruments 176-1 and 176-2 can
establish a peer-to-peer relationship, where they communicate
information between one another or through an associated network.
The interconnecting lines (without arrowheads) of FIG. 5 represent
communication pathways for data and/or control instructions made
possible by the EpiMonitor software platform 100. The directed
arrows show relationships among the interconnected components.
Thus, as illustrated, the ISAP module 172 produces the microfluidic
card 174. In various embodiments, the microfluidic card 174 can be
analyzed by reader-analyzer 176-1, which communicates peer-to-peer
with reader-analyzer 176-2. The reader-analyzer 176-2 reports to
the database 180. The relationships among components, and the
functions that they perform, are managed by the EpiMonitor software
platform 100. The EpiMonitor software platform 100 can include
components associated with the LRN 50, or with other networks 190,
to coordinate analysis and response capabilities.
[0055] FIGS. 6 and 7 each illustrate a possible parallel processing
timing diagram. Referring to FIG. 6, the ISAP module 172 produces a
first microfluidic card 174, which is then processed by the first
reader-analyzer instrument 176-1. While processing is taking place
within the first instrument 176-1, the ISAP module 172 prepares a
second microfluidic card 174 so that it will be ready for
processing by the instrument 176-1 once the first assay processing
is completed. In a second parallel processing arrangement,
illustrated in FIG. 7, the ISAP module 172 successively prepares
three different assays (assay 1, assay 2, assay 3), which are
individually processed by three different reader-analyzer
instruments 176-1, 176-2, and 176-3.
[0056] In each of the reader-analyzer instruments 176 described
above, the sample can be tested against a specific assay panel. In
various embodiments, such a panel can include desired reagents
(e.g., enzymes, primers, probes, etc., when using PCR as discussed
below) that are used to perform an assay for target sequences of
interest. In an exemplary full-featured system application, the
reagents can include a compound set for detecting a plurality of
selected bacterial spores, gram-positive or gram-negative bacteria,
and/or viruses (whether DNA or RNA-based). A combination of these
target sequences can define an assay panel particularly useful for
a particular diagnosis.
[0057] In various embodiments, one example of such an assay panel
can be an upper respiratory panel that includes several of the most
common bacterial and viral pathogens responsible for, or associated
with, upper respiratory infectious disease as shown in Table 1. The
exemplary assay panel includes twenty-one distinct pathogens and
five controls (GAPDH, IPC1, IPC10, IPC0.1, and buffer). In this
example, six of the twenty-one pathogens are included a second time
with the incorporation of an internal positive control (IPC).
TABLE-US-00001 TABLE 1 Assay Name Pathogen B-pert/holm/1000x
Bordetella pertussis + 1000x IPC C-pneu/100x Chlamydia pneumoniae +
100x IPC L-pneu/10x Legionella pneumophila + 10x IPC M-pneu/1x
Mycoplasma pneumoniae + 1x IPC C-botu/0.1x Clostridium botulinum +
0.1x IPC S-pneu/0.01x Streptococcus pneumoniae + 0.01x IPC M-cata
Moraxella catarrhalis N-meni Neisseria meningitidis H-infl
Haemophilus influenzae (Type B) S-aure Stapphylococcus Aureus GAPDH
GAPDH control (for QC purposes) M-tube Mycobacterium tuberculosis
RSV-A Respiratory Syncytial Virus (RSV) A RSV-B Respiratory
Syncytial Virus (RSV) B Hadv-1-2-5-6 Human AdV (Types 1, 2, 5, 6)
EntV Enterovirus SARS3-CoV SARS-CoV Metapneu-V Metapneumovirus
Infl-A Influenza A Infl-B Influenza B CMV Cytomegalovirus PIV
Parainfluenza Virus B-pert/holm Bordetella pertussis C-pneu
Chlamydia pneumoniae L-pneu Legionella pneumoniae M-pneu Mycoplasma
pneumoniae C-botu Clostridium Botulinum S-pneu Streptococcus
pneumoniae IPC1 Internal Positive control IPC10 Internal Positive
control IPC0.1 Internal Positive Control Buffer Negative
Control
[0058] Multiple configurations of such assay panels can be created
and other panels can be configured as desired. The number of target
sequences in the panel may depend on factors, including the nature
of the panel and the implementation of a specific instrumentation
platform of reader-analyzer 176. In one exemplary application, a
laboratory instrument 52 might perform between approximately 10-20
assays while a handheld instrument 56 may perform fewer, possibly
just one assay. In addition to an assay panel that includes
multiple pathogenic species, the assay panel can include multiple
strains of a particular pathogen for purposes such as identifying
potential drug resistances, thereby providing a potential guide to
effective therapy. The assay panel can also contain multiple DNA
targets or other target sequences for a single pathogen to
potentially improve specificity in detection. Other potential assay
panel combinations/formulations can be devised for numerous useful
purposes. For example, an assay panel could include avian flu H5:N1
or a group of strains of pathogenic E. Coli which could include
0157:H7.
[0059] In various embodiments, to create an assay panel, an ISAP
module 172, such as that illustrated in FIG. 8, can be used. The
ISAP module 172 can accept one or more microfluidic cards 174 into
a loading tray 214. A lid 216 of the ISAP module 172 can be raised
so that reagent holding devices 218 can be removed and inserted.
These reagent holding devices 218 provide the ISAP module 172 with
a supply of reagents that are selectively introduced to the
microfluidic card 174.
[0060] The ISAP module 172 can accept samples 170 from the
environment or from a patient, such as nasal, throat, and/or
nasopharyngeal swabs. The ISAP module 172 treats samples of liquid
expressed from these swabs to facilitate lysis and ready the sample
for purification. The nucleic acids produced are highly pure and
free of cross-contamination. Purification reagents can also be
added manually to the microdfluidic card 174 by the ISAP module 172
operator. An optional graphical user interface incorporated to the
ISAP module 172 can provide easy access to pre-programmed methods,
and affords the ability to create, edit, and store custom
purification routines. It should also be appreciated that the
present teachings may be used in connection with microfluidic cards
174 and other principles, such as set forth in U.S. Pat. Nos.
6,124,138 and 6,126,899.
[0061] Table 2 depicts an exemplary layout of a microfluidic card
174, given the pathogen panel of Table 1. There are sixteen rows
(A-P), and twenty-four columns (1-24), yielding 384 (16*24=384)
wells. Because each target sequence/control can be repeated at
least eight times in the card layout, this card can simultaneously
process eight samples. TABLE-US-00002 TABLE 2 1 2 3 4 5 6 7 8 9 10
A B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure B B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure C
B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure D B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure E
B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure F B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure G
B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure H B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure I
B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure J B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure K
B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure L B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure M
8-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure N B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure O
B-pert/holm/1000x C-pneu/100x L-pneu/10x M-pneu/1x C-botu/0.1x
S-pneu/0.01x M-cata N-meni H-infl S-aure P B-pert/holm C-pneu
L-pneu M-pneu C-botu S-pneu M-cata N-meni H-infl S-aure 11 12 13 14
15 16 17 18 19 20 21 22 23 24 A GAPDH M-tube RSV-A RSV-B
Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV IPC10
IPC1 B GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL C GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 D GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL E GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 F GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL G GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 H GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL I GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 J GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL K GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 L GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL M GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 N GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL O GAPDH M-tube RSV-A
RSV-B Hadv-1-2-5-6 EntV SARS3-CoV Metapneu-V Infl-A Infl-B CMV PIV
IPC10 IPC1 P GAPDH M-tube RSV-A RSV-B Hadv-1-2-5-6 EntV SARS3-CoV
Metapneu-V Infl-A Infl-B CMV PIV IPC0.1 BL
[0062] In various embodiments, microfluidic card 174 may be other
than the 384-well microfluidic card 174 layout and filling systems
and/or microfluidics can also be used in implementing loading
samples and reagents to the microfluidic card 174. By way of
non-limiting illustration, a centrifugal filling system and
microfluidic card system described in U.S. Pat. No. 6,627,159 can
be used to fill the card from the loading ports. An exemplary
centrifuge can be the Sorvall.RTM. Legend T Centrifuge with a
4-Place Swinging Bucket Rotor twist-on fixture, which does not
require a tool to secure it to the centrifuge.
[0063] Referring now to FIG. 9, an example of a microfluidic card
174, which may be injection molded, serves as the base for
microfluidic card assembly 246. A gas-permeable membrane 244 can be
placed onto the microfluidic card 174. Above the membrane 244 can
be situated a thin film cover layer 242, including vent holes 248.
Referring now to FIG. 10, a thermal transfer plate 260 can be
demonstrated. The thermal transfer plate 260 can be interfaced with
the microfluidic card assembly 246 of FIG. 9. The thermal transfer
plate 260 seals inlet and outlet channels of the microfluidic card
assembly 246 to isolate reaction chambers 264. Circular thermal
dies 262 (which have an internal diameter of 2.5 mm in various
embodiments) of the thermal transfer plate 260 create a heat seal
around each reaction chamber 264.
[0064] FIG. 11 illustrates a top view of the microfluidic card
assembly 246. The gas permeable membrane 244 holds up liquid during
filling. A vent hole 248 can be located above the gas permeable
membrane 244. A reaction chamber 264 and a sample inlet port 282 is
shown, into which samples can be loaded from an ISAP module 172, or
manually with a syringe. In various embodiments, the microfluidic
card 174 can be loaded with a volume of 100 .mu.L, and each well
has a volume of 1.5 .mu.L.
[0065] FIG. 12 illustrates a perspective view of the thermal
transfer plate 260 of FIG. 10. Each of the 384 thermal transfer
dies 262 isolates reaction chambers 264 (not shown) in the
microfluidic card 174. The size of the circular dies 262 depends
upon reaction chamber 264 size, but in various embodiments, can be
about a 2.5 mm inside diameter. Referring now to FIG. 15, a
perspective view of the microfluidic card 174 comprising
microchannels within the microfluidic card 174 can be routed to
create any arbitrary layout desired. In various embodiments, the
card can be about 85.7 mm in width and about 127.0 mm in
length.
[0066] In various embodiments, microfluidic card 174 themselves can
be provided with embedded processor capability. For example, the
microfluidic card 174 can be provided with one or more thermal
sensors, thereby allowing actual thermal data to be collected by
the reader-analyzer instrument 176. In various embodiments, the
EpiMonitor software platform 100 can supply the microfluidic card
174 with data, which can be used in the event that subsequent tests
or quality control procedures may be needed. Such a capability can
be provided by including a SmartCard, RFID, or other such
semiconductor device mounted in the microfluidic card 174. In
various embodiments, microfluidic card 174 can also communicate
with the rest of the system 10 using the EpiMonitor software
platform 100. In various embodiments, a reader-analyzer instrument
176 can perform PCR on prepared assay panels, and detect resulting
fluorescence. The reader-analyzer instrument 176 can also process
this data to estimate the number of copies of a target sequence
initially present in a sample, or whether a particular target
sequence may be present. In various embodiments, the
reader-analyzer instrument 176 can be controlled by a computer or
laptop, so that processing power can be A connection between the
reader-analyzer instrument 176 and the computer can be wired or
wireless, and the connection between the computer and the server
hosting EpiMonitor software platform 100 may be wired or wireless.
In various embodiments, reader-analyzer instrument 176 is connected
to a computer that can be part of a client server system and, in
various embodiments, at least part of the EpiMonitor software 100
host at a server may be downloaded to the chart for numbering
crunching and/or data analysis at the client.
[0067] In various embodiments, a Fast real-time PCR option can give
real-time PCR results in a 96-well format in approximately 35
minutes, inclusive of sample preparation. In various embodiments,
reader-analyzer instruments 176 used for the amplification of
polynucleic acids, such as by PCR. Briefly, by way of background,
PCR can be used to amplify a sample of target Deoxyribose Nucleic
Acid (DNA) for analysis. Typically, the PCR reaction involves
copying the strands of the target DNA and then using the copies to
generate additional copies in subsequent cycles. Each cycle doubles
the amount of the target DNA present, thereby resulting in a
geometric progression in the number of copies of the target DNA.
The temperature of a double-stranded target DNA is elevated to
denature the DNA, and the temperature is then reduced to anneal at
least one primer to each strand of the denatured target DNA. In
various embodiments, the target DNA can be a cDNA.
[0068] In various embodiments, primers are used as a pair--a
forward primer and a reverse primer--and can be referred to as a
primer pair or primer set. In various embodiments, the primer set
comprises a 5' upstream primer that can bind with the 5' end of one
strand of the denatured target DNA and a 3' downstream primer that
can bind with the 3' end of the other strand of the denatured
target DNA. Once a given primer binds to the strand of the
denatured target DNA, the primer can be extended by the action of a
polymerase. In various embodiments, the polymerase can be a
thermostable DNA polymerase, for example, a Taq polymerase. The
product of this extension, which sometimes may be referred to as an
amplicon, can then be denatured from the resultant strands and the
process can be repeated. Temperatures suitable for carrying out the
reactions are well known in the art. Certain basic principles of
PCR are set forth in U.S. Pat. Nos. 4,683,195, 4,683,202,
4,800,159, and 4,965,188, each issued to Mullis et al.
[0069] In various embodiments, PCR can be conducted under
conditions allowing for quantitative and/or qualitative analysis of
one or more target DNA. Accordingly, detection probes can be used
for detecting the presence of the target DNA in an assay. In
various embodiments, the detection probes can comprise physical
(e.g., fluorescent) or chemical properties that change upon binding
of the detection probe to the target DNA. Various embodiments of
the present teaching can provide real time fluorescence-based
detection and analysis of amplicons as described, for example, in
PCT Publication No. WO 95/30139 and U.S. patent application Ser.
No. 08/235,411.
[0070] In various embodiments, a sample can be analyzed as a
homogenous polynucleotide amplification assay, for coupled
amplification and detection, wherein the process of amplification
generates a detectable signal and the need for subsequent sample
handling and manipulation to detect the amplified product is
minimized or eliminated. Homogeneous assays can provide for
amplification that is detectable without opening a sealed well or
further processing steps once amplification is initiated. Such
homogeneous assays can be suitable for use in conjunction with
detection probes. For example, in various embodiments, the use of
an oligonucleotide detection probe, specific for detecting a
particular target DNA can be included in an amplification reaction
in addition to a DNA binding agent of the present teachings.
[0071] Homogenous assays among those useful herein are described,
for example, in commonly assigned U.S. Pat. No. 6,814,934. In
various embodiments, methods are provided for detecting a plurality
of targets. Such methods include those comprising forming an
initial mixture comprising an analyte sample suspected of
comprising the plurality of targets, a polymerase, and a plurality
of primer sets. In various embodiments, each primer set comprises a
forward primer and a reverse primer and at least one detection
probe unique for one of the plurality of primer sets. In various
embodiments, the initial mixture can be formed under conditions in
which one primer elongates if hybridized to a target.
[0072] In various embodiments, reagents are provided comprising a
master mix comprising at least one of catalysts, initiators,
promoters, cofactors, enzymes, salts, buffering agents, chelating
agents, and combinations thereof. In various embodiments, reagents
can include water, a magnesium catalyst (such as MgCl2),
polymerase, a buffer, and/or dNTP. In various embodiments, specific
master mixes can comprise AmpliTaq.RTM. Gold PCR Master Mix,
TaqMan.RTM. Universal Master Mix, TaqMan.RTM. Universal Master Mix
No AmpErase.RTM. UNG, Assays-by-Design.sup.SM, Pre-Developed Assay
Reagents (PDAR) for gene expression, PDAR for allelic
discrimination and Assays-On-Demand.RTM., (all of which are
marketed by Applied Biosystems). However, the present teachings
should not be regarded as being limited to the particular
chemistries and/or detection methodologies recited herein, but may
employ Taqman.RTM.; Invader.RTM.; Taqman Gold.RTM.; protein,
peptide, and immuno assays; receptor binding; enzyme detection; and
other screening and analytical methodologies.
[0073] In various embodiments, a solid support such as, for
example, a microplate or a microfluidic card 174, can be covered
with a sealing liquid prior to performance of analysis or reaction
of assay. For example, in various embodiments, a sealing liquid can
be applied to the surface of a microplate comprising reaction spots
comprising an assay or for amplification of polynucleotides. In
various embodiments, a sealing liquid can be a material which
substantially covers the material retention regions (e.g., reaction
spots) on the microplate so as to contain materials present in the
material retention regions, and substantially prevent movement of
material from one reaction region to another reaction region on the
substrate. In various embodiments, the sealing liquid can be any
material which is not reactive with assay under normal storage or
usage conditions. In various embodiments, the sealing liquid can be
substantially immiscible with assay.
[0074] In various embodiments, the sealing liquid can be
transparent, have a refractive index similar to glass, have low or
no fluorescence, have a low viscosity, and/or be curable. In
various embodiments, the sealing liquid can comprise a flowable,
curable fluid such as a curable adhesive selected from the group
consisting of: ultra-violet-curable and other light-curable
adhesives; heat, two-part, or moisture activated adhesives; and
cyanoacrylate adhesives. In various embodiments, the sealing liquid
can be selected from the group consisting of mineral oil, silicone
oil, fluorinated oils, and other fluids that are substantially
non-miscible with water. In various embodiments, the sealing liquid
can be a fluid when it is applied to the surface of the microplate
and in various embodiments, the sealing liquid can remain fluid
throughout an analytical or chemical reaction using the microplate.
In various embodiments, the sealing liquid can become a solid or
semi-solid after it is applied to the surface of the
microplate.
[0075] As should be appreciated from the discussion herein, the
present teachings can find utility in a wide variety of
amplification methods, such as PCR, Reverse-Transcription PCR
(RT-PCR), Ligation Chain Reaction (LCR), Nucleic Acid Sequence
Based Amplification (NASBA), self-sustained sequence replication
(3SR), strand displacement activation (SDA), Q (3replicase) system,
isothermal amplification methods, and other known amplification
method or combinations thereof. Additionally, the present teachings
can find utility for use in a wide variety of analytical
techniques, such as ELISA; DNA and RNA hybridizations; antibody
titer determinations; gene expression; recombinant DNA techniques;
hormone and receptor binding analysis; and other known analytical
techniques. Still further, the present teachings can be used in
connection with such amplification methods and analytical
techniques using not only spectrometric measurements, such as
absorption, fluorescence, luminescence, transmission,
chemiluminescence, and phosphorescence, but also colorimetric or
scintillation measurements or other known detection methods.
[0076] In various embodiments, the reagents can comprise first and
second oligonucleotides effective to bind selectively to adjacent,
contiguous regions of target DNA and that can be ligated covalently
by a ligase enzyme or by chemical means. Such oligonucleotide
ligation assays (OLA) are described, for example, in U.S. Pat. No.
4,883,750; and Landegren, U., et al., Science 241:1077 (1988). In
various embodiments, a detection probe comprises a moiety that
facilitates detection of a nucleic acid sequence, and in various
embodiments, quantifiably. In various embodiments, a detection
probe can comprise, for example, a fluorophore such as a
fluorescent dye, a hapten such as a biotin or a digoxygenin, a
radioisotope, an enzyme, or an electrophoretic mobility modifier.
In various embodiments, the level of amplification can be
determined using a fluorescently labeled oligonucleotide. In
various embodiments, a detection probe can comprise a fluorophore
further comprising a fluorescence quencher.
[0077] In various embodiments, a detection probe can comprise a
fluorophore and can be, for example, a 5'-exonuclease assay probe
such as a TaqMan.RTM. probe (marketed by Applied Biosystems), a
stem-loop Molecular Beacon (see, e.g., U.S. Pat. Nos. 6,103,476 and
5,925,517, Nature Biotechnology 14:303-308 (1996); Vet et al., Proc
Natl Acad Sci USA. 96:6394-6399 (1999)), a stemless or linear
molecular beacon (see., e.g., PCT Patent Publication No. WO
99/21881), a Peptide Nucleic Acid (PNA) Molecular Beacon.TM. (see,
e.g., U.S. Pat. Nos. 6,355,421 and 6,593,091), a linear PNA
Molecular Beacon (see, e.g., Kubista et al., SPIE 4264:53-58
(2001)), a flap endonuclease probe (see, e.g., U.S. Pat. No.
6,150,097), a Sunrise.RTM./Amplifluor.RTM. probe (see, e.g., U.S.
Pat. No. 6,548,250), a stem-loop and duplex Scorpion.TM. probe
(see, e.g., Solinas et al., Nucleic Acids Research 29:E96 (2001),
and U.S. Pat. No. 6,589,743), a bulge loop probe (see, e.g., U.S.
Pat. No. 6,590,091), a pseudo knot probe (see, e.g., U.S. Pat. No.
6,589,250), a cyclicon (see, e.g., U.S. Pat. No. 6,383,752), an MGB
Eclipse.TM. probe (Marketed by Epoch Biosciences), a hairpin probe
(see, e.g., U.S. Pat. No. 6,596,490), a peptide nucleic acid (PNA)
light-up probe, a self-assembled nanoparticle probe, or a
ferrocene-modified probe described, for example, in U.S. Pat. No.
6,485,901; Mhlanga et al., Methods 25:463-471 (2001); Whitcombe et
al., Nature Biotechnology 17:804-807 (1999); Isacsson et al.,
Molecular Cell Probes 14:321-328 (2000); Svanvik et al., Anal.
Biochem. 281:26-35 (2000); Wolffs et al., Biotechniques 766:769-771
(2001), Tsourkas et al., Nucleic Acids Research 30:4208-4215
(2002); Riccelli et al., Nucleic Acids Research 30:4088-4093
(2002); Zhang et al., Sheng Wu Hua Xue Yu Sheng Wu Li Xue Bao
(Shanghai) (Acta Biochimica et Biophysica Sinica) 34:329-332
(2002); Maxwell et al., J. Am. Chem. Soc. 124:9606-9612 (2002);
Broude et al., Trends Biotechnol. 20:249-56 (2002); Huang et al.,
Chem Res. Toxicol. 15:118-126 (2002); Yu et al., J. Am. Chem. Soc
14:11155-11161 (2001).
[0078] In various embodiments, a detection probe can comprise a
sulfonate derivative of a fluorescent dye, a phosphoramidite form
of fluorescein, or a phosphoramidite forms of CY5. Detection probes
among those useful herein are also disclosed, for example, in U.S.
Pat. Nos. 5,188,934, 5,750,409, 5,847,162, 5,853,992, 5,936,087,
5,986,086, 6,020,481, 6,008,379, 6,130,101, 6,140,500, 6,140,494,
6,191,278, and 6,221,604. Energy transfer dyes among those useful
herein include those described in U.S. Pat. Nos. 5,728,528,
5,800,996, 5,863,727, 5,945,526, 6,335,440, 6,849,745, U.S. Patent
Application Publication No. 2004/0126763 A1, PCT Publication No. WO
00/13026A1, PCT Publication No. WO 01/19841A1, U.S. Patent
Application Ser. No. 60/611,119, filed Sep. 16, 2004, and U.S.
patent application Ser. No. 10/788,836, filed Feb. 26, 2004. In
various embodiments, a detection probe can comprise a fluorescence
quencher such as a black hole quencher (marketed by Metabion
International AG), an Iowa Black.TM. quencher (marketed by
Integrated DNA Technologies), a QSY quencher (marketed by Molecular
Probes), and Dabsyl and Eclipse.TM. Dark Quenchers (marketed by
Epoch).
[0079] In various embodiments, amplified sequences can be detected
in double-stranded form by a detection probe comprising an
intercalating or a crosslinking dye, such as ethidium bromide,
acridine orange, or an oxazole derivative, for example, SYBR
Green.RTM. (marketed by Molecular Probes, Inc.), which exhibits a
fluorescence increase or decrease upon binding to double-stranded
nucleic acids. In various embodiments, a detection probe comprises
SYBR Green.RTM. or Pico Green.RTM. (marketed by Molecular Probes,
Inc.). In various embodiments, a detection probe can comprise an
enzyme that can be detected using an enzyme activity assay. An
enzyme activity assay can utilize a chromogenic substrate, a
fluorogenic substrate, or a chemiluminescent substrate. In various
embodiments, the enzyme can be an alkaline phosphatase, and the
chemiluminescent substrate can be
(4-methoxyspiro[1,2-dioxetane-3,2'(5'-chloro)-tricyclo[3.3.1.13,7]decan]4-
-yl)phenylphosphate. In various embodiments, a chemiluminescent
alkaline phosphatase substrate can be CDP-Star.RTM.
chemiluminescent substrate or CSPD.RTM. chemiluminescent substrate
(marketed by Applied Biosystems).
[0080] In various embodiments, the present teachings provide
methods and apparatus for Reverse Transcriptase PCR (RT-PCR), which
include the amplification of a Ribonucleic Acid (RNA) target. In
various embodiments, assay can comprise a single-stranded RNA
target, which comprises the sequence to be amplified (e.g., an
mRNA), and can be incubated in the presence of a reverse
transcriptase, two primers, a DNA polymerase, and a mixture of
dNTPs suitable for DNA synthesis. During this process, one of the
primers anneals to the RNA target and can be extended by the action
of the reverse transcriptase, yielding an RNA/cDNA doubled-stranded
hybrid. This hybrid can be then denatured and the other primer
anneals to the denatured cDNA strand. Once hybridized, the primer
can be extended by the action of the DNA polymerase, yielding a
double-stranded cDNA, which then serves as the double-stranded
target for amplification through PCR, as described herein. RT-PCR
amplification reactions can be carried out with a variety of
different reverse transcriptases, and in various embodiments, a
thermostable reverse-transcriptions can be used. Suitable
thermostable reverse transcriptases can comprise, but are not
limited to, reverse transcriptases such as AMV reverse
transcriptase, MuLV, and Tth reverse transcriptase.
[0081] In various embodiments, assay can be an assay for the
detection of RNA, including small RNA. Detection of RNA molecules
can be, in various circumstances, very important to molecular
biology, in research, industrial, agricultural, and clinical
settings. Among the types of RNA that are of interest in various
embodiments are, for example, naturally occurring and synthetic
regulatory RNAs such as small RNA molecules (Lee, et al., Science
294: 862-864, 2001; Ruvkun, Science 294: 797-799; Pfeffer et al.,
304: Science 734-736, 2004; Ambros, Cell 107: 823-826, 2001; Ambros
et al., RNA 9: 277-279, 2003; Carrington and Ambros, Science 301:
336-338, 2003; Reinhart et al., Genes Dev. 16: 1616-1626, 2002
Aravin et al., Dev. Cell 5: 337-350, 2003, Tuschel et al., Science
294: 853-858, 2001; Susi P. et al., Plant Mol. Biol. 54: 157-174,
2004; Xie et al., PLoS Biol. 2: E104, 2004). Small RNA molecules,
such as, for example, micro RNAs (mRNA), short interfering RNAs
(siRNA), small temporal RNAs (stRNA) and short nuclear RNAs
(snRNA), can be, typically, less than about 40 nucleotides in
length and can be of low abundance in a cell.
[0082] With appropriate detection probes, reader-analyzer
instrument 176 can detect mRNA expression found in, for instance,
cell samples taken at different stages of development. In various
embodiments, coexpression patterns can be analyzed across
microfluidic card 174 with TaqMan.RTM. sensitivity, specificity,
and dynamic range. In various embodiments, such methods obviate the
need for running further assays to validate the expression levels.
In various embodiments, reader-analyzer instrument 176 can be used
to validate that siRNA molecules have successfully,
post-translationally regulated the gene expression patterns of
interest. In various embodiments, such methods may be useful during
the manipulation of gene expression patterns using siRNAs in order
to elucidate gene function and/or interrelationships amongst genes.
In various embodiments, gene expression patterns can be introduced
into living cells, cellular assays can be seen on reader-analyzer
instrument 176 and can reveal gene functions. In various
embodiments, analysis for small RNA can be run on reader-analyzer
instrument 176 allowing for a high number of simultaneous assays on
a single sample with performance that obviates the need for
secondary assays to validate the gene expression results.
[0083] In various embodiments, multiplex methods are provided
wherein assay comprises a first universal primer that binds to a
complement of a first target, a second universal primer that binds
to a complement of a second target, a first detection probe
comprising a sequence that binds to the sequence comprised by the
first target, and a second detection probe comprising a sequence
that binds to a sequence comprised by the second target. In various
embodiments, at least some of the plurality of wells of comprise a
solution operable to perform multiplex PCR. The first and second
detection probes can comprise different labels, for example,
different fluorophores such as, in non-limiting example, VIC and
FAM. Sequences of the first and second detection probes can differ
by as little as one nucleotide, two nucleotides, three nucleotides,
four nucleotides, or greater, provided that hybridization occurs
under conditions that allow each detection probe to hybridize
specifically to its corresponding detection probe.
[0084] In various embodiments, multiplex PCR can be used for
relative quantification, where one primer set and detection probe
amplifies the target DNA and another primer set and detection probe
amplifies an endogenous reference. In various embodiments, the
present teachings provide for analysis of at least four DNA targets
in each of the plurality of wells and/or analysis of a plurality of
DNA targets and a reference in each of a plurality of wells in
microfluidic card 174.
[0085] In various embodiments, DNA applications such as, for
example, PCR, may be detected using electrochemical detection
methods. In various embodiments, a hand held pathogenic detection
device utilizes electrochemical detection. In various embodiments,
such electrochemical detection methods employ Taq polymerase and
5.sup.1-exonucleoase activity preamplification, as described below.
In such electrochemical detection, the use of a fluorescent probe
as described above may not be needed. In various embodiments,
during the PCR extension step, a unique oligo probe may be cleaved
by attack polymerase after completion of the PCR, the releasable
oligo probe may be hybridized to a capture anti-sense oligo
immobilized on the surface of the electrochemical detector. In
various embodiments, the oligo probe which can be hybridized to a
surface of the electrochemical detector may generate a yes answer
and lack of hybridization may generate a no answer for the target
related to a pathogen or virus for which it is being analyzed. In
various embodiments, such a handheld may be able to multiplex
several targets by designing a multiple of unique probes that may
hybridize to a unique detector thus providing a yes/no answer for
each of multiple targets for a group of pathogens or viruses being
analyzed. Examples of use of DNA amplification assay employing
electrochemical detection may be found in U.S. Provisional Patent
Application No. 60/699,950, filed Jul. 7, 2005 and commonly
assigned.
[0086] An example of a portable reader-analyzer instrument 54 is
illustrated in FIG. 14 as an exemplary device. In various
embodiments, portable instrument 54 can utilize six fluidic
cartridges 322. The portable instrument 54 can be capable of
analyzing a variety of different sample types. In various
embodiments, it may be powered using AC power from a standard
outlet, or by battery power, or by solar power. Further, the
portable instrument 54 can have no processing ability, relying
instead on connection to, and control by, a computer. This computer
can be a laptop, so not to limit the portability of the portable
instrument 54. In various embodiments, the portable instrument 54
can be configured to detect on the order of ten strains of bacteria
or virus (although smaller and larger numbers of strains are also
possible).
[0087] In various embodiments, the portable instrument 54 employs
up to approximately 50 detection wells and can be capable of
analyzing multiple samples per run. In various embodiments,
portable instrument 54 can be configured to perform multiplex PCR
(as discussed above) in at least one pre-filled reagent cartridges
336. For example, with 50 detection wells, five patient samples
could be analyzed for ten agents each. One or more of the agents
can be controls, which are used to calibrate the portable
instrument. Calibration is discussed in more detail below. FIG. 15
illustrates a cutaway view of a fluidic cartridge 322, including a
cartridge housing 338, a flexible printed circuit board (PCB)
interconnect 332, a sample inlet 334 for a 5 mL syringe 330, and
pre-filled reagent cartridges 336. In various embodiments, portable
instrument 54 may perform PCR utilizing electrochemical
detection.
[0088] FIG. 16 shows a handheld instrument 56. The handheld
instrument 56 can be configured to analyze a single sample per run.
For example, this sample can be a sputum sample from a patient. The
handheld instrument 56 can be pocket-sized or about the size of a
deck of playing cards to allow for easy storage and portability. To
this end, the processing ability of the handheld instrument 56 may
be limited, relying on externally located resources for more
sophisticated analysis.
[0089] The handheld instrument 56 can be configured to detect
multi-drug-resistant tuberculosis, a very useful application in
developing countries. The handheld instrument 56 may be capable of
running on batteries for situations where electrical power may be
not present or may not be reliable. An internal controller can
automatically coordinate transfer of data acquired by the handheld
instrument 56 to another device for further analysis such as P2P
communication to another handheld instrument 56, a portable
instrument 54, a laboratory instrument 52, a local computer, a
network, or a distant server. Such communication may be wired,
wireless, or a combination thereof. In various embodiments,
handheld instrument 56 may include a GPS device to identify the
location of the where the sample was analyzed and such resulting
spatial data can be communication along with PCR results for
further analysis.
[0090] Referring to FIG. 17, components of handheld instrument 56
can include an enclosure back 360, microfluidic device 362, an
enclosure front 364, and an activation slider 366. FIG. 18
demonstrates the activation of the handheld instrument 56 by
sliding the activation slider 366 in the direction of the arrow
toward the top of the handheld instrument 56. FIG. 19 demonstrates
protusions 380 on the inside of the activation slider 366 that
activate the PCR process. In various embodiments, handheld
instrument 56 can be preloaded with PCR reagents. In various
embodiments, handheld instrument 56 may perform PCR utilizing
electrochemical detection, as discussed above.
[0091] Although not specifically illustrated, each of the above
reader-analyzer instruments 176 can be provided with a visual
readout. This readout can be used to display operating instructions
or messages to the user, including alert messages about tests that
should be performed on the reader-analyzer instrument 176. Such
messages would be provided using the communication capability of
the instrument. In various embodiments, reader-analyzer instrument
176 can include a MMI such as, for example, a keyboard. The MMI may
be useful for entering spatial and/or demographic data, and/or
confirming each step performed during an analysis, and/or to
communicate with the network, a computer or another reader-analyzer
instrument 176. In various embodiments, the MMI can be a computer
in bi-directional communication with reader-analyzer instrument
176. In various embodiments, cellular phone capabilities may be
included in the reader-analyzer instrument 176. In various
embodiments, the reader-analysis instruments 176 utilize a common
genetic assay analysis platform, such as a TaqMan.RTM. assay-based
platform, as discussed herein, which utilizes PCR techniques. A
collection 102 of reader-analyzer instruments 176 may include other
types of analysis platforms can additionally or alternatively be
used, such as, for example, hybridization array (microarray)
platforms. In some applications, it may be beneficial to utilize
both hybridization array and PCR platforms together. For example, a
hybridization array technology can be employed first to screen a
sample over a large number of different targets (e.g., different
bacteria, viruses, pathogens, and/or other target sequences).
[0092] In various embodiments, the results of the initial
hybridization array analysis can then indicate a PCR analysis to
select for subsequent testing. As will be more fully explained
herein, the reader-analyzer instruments 176 can be equipped with
bidirectional communication capability such as P2P or through a
network, and this communication capability can be utilized, for
example, to send control instructions and/or data from a
hybridization array system to the PCR system, so that the PCR
system will know, as identified by hybridization array system, what
specific bacteria, virus, pathogen, and/or target sequence to
target.
[0093] Environmental samplers 60, 62, such as, for example, air
sampler 60 and water sampler 62, can be used. In various
embodiments, data collected from any environmental samples can be
included in the spatial data that is uploaded to the system 10. In
various embodiments, these environmental samplers 60, 62 can simply
be a front-end to the PCR process detailed above, containing an
apparatus to capture a sample, and suspend it in solution for
processing by an ISAP module 172. In various embodiments, the
samplers 60, 62 can include specific PCR instruments designed to
perform PCR analysis on environmental samples. Similarly, PCR can
be employed in medical diagnostics, environmental studies, clinical
studies, food/agricultural analysis, animal/organism testing, and
chemical content analysis.
[0094] In various embodiments, PCR can be adapted to perform
quantitative PCR. In various embodiments, two different methods of
analyzing data from PCR experiments can be used: absolute
quantification and relative quantification. In various embodiments,
absolute quantification can determine an input copy number of the
target DNA of interest. This can be accomplished by relating a
signal from a detection probe to a standard curve. In various
embodiments, relative quantification can describe the change in
expression of the target DNA relative to a reference or a group of
references such as, for example, an untreated control, an
endogenous control, a passive internal reference, a universal
reference RNA, or a sample at time zero in a time course study.
When determining absolute quantification, the expression of the
target DNA can be compared across many samples, for example, from
different individuals, from different tissues, from multiple
replicates, and/or serial dilution of standards in one or more
matrices.
[0095] In various embodiments of the present teachings, PCR can be
performed using relative quantification and the use of standard
curve may not be required. Relative quantification can compare the
changes in steady state target DNA levels of two or more genes to
each other with one of the genes acting as an endogenous reference,
which may be used to normalize a signal from a sample gene. In
various embodiments, in order to compare between experiments,
resulting fold differences from the normalization of sample to the
reference can be expressed relative to a calibrator sample. In
various embodiments, the calibrator sample can be included in each
sample well of the assay panel. The analysis system can determine
the amount of target DNA, normalized to a reference, by determining
.DELTA.C.sub.T=C.sub.Tq-C.sub.Tendo where C.sub.T is the threshold
cycle for detection of a fluorophore in real time PCR; C.sub.Tq is
the threshold cycle for detection of a fluorophore for a target DNA
in sample; and C.sub.Tendo is the threshold cycle for detection of
a fluorophore for an endogenous reference or a passive internal
reference in assay. In various embodiments, a gene expression
analysis system can determine the amount of target DNA, normalized
to a reference and relative to a calibrator, by determining:
.DELTA..DELTA.C.sub.T=.DELTA.C.sub.Tq-.DELTA.C.sub.Tcb where
C.sub.Tq is the threshold cycle for detection of a fluorophore for
the target DNA in sample; C.sub.Tcb is the threshold cycle for
detection of a fluorophore for a calibrator sample; .DELTA.C.sub.Tq
is a difference in threshold cycles for the target DNA and an
endogenous reference; and .DELTA.C.sub.Tcb is a difference in
threshold cycles for the calibrator sample and the endogenous
reference If .DELTA..DELTA.C.sub.T is determined, the relative
quantity of the target DNA can be determined using a relationship
of relative quantity of the target DNA, which can be equal to
2.sup.-.DELTA..DELTA.C.sup.T. In various embodiments,
.DELTA..DELTA.C.sub.T can be about zero. In various embodiments,
.DELTA..DELTA.C.sub.T can be less than .+-.1. In various
embodiments, the above calculations can be adapted for use in
multiplex PCR (See, for example, Livak et al. Applied Biosystems
User Bulletin #2, updated October 2001, and Livak and Schmittgen,
Methods (25) 402-408 (2001). In various embodiments, once
calibration has been performed on all target sequence C.sub.T
values to produce their respective copy numbers, the data can be
analyzed in various ways.
[0096] A knowledge base comprises a set of sentences (or rules,
etc.) that assert something about the context within which they
exist. For example, in the real-time PCR context, asserting that "a
C.sub.T value less than twenty for a target sequence X means the
target sequence level of X is high" is an application of knowledge
that originates from data in the EpiMonitor domain. The knowledge
being represented in this example is when a target sequence level
is high. Knowledge base construction involves structuring the
domain so that knowledge-creating methods or rules, which end users
may devise, provide a framework for inference.
[0097] In various embodiments, a rules engine is described to
flexibly create and process rules to apply a qualitative label or
labels to quantitative results. Rules may be defined a priori by a
user, or determined by the rules engine based upon a learning
algorithm. A simple example of a rule is the application of a PLUS
label when a C.sub.T value is less than 30 and a MINUS label when
the C.sub.T value is greater than or equal to 30. Such a simple
inequality may not fully encapsulate the logical procedure a
skilled user would undertake to reach a qualitative result. For
example, a user can perform other evaluations related to real-time
PCR experiments to reach the conclusion that a PLUS label is
appropriate. These evaluations include assessing data validity by
looking at reaction controls, using quality control (QC) metrics to
determine reproducibility, and looking at the C.sub.T data to see
if the value falls within an expected numerical range.
[0098] Each of the steps in the process can be defined using
first-order logic to automate the application of a qualitative
label to quantitative data. This definition can be achieved by
codifying each of the process steps as a Rule composed of
Statements, building a ruleset that is a series of these rules, and
examining the data against the ruleset (instantiation). Additional
logical steps can be performed in the form of a decision tree or a
forward- or backward-chaining program.
[0099] In various embodiments, a Pathogen Calculator software tool
can implement such a rules engine, which can apply a label of high,
medium, or low to PCR data. Additionally, error labels such as
invalid, unrepeatable, or out of bounds can be applied. A label of
invalid can be applied if measurement of reaction controls
indicates a failure occurred in the reaction process. A label of
unrepeatable can be applied if the data does not meet QC metrics,
such as records of time and temperature recorded by the instrument
performing PCR. A label of unrepeatable can also be applied if
statistical parameters of the data, such as standard deviation, are
outside of permissible boundaries. A label of out of bounds can be
applied if the C.sub.T value is less than a lower limit, indicating
too much fluorescence (or other indicator) at too early a stage,
and thus invalid data. The label of out of bounds can also be
applied if the C.sub.T value is too great, indicating a result
beyond the accepted resolution of the instrument.
[0100] The Pathogen Calculator tool can define certain thresholds
based upon the sample card 174 configuration to flag percentages,
quantities, and/or qualitative results. Threshold violations and
other results, whether qualitative or quantitative, can be
demonstrated graphically to the user. In various embodiments, the
Pathogen Calculator includes a percentage calculator that can be
used to determine respective quantities of the various target
sequences present. The target sequence percentage can be calculated
by dividing the copy number of a selected target sequence by the
sum of all target sequence copy numbers, then multiplied by 100%.
This information can be displayed in various ways, including tables
and bar charts. In various embodiments, the Pathogen Calculator
tool may be implemented within one of the reader-analyzer
instruments 176, or within a computer in communication with the
reader-analyzer instrument 176. Data, qualitative or otherwise,
that is generated by the Pathogen Calculator can be communicated to
the EpiMonitor software platform 100, instead of, or in addition
to, the reaction data. In various embodiments, the Pathogen
Calculator can be located in a reader-analyzer instrument 176, or
in a computer associated with a reader-analyzer instrument 176. The
Pathogen Calculator can also be implemented in the EpiMonitor
software platform 100 itself.
[0101] Because C.sub.T values may vary based upon a number of
factors, including the reader-analyzer instrument 176 platform
type, the assay type, and the genetic material sample type, a rules
engine can take these factors into account. For instance, different
rulesets can be defined for each platform, such as one ruleset for
a BioRad LightCycler, and another for an ABI 7900. Within each
platform ruleset, there can be groups of rules for each sample
type, such as blood, sputum, hair, dirt, saliva, etc. Each group of
sample type rules can contain individual rules for each assay type,
such as a particular manufacturer's primer/probe set used for
detecting bordetella pertussis. This linear model can be
extrapolated to greater or fewer numbers of factors.
[0102] Other rules may be included for each individual target
sequence, for example, different target sequences out of each of
two pathogenic E. coli strains, such as O127:H7 and O157:H7. Still
other rules can include normalizing to a variety of different
endogenous controls that can be used in individual assays.
Combinations of all or a subset of these rules can be used in
various embodiments. Standardized chemistry and controls can be
used to help limit the amount of rules to a manageable number.
[0103] In various embodiments, hierarchical rules can be defined.
For example, a ruleset can be defined for platform type, a ruleset
can be defined for sample type, and a ruleset can be defined for
assay type. These rulesets can then be applied serially. For
example, rules within the platform type ruleset can be applied
based upon the type of platform used to acquire PCR data. Then
rules within the sample type ruleset can be applied based upon the
type of sample from which genetic information was extracted. Then
rules within the assay type ruleset can be applied based upon the
assay type, for example, controls, PCR chemistry, probes, etc.
[0104] In various embodiments, a global ruleset can be defined that
operates on normalized values, whether normalized C.sub.T values,
normalized copy count numbers, or other suitable values.
Normalization, as described below, can account for variations in
factors such as platform type, sample type, and assay type. Then a
global ruleset can be applied equally to the normalized numbers,
regardless of platform, sample type, assay type, etc.
[0105] The following exemplary XML (extensible markup language)
code demonstrates a data structure containing rules that can be
passed to the Pathogen Calculator. This data structure can be
stored within the EpiMonitor platform 100 or communicated to
reader-analyzer instruments 176. These rules can be used by the
Pathogen Calculator to qualitatively label quantitative results
from a real-time PCR run. TABLE-US-00003 <?xml version="1.0"
?> - <qualresult type="linearrulesresult"> -
<linearrulesresult owner ="B-pert" sample_name="Sample01"
description="General Linear Evaluation"> - <rulesresult owner
="B-pert" sample_name="Sample01" description="Poor Replicate Data
Quality" true_result="Pathogen QC: Fail" false_result="ok"
true_color="205,92,92" false_color="152,251,152"
operators="NONE"> - <rule owner ="B-pert"
sample_name="Sample01" operators="AND" datatype="StdDev(Ct)">
<statement operator="GREATER THAN" value="2" /> <statement
operator="NOT EQUAL" value="NaN" /> </rule>
</rulesresult> - <rulesresult owner ="B-pert"
sample_name="Sample01" description="Low Pathogen Quality"
true_result="low" false_result="not low" true_color="152,251,152"
false_color="205,92,92" operators="NONE"> - <rule owner
="B-pert" sample_name="Sample01" operators="OR"
datatype="Mean(Ct)"> <statement operator="GREATER THAN"
value="35" /> <statement operator="EQUAL" value="NaN" />
</rule> </rulesresult> - <rulesresult owner
="B-pert" sample_name="Sample01" description="Medium Pathogen
Quality" true_result="medium" false_result="not medium"
true_color="238,221,130" false_color="152,251,152"
operators="NONE"> - <rule owner ="B-pert"
sample_name="Sample01" operators="AND" datatype="Mean(Ct)">
<statement operator="LESS THAN" value="35" /> <statement
operator="GREATER THAN" value="25" /> </rule>
</rulesresult> - <rulesresult owner ="B-pert"
sample_name="Sample01" description="High Pathogen Quality"
true_result="high" false_result="not high" true_color="238,92,66"
false_color="152,251,152" operators="NONE"> - <rule owner
="B-pert" sample_name="Sample01" operators="AND"
datatype="Mean(Ct)"> <statement operator="LESS THAN"
value="25" /> </rule> </rulesresult>
</linearrulesresult> </qualresult>
[0106] This data structure defines a decision tree type of analysis
for the B-pert assay for a sample named Sample01. Each rule is
evaluated in order until a true result is found. The first rule
defines "Poor Replicate Data Quality." This rule states that the
replicate data is poor when this target sequence's standard
deviation of C.sub.T is greater than 2 and not equal to "NaN." When
true, the rules engine will return the qualitative result "Pathogen
QC: Fail," which denotes a failure in the real-time PCR.
[0107] The second rule defines a "Low Pathogen Quantity," which is
present when an arithmetic mean of C.sub.T values is greater than
35 or equal to "NaN." This will return a qualitative result of
"Low" when true. The third rule defines a "Medium Pathogen
Quantity," which is expressed by a mean (C.sub.T) less than 35 and
greater than 25. This will return a qualitative result of "Medium"
when true.
[0108] The last rule is a "High Pathogen Quantity," which is
expressed by a mean C.sub.T value less than 25. This will return a
qualitative result of "High" when true. This example demonstrates
how knowledge of assay parameters can be codified, in this case
knowledge of the Bordetella pertussis assay, and what sorts of
qualitative results can be generated.
[0109] A ruleset data structure can be encoded to be easily
readable by both humans and computer programs such as by using XML,
as demonstrated above. Such a ruleset may be coded in any
machine-readable language. In addition to the qualitative results
returned by the decision tree, each rule can return other types of
data such as strings (in this case, these rules also return text
indices for RGB color in order to give a color representation along
with the qualitative result), other rules, or other sets of
rules.
[0110] Normalization allows data to be compared without regard to
systematic variations. Such systematic variations include
differences between platforms, between different sample types, and
between different assay types. Each machine that performs PCR may
have slightly different operating parameters, and differences
between manufacturers may be even greater. Various sample types
entail differences in the difficult of purifying the nucleic acid
content in the sample, whether and to what extent PCR inhibitors
are present, and quantity of nucleic acid per volume. Different
assay types produce different reaction rates, and each may interact
with a sample differently. The linear rules engine model described
above is one approach to normalization. By generating a qualitative
tag for each set of reaction data, disparate reaction data can be
compared, regardless of PCR platform, symptoms, illness, etc. The
normalization is accomplished by having rules specifically tailored
to each combination of variable, such as assay X, taken on
instrument Y, originating from sample Z.
[0111] Quantitative normalization is also possible. One approach is
to convert C.sub.T to a genomic copy number. This conversion can be
accomplished through the use of absolute or relative quantitation.
Relative quantitation relies on comparing the fluorescence (or
other indicia) of probes for the target sequence of interest to
fluorescence (or other indicia) of probes for a genetic standard
within the same reaction well. This standard can be genetic data
assumed to be present in substantially consistent quantity (such as
GAPDH, discussed below), or added to the sample. Absolute
quantitation relies on forming a standard curve for an assay via a
dilution series prepared a priori. The dilution series records
fluorescence (or other indicia) data (often measured by C.sub.T) at
various starting copy numbers of the target sequence of interest.
Then, a linear best fit is determined for C.sub.T vs. the logarithm
(such as base 10) of copy number, yielding a line described by a
slope and y-intercept. Unknown C.sub.Ts (those measured in the
field) can be converted to copy number by interpolating the value
from this line.
[0112] Each PCR assay and instrument platform can be described by
standard curve parameters that convert threshold cycle to copy
number. This copy number is then comparable across assays and
instrument platforms. Copy number can further be normalized against
sample type by adjusting to a standard sample type, such as blood.
A similar procedure could be used, wherein levels of known genetic
sequences are measured within each of the various sample types,
such as blood and sputum. A correlation, such as a best-fit line,
can then be fitted to the plot of copy number of each sample type
of interest to copy number of the standard sample type. In various
embodiments, triple delta C.sub.T, or delta delta C.sub.T,
described below, can be used to normalize reaction data in the gene
expression domain.
[0113] Benefits of normalization can include, for example, system
10 is not reliant on just one or two types of reader-analyzer
instruments 176, or reader-analyzer instruments 176 exclusively
from one manufacturer, or using one type of chemistry. Such
benefits allow EpiMonitor software platform 100 to encompass a
greater universe of reader-analyzer instruments 176 without
additional capital expenditures or major instrument replacement,
and thus allows for a greater quantity of data to be captured and
participation of a larger group of labs.
[0114] In various embodiments of the present teachings, an analysis
system can use .DELTA..DELTA.C.sub.T values computed for the same
target DNA but in different samples (Sample A (S.sub.A) and Sample
B (S.sub.B)) in order to determine the accuracy of subsequent
relative expression computations. This results in the equation as
shown in FIG. 20,
.DELTA..DELTA..DELTA.C.sub.TT.sub.x=.DELTA..DELTA.C.sub.TT.sub.xS.sub.A-.-
DELTA..DELTA.C.sub.TT.sub.xS.sub.B
[0115] In various embodiments, a value for
.DELTA..DELTA..DELTA.C.sub.TT.sub.x can be zero, or reasonably
close to zero, which can indicate that the preamplified
.DELTA.C.sub.T values for T.sub.x (.DELTA.C.sub.T preamplified
T.sub.xS.sub.A and .DELTA.C.sub.T preamplified T.sub.xS.sub.B) can
be used for relative gene expression computation between different
samples via a standard relative gene expression calculation. Such
calculation may be useful in normalizing data from different
instruments 176 or as a QC step to accept or reject normalized
data.
[0116] In various embodiments, a standard relative gene expression
calculation can determine the amount of the target DNA. In various
embodiments, a standard relative gene expression calculation
employs a comparative C.sub.T. In various embodiments, the above
methods can be practiced during experimental design and once the
conditions have been optimized so that the
.DELTA..DELTA..DELTA.C.sub.TT.sub.x is reasonably close to zero,
subsequent experiments only require the computation of the
.DELTA.C.sub.T value for the preamplified reactions. In various
embodiments, .DELTA..DELTA.C.sub.TT.sub.xS.sub.A values can be
stored in a database or other storage medium. In various
embodiments, these values can then be used to convert
.DELTA..DELTA.C.sub.TpreamplifiedT.sub.xS.sub.A values to
.DELTA..DELTA.C.sub.T not preamplifiedT.sub.xS.sub.A values. In
various embodiments, the .DELTA..DELTA.C.sub.T
preamplifiedT.sub.xS.sub.y values can be mapped back to a common
domain. In various embodiments, a not preamplified domain can be
calculated using other gene expression instrument platforms such
as, for example, a microarray. In various embodiments, the
.DELTA..DELTA.C.sub.TT.sub.xS.sub.A values need not be stored for
all different sample source inputs (S.sub.A) if it can be
illustrated that the .DELTA..DELTA.C.sub.T preamplifiedT.sub.x is
reasonably consistent over different sample source inputs.
[0117] In various embodiments, microarray technology, which can
provide data to system 10. In various embodiments, a microarray can
be a piece of glass or plastic on which single-stranded pieces of
DNA are affixed in a microscopic array as probes. In various
embodiments, thousands of identical probes can be affixed at each
point in the array which can make effective detectors.
[0118] Typically, arrays can be used to detect the presence of
mRNAs that may have been transcribed from different genes and which
encode different proteins. The RNA can be extracted from many
cells, ideally from a single cell type, then converted to cDNA. In
various embodiments, the cDNA may be amplified in quantity by PCR.
Fluorescent tags can be enzymatically incorporated into the or can
be chemically attached to strands of cDNA. In various embodiments,
a cDNA molecule that contains a sequence complementary to one of
the probes will hybridize via base pairing to the point at which
the complementary probes are affixed. In various embodiments, the
point on the array can then fluoresce when examined using a
microarray scanner. In various embodiments, the intensity of the
fluorescence can be proportional to the number of copies of a
particular mRNA that were present and calculates the activity or
expression level of that gene.
[0119] In various embodiments, a microarray can be, for example, a
cDNA array, a hybridization array, a DNA microchip, a high density
sequence oligonucleotide array, or the like. In various
embodiments, a microarray can be available from a commercial source
such as, for example, Applied Biosystems, Affymetrix, Agilent,
Illumina, or Xeotron. In various embodiments, a microarray can be
made by any number of technologies, including printing with
fine-pointed pins onto glass slides, photolithography using
pre-made masks, photolithography using dynamic micromirror devices,
or ink-jet printers. The lack of standardization in microarrays can
present an interoperability problem in bioinformatics since it can
limit the exchange of array data.
[0120] In various embodiments, microarray output data can be in a
format of fluorescence intensity and in various embodiments,
microarray output data may be in a format of chemiluminescence
intensity. In various embodiments, an intensity value from a
microarray output data can be globally normalized. In various
embodiments, total difference values can be determined by
subtracting background noise and normalizing the array signal
intensity, then dividing experimental sample signal intensity by a
control sample signal intensity yielding net sample intensity. In
various embodiments, a control sample used to generate the control
sample signal intensity can be, for example, Stratagene.RTM., UHR,
or the like. In various embodiments, a total difference can be
converted to a log.sub.2 by the following equation:
2.sup..DELTA..DELTA.C.sup.T=3.3 log.sub.10 (net intensity sample
1/net intensity sample 2)
[0121] In various embodiments, microarray output data is in a
.DELTA..DELTA.C.sub.T format. In various embodiments, microarray
output data can be converted into a .DELTA..DELTA.C.sub.T format by
the following equation: R=(1/2).sup..DELTA..DELTA.C.sup.T where R
is the resulting measurement from a microarray. Such calculations
are available commercially, such as GeneSpring from Silicon
Genetics. Various embodiments include converting microarray output
data into a .DELTA..DELTA.C.sub.T format using a Global Pattern
Recognition (GPR) algorithm which can convert intensity values
generated from microarrays from linear values to algorithmic values
and can use transformed intensity cutoffs to affect gene and
normalizer filters. In various embodiments, GPR software algorithm
may be available from The Jackson Laboratory. In various
embodiments, microarray output data can be in a standard language
or format such as MAGE-ML (microarray and gene expression markup
language), MAML (microarray markup language), or MIAME (minimum
information about microarray experiments). In various embodiments,
such standardized formats and language can be converted to a
.DELTA..DELTA.C.sub.T format.
[0122] In various embodiments, microarray output data can be in a
.DELTA..DELTA.C.sub.T format, then PCR data can be directly
compared to data from microarray platforms as shown in FIG. 21. In
various embodiments, a .DELTA..DELTA..DELTA.C.sub.T calculation can
be a validation tool to confirm that relative quantitation data can
be compared from one amplification/detection process to another. In
various embodiments, .DELTA..DELTA..DELTA.C.sub.T calculation can
be a validation tool to confirm that relative quantitation data can
be compared from one sample input source to another sample input
source, for example, comparing a sample from liver to a sample from
brain in the same individual. In various embodiments,
.DELTA..DELTA..DELTA.C.sub.T calculation can be a validation tool
to confirm that relative quantitation data can be compared from one
high-density sequence detector system to another high-density
sequence detection system.
[0123] In various embodiments, .DELTA..DELTA..DELTA.C.sub.T
calculation can be a validation tool to confirm that relative
quantitation data can be compared from one platform to another, for
example, data from real time PCR to data from a hybridization array
is especially valuable for cross-platform validation. In various
embodiments, real-time PCR and hybridization array data can be
directly compared. In various embodiments, a TaqMan.RTM.
.DELTA..DELTA.C.sub.T can be compared to a microarray output
converted to the .DELTA..DELTA.C.sub.T format. In various
embodiments, the resultant .DELTA..DELTA..DELTA.C.sub.T, if within
+/-1 C.sub.T of zero, can determine a high-degree of confidence
that the actual total difference observed within each of the two
platforms is correlative and, as such, may be normalized for entry
into system 10. Further discussion of .DELTA..DELTA..DELTA.C.sub.T
can be found in commonly assigned U.S. patent application Ser. No.
11/086,253.
[0124] In various embodiments, a correction, which can be a
quantity added to a calculated or observed value to obtain the true
value, may be used so that data generated on two different
platforms can be used together in further calculations and
analysis. Various embodiments allow for larger and sometimes more
complete data sets to be used in gene expression studies. In
various embodiments, the correction can be calculated from a
resulting .DELTA..DELTA..DELTA.C.sub.T. In various embodiments, a
correction can be a bias correction.
[0125] Referring now to FIG. 22, a graphical representation
illustrates some of the information that can be acquired and
transmitted by the reader-analyzer instruments 176 to the
EpiMonitor software platform 100. The reader-analyzer instruments
176 may provide PCR analysis results or other genetic data 452 to
the EpiMonitor software platform 100. These analysis results can be
in the form of raw data, can be pre-processed in some respect, or
can even be a diagnosis (such as a determination that the patient
is infected with a particular illness). Pre-processing
possibilities are discussed in greater detail below.
[0126] EpiMonitor software platform 100 can also store an
identifier for each assay performed on a sample as part of the PCR
analysis results or other genetic data 452. This can be based upon
Logical Observation Identifiers Names and Codes (LOINC), a standard
that codifies laboratory and clinical observations and can be
applied by the EpiMonitor administrator when creating a panel and a
probe (see below).
[0127] Reader-analyzer instruments 176 can also capture contextual
information 462, including spatial, temporal, climate, and priority
information. Spatial (e.g., geographic) information describes where
the sample was obtained, where the sample was prepared for
processing, and/or where the sample analysis was performed. When
analyzing genetic material of an entire population (whether of a
community, a country, the world, etc.), this spatial component is
useful for such purposes as analyzing how a target sequence is
spreading through a population.
[0128] Spatial information can be provided by a user (including the
patient or clinician) or automatically by the reader-analyzer
instrument 176. In various embodiments, the reader-analyzer
instrument 176 includes a system for ascertaining its geographic or
spatial position. This can be provided by a GPS (Global Positioning
System) device that is either embedded in, or in communication
with, the reader-analyzer instrument 176. Additionally, the
location of the reader-analyzer instrument 176 can be obtained by
determining its IP (Internet Protocol) address and using a suitable
lookup table to convert the IP address into a geographic location.
While IP addresses are not uniformly accurate as indicators of
physical location, the EpiMonitor software platform 100 can
circumvent this limitation by requiring that the user or instrument
register its geographic location once the instrument is connected
to the communication network via the EpiMonitor software platform
100.
[0129] In addition to spatial information, temporal information can
be retained for historical analysis. Reader-analyzer instruments
176 can synchronize their internal clocks with a reference clock of
the EpiMonitor platform 100 to ensure accurate temporal
information. As time-correlated historical data is accumulated,
analysis can become increasingly powerful. For example, more
thorough "baselines" can be collected to discern true signals from
noise, and cyclical patterns may emerge that aid prediction or
diagnosis.
[0130] Climate information can be useful to analyze results with
regard to seasonal, weather, and/or pollution effects. Climate
information includes temperature, humidity, precipitation, wind
speed, and air quality. This information can be correlated with the
temporal information to determine disease or other factors that
might be more closely correlated with temperature than with
season.
[0131] Priority level data can include information about conditions
under which the reader-analyzer instrument 176 being used, as that
information might be indicative of whether a positive detection of
a particular bacteria, virus, pathogen or other target sequence
should be used to trigger a public health warning or other action.
In this regard, a positive detection from a single handheld
instrument 56 might not warrant a public health alert; however, a
single report from a laboratory instrument 52 associated with a
reference laboratory or national laboratory might well warrant a
public alert. The priority level data can be used to allow the
laboratory response network 50 to interpret the reported
information properly.
[0132] Subject information 472 can be recorded as well, and may
include identification data, demographic data, diagnostic data, and
clinical observations. Identification data, stored confidentially,
is valuable for a number of reasons. A patient whose biological
sample is later determined to contain a pathogen could be alerted
to this fact. If the biological sample was taken from an animal,
the animal may need to be quarantined or put down. If an infected
patient visits multiple clinics or has multiple samples taken, it
is useful to allow the system to identify that each of the samples
came from the same subject. Any sample source can be recorded in
the EpiMonitor software platform 100, including humans, animals,
environmental samples, and plants. A population that can be
analyzed on the EpiMonitor software platform 100 can be a group any
living organism including plant for example filed of GMO crops.
Identification information may differ for different types of sample
sources, and such provision can be made in the database.
[0133] The Health Insurance Portability and Accountability Act
(HIPAA) is the code of national standards for protecting the
privacy of personal health information set forth by the U.S. Health
and Human Services (HHS) department. In compliance with HIPAA, the
EpiMonitor software 100 can store a unique key assigned to the
patient by the clinician or physician. Certain applications,
regulations, or privacy concerns may dictate that personal
information not be obtained in particular circumstances.
Demographic data, such as age and gender of the patient, can be
stored. Correlating this data may lead to determinations of
particular susceptibility of a certain age group or gender to a
certain target sequence.
[0134] Diagnostic data includes information provided by the patient
and information determined by the clinician by observing or
analyzing the human or animal subject. In the case of a human
subject, a chief complaint can be recorded. This is the complaint
voiced by the patient and recorded by the clinician. The complaint
can be coded by ICD-9 (International Classification of Diseases,
ninth revision), a uniform code that can be used to tag each
patient's syndrome or diagnosis (e.g., fever=12345, cough=12346,
etc.), or can be stored as a physician's free text remarks (e.g.,
"fever," "cough," etc.). The physician's diagnosis of the patient
can also be stored as an ICD-9 code or free text. Other storage
possibilities are CPT (Current Procedural Terminology) code,
commonly used for medical billing, and SNOMED (Systematized
Nomenclature of Medicine) clinical terms.
[0135] To standardize input arriving as free text, natural language
processing techniques can be used to convert free text into a code
that can be used by a computer. For example, if the chief complaint
reads "cough, sneezing, some fever," a text classifier can
translate this into ICD-9 code 122.3 ("Respiratory Illness with
Fever"). If samples are from plants and/or animals, observable
characteristics can also be recorded. This can include, for
instance, color, flowering patterns, yields, insect infestation,
pesticide and/or herbicide application, and/or observed resistance
to disease/pesticides.
[0136] Referring now to FIG. 23, a database implementation capable
of storing the above information is depicted. In the exemplary
database implementation, a variety of interrelated tables can be
used. These tables can include a Detection_Software_Type table 502
and a Panel table 504, which links to a Device table 506 and the
Detection_Software_Type table 502. A Probe table 508 and a
Probe_location table 518 link to the Panel table 504. An Instance
table 510 also links to the Panel table 504. A Sample table 512
links to the Instance table 510 and to a Patient Information table
516. A Clinical Data table 514 and an Interp_Data table 522 link to
the Sample table 512. A Raw_data table 524 links to the Interp_Data
table 522. A Probedata table 520 and the Interp_Data table 522 link
to the Probe table 508. A Data Received table 526, an XML Exception
table 520, and a Users table 530 are unlinked.
[0137] The Data Received table 526 includes XMLData, Date_received,
and Chunk_num. The XML Exception table 528 includes XMLData,
Date_received, Chunk_num, and XML_message. The Users table 530
includes Username, Full Name, Role, and Date_created. The
Detection_Software_Type table 502 includes Name, Description, and
Version.
[0138] The Panel table 504 includes Name, Description, Version,
Create_Date, Device_id, which links to the Device table 506, and
Detection_software_id, which links to the Detection_Software_Type
table 502. The Device table 506 includes Name and Description. The
Patient Information table 516 includes HIPAA_Patient_IDs,
Date_of_birth, and Sex. The Raw_data table 524 includes
Interp_data_id, which links to the Interp_Data table 522, C.sub.T,
Quantity, well_num, Reporter, and Task.
[0139] The Interp_Data table 522 includes Probe_id, which links to
the Probe table 508, Agg_C.sub.T, Threshold, Sample_id, which links
to the Sample table 512, and interpolated_copy_num. The Probedata
table 520 includes Probe_id, which links to the Probe table 508,
Ct_mean, Ct_std, and Quantity. The Probe_location table 518
includes Panel_id, which links to the Panel table 504, Probe_id,
which links to the Probe table 508, and well_num. The Probe table
508 includes Panel_id, which links to the Panel table 504,
Description, calibration_slope, calibration_yint, detector_name,
create_date, is_standard, and LOINC_code.
[0140] The Clinical Data table 514 includes Diagnosis ID, Diagnosis
Type, Chief Complaint, Chief Complaint Type, and Sample_id, which
links to the Sample table 512. The Sample table 512 includes
Instance_id, which links to the Instance table 510, Description,
Sample_number, Name, Location_zip, Location_city, Location_state,
and Patient_id, which links to the Patient Information table 516.
The Instance table 510 includes Upload_time, Location_zip,
Location_city, Location_state, Panel_id, which links to the Panel
table 504, file_version, and date_received. The Panel table 504
includes Name, Description, Version, Create_Date, Device_id, which
links to the Device table 506, and Detection_software_id, which
links to the Detection_Software_Type table 502.
[0141] The Data Received table 526 and XML Exception table 528
serve as temporary data stores for XML uploads used for
authentication and debugging. The Users table 530 contains the
names of users allowed access to the system and the roles, or user
access rights, that they have (discussed in more detail below).
Mapping the data types of FIG. 23 to those adopted by other
institutions, such as the Public Health Information Network (PHIN)
allows others, such as the CDC, to incorporate EpiMonitor data into
their analysis.
[0142] The EpiMonitor platform 100 allows users to log in to the
system and define assay panels, configure individual gene probes,
and view uploaded instances. Instance is the term used for the
information related to the PCR analysis of a biological sample. A
web interface provides a convenient and widely accessible mode of
operation. In various embodiments, the EpiMonitor web interface
includes a home page that provides a navigation index of other
pages, including panels, probes, PCR devices, detection software
types, and instances.
[0143] The home page can also display whether there are any
identified outbreaks or system warnings. Statistics can also be
displayed regarding timing of data uploads to the system, such as
time of last upload, number of uploads for the current day, and
total number of uploads. Clicking on the panel's link displays a
list of currently defined panels. Clicking on one of the panels
produces a "view panel" page. The information including the panel
includes a description, a unique identifier, a version number, the
number of wells per sample, the PCR detection software type (such
as Sequence Detection Systems v. 2.2), the associated PCR device
type, the date of panel creation, and the probes assigned to the
panel. The view panel page can also display the uploaded instances
that were based upon this panel.
[0144] A possible XML data structure that describes the panel is
shown with exemplary data: TABLE-US-00004 <?xml version="1.0"
?> - <panel id="3" description="Tony's Smaller Panel"
device_name="7900" device_description="AB7900" software_name="SDS"
software_version="2.2" version="1.0" wellspersample="48"
create_date="2005- 07-22 07:07:02"> <probe id="9"
name="B-pert" slope="-3.3547" yint="35.9770"
description="Bordetella pertussis" create_date="2005-07-22
07:07:02" is_standard="false" /> <probe id="10" name="M-pneu"
slope="-3.4563" yint="43.9540" description="Mycoplasma pneumoniae"
create_date="2005-07-22 07:07:02" is_standard="false" />
<probe id="11" name="S-pneu" slope="-3.5956" yint="43.0410"
description="Streptococcus pneumoniae" create_date="2005-07-22
07:07:02" is_standard="false" /> - <probe id="12" name="IPC"
slope="0" yint="0" description="Internal Positive Control"
create_date="2005-07-22 07:07:02" is_standard="true">
<probedata probeid="9" quantity="0.10" ctmean="27.6030"
ctstd="0.4180" /> <probedata probeid="9" quantity="1"
ctmean="24.6630" ctstd="0.2350" /> <probedata probeid="9"
quantity="10" ctmean="21.0340" ctstd="0.1840" /> </probe>
</panel>
[0145] A subset of this data is transferred to the reader-analyzer
instrument 176 so that it can accurately report back the PCR data.
An Assay Information File (AIF) includes the sample name, detector,
task (either a standard or an unknown), and copy number quantity
(known a priori for standards) for each well of the microfluidic
card 174. The first ten rows of an exemplary AIF are depicted in
Table3: TABLE-US-00005 TABLE 3 Well Sample Name Detector Task
Quantity 1 Sample 01 B-pert UNKN 0 2 Sample 01 C-pneu UNKN 0 3
Sample 01 L-pneu UNKN 0 4 Sample 01 M-pneu UNKN 0 5 Sample 01
C-botu UNKN 0 6 Sample 01 S-pneu UNKN 0 7 Sample 01 M-cata UNKN 0 8
Sample 01 N-meni UNKN 0 9 Sample 01 H-infl UNKN 0 10 Sample 01
S-aure UNKN 0
[0146] In the database, each probe can be defined by a number of
criteria. By clicking on one of the probes listed in the view panel
page, a respective view probe page appears. The probe information
includes a description, a unique identifier, a calibration slope
and y-intercept, the detector name, whether the probe is a
standard, and creation date. Probe data is stored to allow
conversion from C.sub.T to copy number. This probe data can be
stored and viewed in a table with columns for copy number (or
quantity), mean value of C.sub.T, and standard deviation of
C.sub.T. The view probe page can also display the panels that
employ this probe.
[0147] The view instance page, which can be accessed from a listing
of instances linked to from the home page, or from one of the
instances listed in a view panel page, indicates which samples
correspond to the instance. Instance information includes upload
time, upload location (such as city, state, and zip code), version
number, and time received. The view instance page can indicate
which panel this instance used in performing PCR. Further, a list
of samples corresponding to this instance is presented.
[0148] A possible XML data structure for storing instance data is
presented with exemplary data: TABLE-US-00006 <?xml
version="1.0" ?> - <epimonitor time="2005-08-01 09:09:20"
zipcode ="94404" version="1"> <sample number="1"
name="Sample01" description="Sample01" zipcode="94404" />
<sample number="2" name="Sample02" description="Sample02"
zipcode="94404" /> <sample number="3" name="Sample03"
description="Sample03" zipcode="94404" /> <sample number="4"
name="Sample04" description="Sample04" zipcode="94404" />
<sample number="5" name="Sample05" description="Sample05"
zipcode="94404" /> <sample number="6" name="Sample06"
description="Sample06" zipcode="94404" /> <sample number="7"
name="Sample07" description="Sample07" zipcode="94404" />
<sample number="8" name="Sample08" description="Sample08"
zipcode="94404" /> - <panel id="1" detection_software_id="0"
device_id="0"> <probe id="2" name="B-pert" slope="-3.3547"
yint="35.977" is_standard="false" /> <probe id="3"
name="L-pneu" slope="-3.1568" yint="41.495" is_standard="false"
/> <probe id="4" name=`M-pneu" slope="-3.4563" yint="43.954"
is_standard="false" /> <probe id="5" name="S-pneu"
slope="-3.5956" yint="43.041" is_standard="false" /> <probe
id="6" name="M-cata" slope="-3.3986" yint="43.766"
is_standard="false" /> <probe id="7" name="N-meni
slope="-3.6138" yint="45.285" is_standard="false" /> <probe
id="8" name="S-aure" slope="-3.4853" yint="45.472"
is_standard="false" /> - <probe id="1" name="IPC" slope=NaN"
yint="NaN" is_standard="true"> <probedata quantity="0.1"
ctmean="27.603" ctstd="0.418" /> <probedata quantity="1.0"
ctmean="24.6663" ctstd="0.235" /> <probedata quantity="10.0"
ctmean="21.034" ctstd="0.184" /> </probe> </panel> -
<datum samplenumber="1" probeid="2" ct="17.651617"
threshold="0.2" quantity="290134.75"> <sdsfile ct="19.225842"
quantity =`NaN" task="Unknown" reporter="FAM" well_num="1" />
<sdsfile ct="16.077393" quantity="NaN" task="Unknown"
reporter="FAM" well_num="25" /> </datum> - <datum
samplenumber="2" probeid="2" ct="22.861122" threshold="0.2"
quantity="8122.7397"> <sdsfile ct="26.811136" quantity="NaN"
task="Unknown" reporter="FAM" well_num="49" /> <sdsfile
ct="18.911108" quantity="NaN" task="Unknown" reporter="FAM"
well_num="73" /> </datum> - <datum
samplenumber.sup.="3" probeid="2" ct="22.423084" threshold="0.2"
quantity="10971.777"> <sdsfile ct="NaN" quantity=` NaN"
task="Unknown" reporter="FAM" well_num="97" /> <sdsfile
ct="22.423084" quantity="NaN" task="Unknown" reporter=" FAM"
well_num="121" /> </datum> - <datum samplenumber="4"
probeid="2" ct="25.692785" threshold="0.2" quantity="1163.0924">
<sdsfile ct="NaN" quantity="NaN" task="Unknown" reporter="FAM"
well_num="145" /> <sdsfile ct="25.692785" quantity="NaN" task
="Unknown" reporter="FAM" well_num="169" /> </datum> -
<datum samplenumber="5" probeid="2" ct="28.389887"
threshold="0.2" quantity="182.65738"> <sdsfile ct="NaN"
quantity="NaN" task="Unknown" reporter="FAM" well_num="193" />
<sdsfile ct="28.389887" quantity="NaN" task="Unknown"
reporter="FAM" well_num="217" /> </datum>
[0149] Clicking on one of the samples from the view instance page
calls up a view sample page. The view sample page includes the
number of the sample, the name and description of the sample, and
the instance to which the sample corresponds. The sample data can
be presented in a table, listed by probe name. The threshold,
C.sub.T value, and computed copy number are presented for each
probe.
[0150] This web interface can be implemented with hierarchical
access rights granted to different users. A class called
Administrators can create and edit panels, probes, devices, and
instruments. Administrators and a lower privileged group, Viewers,
can view the panel, probe, device, and instrument data, as well as
the C.sub.T information collected by these devices. Data deemed
proprietary, such as calibration parameters, could be hidden from
various users, and entered into the EpiMonitor database directly
from a private database, inaccessible even to Administrators.
Instances can only be viewed, not edited, as they represent
acquired data, not settings.
[0151] Referring now to FIG. 24, a functional flow diagram of an
exemplary communication strategy between the EpiMonitor server 550
and a reader-analyzer instrument (EpiMonitor client) 176 is
presented. In step 552, the EpiMonitor client requests information
from the EpiMonitor server 550 through a web services method
regarding the panel to be run, and the EpiMonitor server 550 sends
the corresponding information back to the client. This information
identifies probe data for each well location. The information
returned by the EpiMonitor server 550 can be embodied in an Assay
Information File (AIF), described above. This panel information can
be used in sample preparation to generate a microfluidic card 174
arranged according to the panel information.
[0152] Web services provide a standard means of interoperating
between different software applications running on a variety of
platforms and/or frameworks. Web services are characterized by
their great interoperability and extensibility, and can be combined
in a loosely coupled way in order to achieve complex operations.
Programs providing simple services can interact with each other in
order to deliver sophisticated services. With web services, methods
on other computer systems can be invoked through a request over
HTTP. The web services can be accessed in a variety of ways,
including over the public Internet, Virtual Private Networks, and
private networks. In addition, data can be passed through HTTP,
structured as an XML file.
[0153] In step 554, after PCR has been performed, raw data is
available. In some embodiments, a cycle threshold (C.sub.T) can be
computed for each probe and sample combination by detection
software. This data can be further processed by the EpiMonitor
client. For example, if more than one C.sub.T value exists for a
probe and sample combination (when there are replicates, for
example), an aggregate statistic (mean, median, standard deviation,
etc.) can be determined instead of reporting each C.sub.T value. In
step 556, the client calls a web services method on the EpiMonitor
server 550 to obtain target sequence panel data.
[0154] If implemented, the Pathogen Calculator, as described above,
receives C.sub.T values in step 558. Based upon probe calibration
parameters, the Pathogen Calculator can transform C.sub.T values
into copy numbers. The calibration parameters can include
parameters describing a linear relationship between C.sub.T value
and copy number, such as a slope and an intercept. The Pathogen
Calculator can also perform other analysis of target sequence
presence in a sample. A flexible rules-based embodiment of
qualitative analysis performed by the Pathogen Calculator is
described above. This analysis can be provided to a user of the
client device and/or communicated to the EpiMonitor server 550.
[0155] In step 560, PCR data (e.g., C.sub.T data, raw fluorescence
or other TaqMan.RTM. data), copy number and other information
computed by the Pathogen Calculator, corresponding panel
information, and spatial/temporal/subject context information are
integrated into an XML data structure by the EpiMonitor client.
This data can be encoded and formatted according to Health Level 7
(a Standards Developing Organization accredited by the American
National Standards Institute) standards. The data structure can
also be encapsulated in a suitable transmission protocol, such as
the Simple Object Access Protocol (SOAP).
[0156] In step 562, the client calls the web services method on the
EpiMonitor server 550 that facilitates data upload, encrypts the
XML data, and uploads the encrypted data. This data is logged by
the EpiMonitor server 550 as an instance of the panel. In various
embodiments, a manually entered zip or postal code can serve as the
spatial record, and the time of execution of step 562 of the client
can be recorded as the temporal component of the instance. In step
564, the XML data is decrypted, authenticated, parsed by EpiMonitor
100, and loaded into the EpiMonitor database tables. In step 566,
information from the database tables is made available to external
systems, such as those compliant with the PHIN (Public Health
Information Network).
[0157] When transporting data, Secure Sockets Layer (SSL) can be
used. In various embodiments, the encryption-decryption standard
algorithm for SSL will be based on the RSA algorithm. A Public Key
Infrastructure (PKI) can be used for end-user or nodal
authentication. The PKI provides for third party vetting of user
identities. PKI arrangements enable users to be authenticated to
each other, and to use the information in identity certificates
(i.e., each other's public keys) to encrypt and decrypt messages.
Once authenticated, a symmetric key system can be used to transmit
data in which the EpiMonitor server 550 and clients share a common
encryption-decryption method outside of the public key
infrastructure to provide a layer of greater security beyond
authentication. In various embodiments, a certificate is issued to
each end-user upon their receipt of an EpiMonitor client
device.
[0158] If desired, the EpiMonitor software platform 100 can be
configured to load, install, or download software to each client
device. This software can share a unique encryption key with the
EpiMonitor for every transaction. Resultantly, the key will differ
from transaction to transaction, and from device to device. This
encryption key can use the current time, in milliseconds, to encode
data differently every time data is sent to the server, making it
extremely difficult to intercept.
[0159] As discussed above, a hybridization array can be used to
prescreen a sample to focus PCR testing upon specific bacteria,
viruses, pathogens, or other target sequences. PCR testing from one
instrument 176 can likewise be used in focusing the analysis of
other instruments 176. A message from a client detecting a certain
target sequence can be used by the EpiMonitor software platform 100
to automatically configure other clients to begin testing for this
detected target sequence. Depending upon the circumstances of the
detection, all units, or only selected ones, could be given
instructions to begin testing for that target sequence. Thus, for
example, detection of a pathogen at a local airport might cause
messages to be sent to other airports that are connected by flight
path with that airport. In this way, the potential spread of an
epidemic can be intelligently tracked without having to alert all
labs throughout the nation.
[0160] The communication capability of the EpiMonitor clients
(reader-analyzer instruments 176) can be employed in paradigms
other than strict client-server. Clients can communicate directly
with other clients to provide input on what target sequences to be
on alert for. Environmental measuring instruments, such as air
sampler 60, can also be of assistance in this function. For
example, if an air sampler 60 at a particular location begins
measuring higher than normal concentrations of a particular
substance, the air sampler 60 could communicate with other clients
(reader-analyzer instruments 176) to alert their respective
operators that they should begin testing for presence of a
respective target sequence.
[0161] In most cases, the EpiMonitor clients provide processed
cycle threshold information to the EpiMonitor server 550. If
desired, however, EpiMonitor software 100 allows for raw data
obtained from PCR (such as optical image or current flow
information) to be transmitted. The server 550 can send a message
to the client that will cause that instrument to transmit its raw
data to the database system. This might be done, for example, when
analytic techniques are desired that the individual instrument is
not equipped to perform. Moreover, because the EpiMonitor software
platform 100 can support peer-to-peer cooperation, one instrument
176 could send its raw data output to another instrument 176,
allowing that other instrument 176 to perform the analysis. This
might be done, for example, when a small handheld unit 56 that does
not have the sophisticated processing capability of a larger
laboratory instrument 52 performs the original analysis.
[0162] FIG. 25 is a functional block diagram of EpiMonitor client
and server components used in aid of communication. Within a client
system 602, data is acquired from PCR (such as fluorescence or
current data) by a PCR data module 604. This data is transmitted to
an XML processing module 606, which organizes the data according to
rules from a data description module 608. The XML processing module
606 can also receive data from a pathogen calculator module 607 and
a context acquisition module 609. The pathogen calculator module
607 receives PCR data from the XML module 606 (or possibly directly
from the PCR data module 604), and can also receive calibration
information from the XML module 606. The pathogen calculator module
607 can calibrate the PCR data, and can perform qualitative or
quantitative analysis on the data before or after calibration.
[0163] The context acquisition module 609 determines contextual
data (such as the spatial/temporal/climate/priority data described
with respect to FIG. 25 at 462). The data description module 608
can also provide data rules to a sample preparation module 610,
which is in communication with a sample assay preparation device
(not shown). In this way, the data description module 608 can
control which samples are prepared for which locations within the
microfluidic card 174, and thus the PCR data from the microfluidic
card 174 can be correctly interpreted.
[0164] Once the data has been transformed into an XML-based
description, the XML module 606 forwards it to a SOAP (originally,
Simple Object Access Protocol) encapsulation module 612. The SOAP
encapsulation module 612 operates as a protocol for exchanging XML
messages between computers, primarily via HTTP (HyperText Transfer
Protocol). The SOAP message (envelope) is encrypted in an
encryption module 614 for transmission over a communications
network 616. The communications network 616 can be the Internet, a
private network, or any other suitable network structure, whether
local- or wide-area. Before or after encryption, the XML data can
be stored in a local storage module 618 for later transmission or
for on-board processing. The local storage module 618 can also
store logs of successful transmissions.
[0165] The PCR data module 604 and sample preparation module 610
include a data gathering group 620, while the XML module 606, data
description module 608, SOAP encapsulation module 612, encryption
module 614, and local storage module 618 include a
client-synchronizing group 622. The data gathering group 620 and
client-synchronizing group 622 can be located within a single
device. Alternately, the client-synchronizing group 622 can be
implemented in a separate computer, which connects to the data
gathering group 620 via a localized network, such as Bluetooth,
Ethernet, or infrared. This configuration can be useful when the
data gathering group 620 is desired to be as portable as possible,
as extra processing can be off-loaded to a separate computer.
[0166] A user interface module 625 communicates with the pathogen
calculator module 607, the context acquisition module 609, and the
local storage module 618. The user interface module 620 can include
a display, a keypad, a touchscreen, a keyboard, a mouse, and/or any
other suitable forms of input and output. The user can provide the
user interface module 625 with instructions for where to send
acquired data, information about the samples undergoing PCR
analysis, and directions for further processing. The user interface
module 625 can display process control information, PCR results,
and/or qualitative analysis determined by the pathogen calculator
module 607.
[0167] Within a server system 630, a security/queue module 632
communicates with the communications network 616. The
security/queue module 632 decrypts incoming data, validates data,
and queues data for processing by a description module 634. The
security/queue module 632 can also be responsible for establishing
a secure connection with the secure connection module 614 of the
client systen 602. The description module 634 parses the received
data for storage in a database 636. This parsing can include such
functions as preprocessing (discussed below), natural language
processing (described above), and data type conversion. Once data
is stored in the database 636, an analysis module 638 can identify
trends and determine if triggering conditions are present.
[0168] A web server 640 communicates with the database 636, and
also with the communications network 616. If the communications
network 616 is not connected to the Internet, the web server 640
can also communicate with the Internet. The web server 640 allows
for remote control and viewing of the database 636 and control of
the analysis module 638, as described above. The web server 640 can
include data visualization and summarization responses to queries,
or can provide customizable real-time streaming of data and
alerts.
[0169] A data integrator module 642 communicates with the database
636. Beyond contextual data obtained from the client system 602 is
contextual data that further describes the environment in which the
sample was taken or that the host existed in. This information
includes environmental/climate data (such as that provided by the
National Oceanic and Atmospheric Administration), demographic data
(such as that provided by the U.S. Census Bureau). Much of this
data may be acquired from data stores distributed throughout the
internet or other computer systems. Patient information, such as
hospital and/or doctor records, may also exist in a digital format
on a computer system.
[0170] Additionally, confirmatory data may be generated after
positive results are detected via PCR. Confirmatory data includes
microbiology culture tests and genetic resequencing
assays/instruments. After identification of an agent via a rapid
biological assay such as real-time PCR, a confirmatory test can be
performed using "gold standard" procedures such as viral/microbial
cultures or Applied Biosystem's MicroSeq microbial identification
system.
[0171] The data integrator module 642 can incorporate this
additional contextual data to help describe and analyze the PCR
results collected by EpiMonitor. The data integrator module 642
locates the physical source of the additional contextual dataset,
parses that information, and associates the contextual data with
uploaded instance data from client systems. To facilitate operation
of the data integrator module 642, an EpiMonitor interface standard
can be made publicly available so that a publisher of a new data
store can design their data store accordingly, or write their own
private embodiment of a data integrator module so that EpiMonitor
100 can attain the new data.
[0172] While useful results are obtained by populating and
analyzing the EpiMonitor database 636, integrating the database
with the above-described laboratory response network (LRN),
pictured diagrammatically at 50, provides additional benefit. To
accomplish this integration, the LRN 50 includes a component of the
EpiMonitor software platform 100, which allows the information
stored in the database 636 to be made available to the LRN 50 and
also to integrate with the hierarchical reporting rules defined by
the LRN 50. The EpiMonitor software platform 100 includes a set of
programmable business rules 652 that define how the database 636
integrates with the LRN 50. With the knowledge of the governing
rule set of the LRN 50, the EpiMonitor software platform 100
integrates its database 636 into the LRN schema.
[0173] The EpiMonitor software platform 100 is designed to be
highly efficient in gathering data from a diverse collection of
instruments, potentially located across a widely dispersed
geographic area. As the results are reported from each instrument,
they are stored in the database 636 and linked with the LRN 50
according to the LRN business rules 652. In this way, if a
suspected target sequence is detected in a statistically
significant amount, the LRN 50 receives instant notification. The
LRN 50 can then immediately forward an alert to other networks,
such as a military network, and also to other systems connected
through the EpiMonitor software platform 100. The response to a
positive detection of statistical significance can be to send
messages, possibly through the EpiMonitor software platform, to
instruments at other geographic locations to begin testing for the
target sequence as well.
[0174] Integration is not limited only to the LRN 50 (in its
present form or future forms). Rather, the EpiMonitor software
platform 100 is flexible and will allow integration of database 636
into any information system. If that information system employs
predefined rules, the EpiMonitor software platform 100 can be
configured to embed those rules in its business rules database
652.
[0175] A general framework for acquiring knowledge is useful as the
distribution of instruments 176, data types (originating from
real-time PCR, sequencing, etc.), end-users (epidemiologists,
clinicians), geographical and temporal points/places of interest,
target sequences, data distribution, etc. may be constantly
changing. EpiMonitor 100 can provide a framework for data analysts
to codify automated ways of creating knowledge most important to
them and their distributions-of-interest.
[0176] Specific examples include an analyst in China who may want
to "weight" "high" findings captured in Shanghai greater than those
from New York. Another end-user may want to assign greater "weight"
to data from assays that target a certain target sequence. To a
clinician, the "co-variation" of a target sequence X with target
sequence Y during the month of December may be of clinical
importance. Additionally, data values produced by a more
sophisticated detection instrument, such as a portable pMD, may be
deemed more "sensitive" than that from a handheld pMD. Further,
statistical rules can be envisioned, such as ruling data from a
small-sampled population as less "important" or "critical" than
data originating from a population that is more highly sampled.
[0177] The qualifiers and conclusions shown above in quotation
marks are examples of assertions in the EpiMonitor knowledge
framework that give qualitative, abstract meaning to the
quantitative data. EpiMonitor provides a framework for codifying
this knowledge and an engine to instantiate this knowledge on the
aggregated data and results fed to EpiMonitor. The framework
consists of an ontology to structure the ideas of the domain (where
ideas such as "assays," "weights," "threshold cycle," "instrument,"
"environment," and "sample" are defined in a computable
environment). A rules engine/interface allows users to code their
assertions and knowledge about the domain using ideas in the
ontology, and an inference engine applies the rules to the data to
produce knowledge.
[0178] In addition, statements, rules, or sentences can be proposed
by EpiMonitor software platform 100 itself after learning how users
shape and codify their own rules. For example, if a user asserts a
statement in the knowledge base such as "a covariation of target
sequence X and Y leads to a clinical implication of Z," then
EpiMonitor software platform 100 can search the space of all X and
Y for other clinical implications of Z. Another example, if a user
asserts that "Influenza A and Human Adenovirus vary in distribution
in a co-variate manner," EpiMonitor software platform 100 could
suggest rules for other pairs of target sequences that appear to
co-vary together given the aggregated results.
[0179] Further examples of the operation of the knowledge framework
within the EpiMonitor software platform 100 are as follows.
EpiMonitor software platform 100 can use statistics to judge
whether or not new data is valid. A simple illustration is that if
only one data point is collected, the confidence of the measured
statistic is very low; as more measurements are collected, the
confidence estimate may go up, and the software can tag the outcome
appropriately (such as by attaching confidences that sampled
results are not false positives or false negatives). The software
can be adapted to use other statistical/machine learning techniques
for anomaly detection as well, including those developed by the
Centers for Disease Control (CDC).
[0180] Weighting techniques can also take into account spatial and
temporal information. For example, if the flu intensifies
cyclically every December, for example, those findings of flu that
occur in the middle of the cycle can be weighted lower than
findings from other seasons because the in-season incidences are
expected. Higher flu detection rates outside of the expected cycle
may point to a pending outbreak. An example of spatial processing
is when an event with international draw, such as a soccer
tournament, is hosted in a city. The influx of people from diverse
locales may cause a target sequence to be detected that is not
commonly found in the city. Spatial recognition might weight this
finding lower because it has a known source. The data is not
discarded, however, and can be used in later analysis. Data can
further be processed using quality-control metrics. Data collected
across laboratories and instruments may be of different quality.
For example, a sample may be PCR-inhibitory, the instrument may not
be calibrated correctly, etc. A quality score reflecting these
deficiencies can be used to appropriately weight or normalize
data.
[0181] Further, EpiMonitor software platform 100 provides a
framework to mine data such as, for example to apply probabilities
and classify trends. Statistical and machine pattern recognition
techniques can accept as input the current body of quantitative and
qualitative results and the contextual variables collected along
with it. The pattern recognition techniques then classify and
assign Bayesian-type probabilities to new data given the present
corpus of data. A real-life exercise involving probabilities
includes gauging a result in a particular context. For example:
"What is the probability of a `positive response` given that the
real-time PCR result=X and the sample collection location is `San
Francisco, Calif.,` the temperature when the sample was collected
was 60 degrees, the instrument was an ABI 7900, the assay
performance characteristics are X, Y, and Z, and the period of
collection is December-January?"
[0182] In various embodiments, EpiMonitor software 100 can identify
trends in previous outbreaks, identify trends in current data, and
compare current trends with previous trends to recognize possible
outbreaks. Real-life examples of data mining include using temporal
analysis techniques to enable the classification of the next
outbreak given the prior temporal data of outbreaks, or classifying
where influenza may spread given the prior spatial distribution of
an influenza epidemic. The sensitivity and specificity of
predictive measures improve, as a function of data and time, as the
distribution of data acquired by EpiMonitor software 100 more
closely resembles the actual population. Further, as temporal and
spatial data points increase, the EpiMonitor software 100 will be
able to better predict yearly, seasonal, migratory, and regional
trends.
[0183] Data mining analysis can also evaluate the effectiveness of
countermeasures, such as travel restrictions, prescribed drugs,
etc., when applied to an outbreak scenario. Much of the information
regarding countermeasures can be found in the public domain: for
example, travel restrictions and medication sales (such as the
National Retail Data Monitor). Another source of information to
make data mining more accurate and powerful can be the inclusion of
syndromic data (such as chief complaints by patients, lab results,
a clinician's findings) captured by syndromic surveillance systems,
such as RODS (Real-time Outbreak and Disease Surveillance). For
example, a positive result for the Influenza A assay in EpiMonitor
software 100 can be bolstered by the patient's chief complaint of
Influenza A-caused syndromes or by the population's collective
syndromic trends presented by these other systems.
[0184] In various embodiments, the EpiMonitor software platform 100
supports learning rules to apply to new data. For example, a
ruleset that is assigned to a particular assay X, instrument Y, or
sample Z, can be labeled XYZ. The aggregated data pertaining to XYZ
may have a certain distribution, such as Gaussian, with parameters
such as mean and variance. In this way, algorithms that are
abstract to distributions can be used, such as support vector
machines. Algorithms can be specific for distributions, such as
expectation-maximization, which uses a labeled data set for a
particular sample as a training set to learn how to label an
unlabeled set. Such algorithms may also suggest alternative labels
for distributions already labeled. More simply, a
maximum-likelihood approach may be taken, whereby a probability is
estimated based on distributions of the existing data set. In
various embodiments, neural-network type classifiers can also be
implemented.
[0185] In various embodiments, the EpiMonitor software platform 100
can determine cyclical patterns of disease migration through time.
Given real-time PCR qualitative data over a period of time (e.g.,
the number of PLUS Bordetella pertussis results in a given period),
an outbreak can be predicted. Relevant knowledge includes how copy
counts of Bordetella pertussis are associated with illness (i.e.,
did a PLUS count of Bordetella pertussis really cause respiratory
disease X?). Seasonal effects are also helpful; for example,
whether copy counts of Bordetella pertussis may be generally higher
during the month of January. Without prior knowledge of an
outbreak's distribution, time domain signal processing techniques
can be used, such as discussed below. In various embodiments, the
EpiMonitor software platform 100 can be populated with historic
data of disease outbreaks, which may or may not include disease
data.
[0186] Methodologies presented here can operate on numerical data
(such as threshold cycles or gene copy numbers) and/or clinical
data. In addition to time-domain processes, information can be
transformed into the frequency domain using common tools such as
the Fourier transform. Then, the frequency content can be filtered
according to the needs of the EpiMonitor platform 100 and the data
transformed back to the time domain. A selection of time domain
techniques that can be employed includes CUSUM (cumulative sum),
Generalized Linear Model, Exponential Weighted Moving Average, and
ARIMA (Auto-Regressive Integrated Moving Average).
[0187] CUSUM, implemented in the CDC's Early Aberration Reporting
System (EARS), involves the following calculation: S_t = max
.times. { 0 , S_t - 1 + X_t - ( mean_t + k * s_t ) s_t } . ##EQU1##
S_t is the CUSUM calculation on day t, X_t is the signal on day t,
mean_t and s_t are the mean and standard deviation, respectively,
of the baseline signal reading (a period, possibly a week, in which
no outbreak has occurred), and k is the shift from the mean to be
detected.
[0188] The Generalized Linear Model, implemented in the CDC's
BioSense program (as part of the Public Health Information Network)
attempts to take into account day-of-week and other temporal, such
as seasonal, factors. It can be calculated as follows:
E(X_t)=B.sub.--0+B.sub.--1(Sunday)+ . . .
+B.sub.--6(Friday)+B.sub.--7(January)+ . . . +B.sub.--17(November)+
. . . +B.sub.--19(Holiday)+ . . . +B.sub.--19 (time trend). The
expected counts on day t are defined using a generalized linear
model with a particular distribution. The test statistic is the
probability of observing at least X_t cases given E(X_t).
[0189] The Exponential Weighted Moving Average, implemented in the
Department of Defense's ESSENCE (Electronic Surveillance System for
the Early Notification of Community-based Epidemics) system, can be
calculated using the equation Y_t=omega*X_t+(1-omega)*Y_t-1, where
Y.sub.--1=X.sub.--1. The test statistic is
(Y_t-mean_t)/(s_t*[omega/(2-omega)] 0.5). Y_t is the smoothed daily
value for some smoothing parameter omega, and X_t, s_t, and mean_t
are defined in the same manner as for the CUSUM method.
[0190] ARIMA (Auto-Regressive Integrated Moving Average). Auto
regression is a linear regression of the current value of a series
against one or more prior values of the series. A moving average
can be calculated as shown above for the Exponential Weighted
Moving Average. ARIMA combines both the auto regression and moving
average methods, which appears to more effectively correct for
seasonal effects.
[0191] In various embodiments, the EpiMonitor software platform 100
can also analyze disease through location data. Spatial domain
techniques include SaTScan and WSARE (What's Strange About Recent
Events). SaTScan software has been developed to analyze spatial,
temporal, and space-time count data using the spatial, temporal, or
space-time scan statistics. In other words, it is used to test
spatial clusters of disease outbreaks to distinguish between random
and statistically significant data. SaTScan relies on events being
defined, which can include whether a patient carries a particular
syndrome based on their PCR data being over a certain threshold for
a particular target sequence. SaTScan can use a Poisson-based
model, where the number of events in an area is Poisson-distributed
according to a known underlying population at risk, a Bernoulli
model with 0/1 event data such as cases and controls, a space-time
permutation model using only case data, an ordinal model for
categorical data, or an exponential model for survival time data
with or without censored variables.
[0192] WSARE searches for uniqueness using a combination of values
(co-variate) under a set of rules. For example, a rule could be
"Gender=Male and Home Location=94404." This rule determines whether
male patients whose location (postal code) is 94404 have a
particularly high reading for some target sequence X. WSARE
searches among possible rules and selects the most statistically
significant rule for the current time period.
[0193] In various embodiments, the EpiMonitor software platform 100
can associate disease diagnoses and symptoms to multivariate PCR
results. When EpiMonitor software platform 100 is first installed,
prior knowledge and archival data will be limited, thus limiting
the effectiveness of the learning methods that rely on a set of
learning data. EpiMonitor software platform 100 can then begin
associating diagnoses and symptoms to PCR results through
correlation. Because EpiMonitor software platform 100 provides an
infrastructure to collect this data about disease, symptoms,
context, and PCR results, this correlation-type of study may be
achieved.
[0194] In various embodiments, the EpiMonitor software platform 100
can be employed to determine the effects of platform and assay on
copy count. Aggregating data over many permutations of assay,
sample, and platform types can yield knowledge of how
sensitive/specific a particular detection combination is within the
context of confirmatory results or patient syndromic information.
Statistically significant numbers of analyses can also be
performed, creating more trustworthy normalization data. Other
factors that the EpiMonitor software platform 100 can analyze
include the host-susceptibility or host-resistance of populations
and regions to a certain pathogen, response of a population to
therapeutics, and mitigation measures. Mitigation measures can
include travel restrictions, prescribed drugs, vaccines, etc.
[0195] The EpiMonitor software platform 100 can be configured into
different layers. For example, if systems using the EpiMonitor
software platform 100 exist for different entities, such as the
CDC, the Army, Navy, private hospitals, etc., the EpiMonitor
software 100 can be readily configured to add another computational
layer to those already utilized by each entity. This higher layer
would have the capability to utilize information from lower layers
(i.e., systems deployed by the different entities) to analyze data
at a higher level of abstraction for an entity such as an
overseeing federal agency, the World Health Organization (WHO),
etc. Because information about assays, targets, and experimental
methods are stored in EpiMonitor databases, the data can be related
between these distinct sources.
[0196] An example application of the EpiMonitor software platform
100 is presented merely to illustrate some of the possibilities of
the software platform. In this example, the Laboratory Research
Network (LRN) 50 is in communication with a military network. The
military network, through methods that do not need to be disclosed
to the LRN 50, may detect an increased probability that a terrorist
group intends to release a pathogen into the United States at a
certain port of entry. Even though the precise nature of the
pathogen may not be known, certain parameters (which may be
associated with efficacy or transportability) might be associated
with several known viral agents. Based on this information, the LRN
50 and/or the EpiMonitor software platform 100 can determine a
battery of genetic assay tests that would be most effective in
detecting the pathogen, should it be introduced.
[0197] Using the EpiMonitor software platform 100, the LRN 50
communicates with reader-analyzer instruments 176 in the geographic
vicinity of the targeted port of entry. The reader-analyzer
instruments 176 can include displays that instruct instrument
operators to begin testing using a prescribed assay panel. The
assay panels can be kept in storage (such as freezers) at central
distribution points and forwarded as needed. In various
embodiments, a library of different assay panels may be available
at the lab or a smaller library may be carried by an operator of a
handheld instrument 56 or portable instrument 54. If ISAP modules
172 are provided with communication capability and able to
custom-fill microfluidics cards, information to assemble suitable
assays can be sent directly to the ISAP modules 172 from the
EpiMonitor software platform 100. Because the EpiMonitor software
platform 100 supports peer-to-peer communication, as well as
communication through a central network (e.g., the Internet), the
alert can propagate quickly. Peer-to-peer communication among
instruments provides further assurance that all instruments receive
the alert, even those that are not communicating directly with the
LRN.
[0198] Once the microfluidics card 174 has been prepared and
inserted into the reader-analyzer instrument 176, the
reader-analyzer instruments 176 will collect data, typically by
optical analysis of fluorescence signals, to determine if the
target sequences are present. In a real-time PCR system, individual
data collection steps can occur after each thermal cycle and these
individual data sets can be analyzed to produce quantitative
information about the suspected target sequence. As data is
collected concerning individual samples, the LRN 50 can construct
an accurate picture of where certain target sequences are
occurring. This information can be fed back to the military network
to improve its understanding of an emerging terrorist incident.
[0199] For example, assay panels can be developed that can test for
DNA regions of interest within plants. This is useful to analyze
whether DNA introduced into genetically modified organisms (GMOs)
is spreading to other non-GMO crops, or even into indigenous plant
species. Additionally, panels can be created that can test for DNA
regions of interest within bacteria or insects. Such regions of
interest can be DNA corresponding to drug or pesticide resistance.
Samples can be obtained by farmers and/or agricultural workers, and
can be processed on-site or submitted to a central or regional
testing center. In various embodiments, PCR may be used to analyze
samples. The information from each sample can be used by EpiMonitor
software platform 100 to assess the spread and prevalence of
sequences of interest.
[0200] In various embodiments, the present teachings can employ any
of a variety of universal detection approaches involving real-time
PCR and related approaches. For example, the present teachings
contemplate various embodiments in which an encoding ligation
reaction is performed in a first reaction vessel (such as for
example, an eppendorf tube), and a plurality of decoding reactions
are then performed in microfluidic card 174 described herein. For
example, a multiplexed oligonucleotide ligation reaction (OLA) can
be performed to query a plurality of target DNA, wherein each of
the resulting reaction products is encoded with, for example, a
primer portion, and/or, a universal detection portion. By including
a distinct primer pair in each of a plurality of wells of
microfluidic card 174 corresponding to the primers sequences
encoded in the OLA, a given encoded target DNA can be amplified by
that distinct primer pair in a given well of plurality of wells.
Further, a universal detection probe (such as, for example, a
nuclease cleavable TaqMan.RTM. probe) can be included in each of
plurality of wells of microfluidic card 174 to provide for
universal detection of a single universal detection probe.
[0201] Such approaches can result in a universal microfluidic card
174 with its attendant benefits including, among other things, one
or more of economies of scale, manufacturing, and/or ease-of-use.
The nature of the multiplexed encoding reaction can comprise any of
a variety of techniques, including a multiplexed encoding PCR
pre-amplification or a multiplexed encoding OLA. Further, various
approaches for encoding a first sample with a first universal
detection probe, and a second sample with a second universal
detection probe, thereby allowing for two sample comparisons in a
single microfluidic card 174, can also be performed according to
the present teachings. Illustrative embodiments of such encoding
and decoding methods can be found for example in PCT Publication
No. WO2003US0029693 to Aydin et al., PCT Publication No.
WO2003US0029967 to Andersen et al., U.S. Provisional Application
Nos. 60/556,157 and 60/630,681 to Chen et al., U.S. Provisional
Application No. 60/556,224 to Andersen et al., U.S. Provisional
Application No. 60/556,162 to Livak et al., and U.S. Provisional
Application No. 60/556,163 to Lao et al.
[0202] In various embodiments, the detection probes can be suitable
for detecting single nucleotide polymorphisms (SNPs). A specific
example of such detection probes comprises a set of four detection
probes that are identical in sequence but for one nucleotide
position. Each of the four detection probes comprises a different
nucleotide (A, G, C, and T/U) at this position. The detection
probes can be labeled with probe labels capable of producing
different detectable signals that are distinguishable from one
another, such as different fluorophores capable of emitting light
at different, spectrally resolvable wavelengths (e.g.,
4-differently colored fluorophores). In various embodiments, for
example SNP analysis, two colors can be used for two known
variants.
[0203] In various embodiments, at least one of the forward primer
and the reverse primer can further comprise a detection probe. A
detection probe (or its complement) can be situated within the
forward primer between the first primer sequence and the sequence
complementary to the target DNA, or within the reverse primer
between the second primer sequence and the sequence complementary
to the target DNA. A detection probe can comprise at least about 10
nucleotides up to about 70 nucleotides and, more particularly,
about 15 nucleotides, about 20 nucleotides, about 30 nucleotides,
about 50 nucleotides, or about 60 nucleotides. In various
embodiments, a detection probe (or its complement) can further
comprise a Zip-Code.TM. sequence (marketed by Applied Biosystems).
In various embodiments, a detection probe can comprise an
electrophoretic mobility modifier, such as a nucleobase polymer
sequence that can increase the size of a detection probe, or in
various embodiments, a non-nucleobase moiety that increases the
frictional coefficient of the detection probe, such as those
mobility modifier described in commonly-owned U.S. Pat. Nos.
5,470,705, 5,514,543, 5,580,732, and 5,624,800 to Grossman.
[0204] A detection probe comprising a mobility modifier can exhibit
a relative mobility in an electrophoretic or chromatographic
separation medium that allows a user to identify and distinguish
the detection probe from other molecules comprised by the sample.
In various embodiments, a detection probe comprising a sequence
complementary to a detection probe and an electrophoretic mobility
modifier can be, for example, a ZipChute.TM. detection probe
(marketed by Applied Biosystems). In various embodiments,
hybridization of a detection probe with an amplicon, followed by
electrophoretic analysis, can be used to determine the identity and
quantity of the target DNA. In various embodiments, the methods of
the present teachings can include forming a detection mixture
comprising a detection probe set ligation sequence, and a primer
set.
[0205] In various embodiments, any detection probe set ligation
sequence comprised by the detection mixture can be amplified using
PCR on reader-analyzer instrument 176 and thereby form an
amplification product. In various embodiments, detection of
amplification of any detection probe ligation sequence of an
analyte. In various embodiments, detection of amplification by
reader-analyzer instrument 176 can comprise detection of binding of
a detection probe to a detection probe hybridization sequence
comprised by a probe set ligation sequence or an amplification
product thereof. In various embodiments, detecting can comprise
contacting a PCR amplification product such as an amplified probe
set ligation sequence with a detection probe comprising a label
under hybridizing conditions.
[0206] In various embodiments for amplification of a
polynucleotide, assay can comprise a preamplification product,
wherein one or more polynucleotides in an analyte have been
amplified prior to being deposited in at least one of the plurality
of wells. In various embodiments, these methods can further
comprise forming a plurality of preamplification products by
subjecting an initial analyte comprising a plurality of
polynucleotides to at least one cycle of PCR to form a detection
mixture comprising a plurality of preamplification products. The
detection mixture of preamplification products can be then used for
further amplification using microfluidic card 174 and
reader-analyzer instrument 176. In various embodiments,
preamplification comprises the use of isothermal methods.
[0207] In various embodiments, a two-step multiplex amplification
reaction can be performed wherein the first step truncates a
standard multiplex amplification round to boost a copy number of
the DNA target by about 100-1000 or more fold. Following the first
step, the resulting product can be divided into optimized secondary
single amplification reactions, each containing one or more of the
primer sets that were used previously in the first or multiplexed
booster step. The booster step can occur, for example, using an
aqueous target or using a solid phase archived nucleic acid. See,
for example, U.S. Pat. No. 6,605,452, Marmaro.
[0208] In various embodiments, preamplification methods can employ
in vitro transcription (IVT) comprising amplifying at least one
sequence in a collection of nucleic acids sequences. The processes
can comprise synthesizing a nucleic acid by hybridizing a primer
complex to the sequence and extending the primer to form a first
strand complementary to the sequence and a second strand
complementary to the first strand. The primer complex can comprise
a primer complementary to the sequence and a promoter region in
anti-sense orientation with respect to the sequence. Copies of
anti-sense RNA can be transcribed off the second strand. The
promoter region, which can be single or double stranded, can be
capable of inducing transcription from an operably linked DNA
sequence in the presence of ribonucleotides and a RNA polymerase
under suitable conditions. Suitable promoter regions may be
prokaryote viruses, such as from T3 or T7 bacteriophage.
[0209] In various embodiments, the primer can be a single stranded
nucleotide of sufficient length to act as a template for synthesis
of extension products under suitable conditions and can be poly (T)
or a collection of degenerate sequences. In various embodiments,
the methods involve the incorporation of an RNA polymerase promoter
into selected cDNA molecule by priming cDNA synthesis with a primer
complex comprising a synthetic oligonucleotide containing the
promoter. Following synthesis of double-stranded cDNA, a polymerase
generally specific for the promoter can be added, and anti-sense
RNA can be transcribed from the cDNA template. The progressive
synthesis of multiple RNA molecules from a single cDNA template
results in amplified, anti-sense RNA (aRNA) that serves as starting
material for cloning procedures by using random primers. The
amplification, which will typically be at least about 20-40,
typically to 50 to 100 or 250-fold, but can be 500 to 1000-fold or
more, can be achieved from nanogram quantities or less of cDNA.
[0210] In various embodiments, a two stage preamplification method
can be used to preamplify assay in one vessel by IVT and, for
example, this preamplification stage can be 100.times. sample. In
the second stage, the preamplified product can be divided into
aliquots and preamplified by PCR and, for example, this
preamplification stage can be 16,000.times. sample or more.
Although the above preamplification methods can be used in
microfluidic card 174, these are only examples and are
non-limiting.
[0211] In various embodiments, the preamplification can be a
multiplex preamplification, wherein the analyte sample can be
divided into a plurality of aliquots. Each aliquot can then be
subjected to preamplification using a plurality of primer sets for
DNA targets. In various embodiments, the primer sets in at least
some of the plurality of aliquots differ from the primer sets in
the remaining aliquots. Each resulting preamplification product
detection mixture can then be dispersed into at least some of the
plurality of wells of microfluidic card 174 comprising an assay
having corresponding primer sets and detection probes for further
amplification and detection according to the methods described
herein. In various embodiments, the primer sets of assay in each of
the plurality of wells can correspond to the primer sets used in
making the preamplification product detection mixture. The
resulting assay 1000 in each of the plurality of wells 26 thus can
comprise a preamplification product and primer sets and detection
probes for amplification for DNA targets, which, if present in the
analyte sample, have been preamplified.
[0212] Since a plurality of different sequences can be amplified
simultaneously in a single reaction, the multiplex preamplification
can be used in a variety of contexts to effectively increase the
concentration or quantity of a sample available for downstream
analysis and/or assays. In various embodiments, because of the
increased concentration or quantity of target DNA, significantly
more analyses can be performed with multiplex amplified samples
than can be performed with the original sample. In various
embodiments, multiplex amplification further permits the ability to
perform analyses that require more sample or a higher concentration
of sample than was originally available. In various embodiments,
multiplex amplification enables downstream analysis for assays that
could not have been possible with the original sample due to its
limited quantity.
[0213] In various embodiments, the plurality of aliquots can
comprise 16 aliquots with each of the 16 aliquots comprising about
1536 primer sets. In various embodiments, a sample comprising a
whole genome for a species, for example a human genome, can be
preamplified. In various embodiments, the plurality of aliquots can
be greater than 16 aliquots. In various embodiments, the number of
primer sets can be greater than 1536 primer sets. In various
embodiments, the plurality of aliquots can be less than 16 aliquots
and the number of primer sets can be greater than 1536 primer sets.
For examples of various embodiments, see PCT Publication No. WO
2004/051218 to Andersen and Ruff.
[0214] In various embodiments, assay can be preamplified, as
discussed herein, in order to increase the amount of target DNA
prior to distribution into a plurality of wells of a microplate. In
various embodiments, assay can be collected, for example, via a
needle biopsy that typically yields a small amount of sample.
Distributing this sample across a large number of wells can result
in variances in sample distribution that can affect the veracity of
subsequent gene expression computations. In such situations, assay
can be preamplified using, for example, a pooled primer set to
increase the number of copies of all target DNA simultaneously.
[0215] In various embodiments, preamplification processes can be
non-biased, such that all target DNA are amplified similarly and to
about the same power. In various embodiments, each target DNA can
be amplified reproducibly from one input sample to the next input
sample. For example, if target DNA X is initially present in sample
A at 100 target molecules, then after 10 cycles of PCR
amplification (1000-fold), 100,000 target molecules should be
present. Continuing with the example, if target DNA X is initially
present in sample B at 500 target molecules, then after 10 cycles
of PCR amplification (1000-fold), 500,000 target molecules should
be present. In this example, the ratio of target DNA X in samples
A/B remains constant before and after the amplification
procedure.
[0216] In various embodiments, a minor proportion of all target DNA
can have an observed preamplification efficiency of less than 100%.
In various embodiments, if the amplification bias is reproducible
and consistent from one input sample to another, then the ability
to accurately compute comparative relative quantitation between any
two samples containing different relative amounts of target can be
maintained. Continuing the example from above and assuming 50%
reproducible amplification efficiency, if target DNA X is initially
present in sample A at 100 target molecules, then after 10 cycles
of PCR amplification (50% of 1000-fold), 50,000 target molecules
should be present. Further continuing the example, if target X is
initially present in sample B at 500 target molecules, then after
10 cycles of PCR amplification (50% of 1000-fold), 250,000 target
molecules should be present. In this example, the ratio of template
X in samples A/B remains constant before and after the
amplification procedure and is the same ratio as the 100%
efficiency scenario.
[0217] In various embodiments, an unbiased amplification of each
target DNA (x, y, z, etc.) can be determined by calculating the
difference in C.sub.T value of the target DNA (x, y, z, etc.) from
the C.sub.T value of a selected endogenous reference, and such
calculation is referred to as the .DELTA.C.sub.T value for each
given target DNA, as described above. In various embodiments, a
reference for a bias calculation can be non-preamplified, amplified
target DNA and an experimental sample can be a preamplified
amplified target DNA. In various embodiments, the standard sample
and experimental sample can originate from the same sample, for
example, same tissue, same individual and/or same species. In
various embodiments, comparison of .DELTA.C.sub.T values between
the non-preamplified amplified target DNA and preamplified
amplified target DNA can provide a measure for the bias of the
preamplification process between the endogenous reference and the
target DNA (x, y, z, etc.).
[0218] In various embodiments, the difference between the two
.DELTA.C.sub.T values (.DELTA..DELTA.C.sub.T) can be zero and as
such there is no bias from preamplification. This is explained in
greater detail below with reference to FIG. 20. In various
embodiments, the gene expression analysis system can be calibrated
for potential differences in preamplification efficiency that can
arise from a variety of sources, such as the effects of multiple
primer sets in the same reaction. In various embodiments,
calibration can be performed by computing a reference number that
reflects preamplification bias. Reference number similarity for a
given target DNA across different samples is indicative that the
preamplification reaction ACTS can be used to achieve reliable gene
expression computations.
[0219] In various embodiments of the present teaching, a gene
expression analysis system can compute these reference numbers by
collecting a sample (designated as Sample A (S.sub.A)) and
processing it with one or more protocols. A first protocol
comprises running individual PCR gene expression reactions for each
target DNA (T.sub.x) relative to an endogenous reference (endo),
such as, for example, 18s or GAPDH. These reactions can yield cycle
threshold values for each target DNA relative to the endogenous
control; as computed by: .DELTA.C.sub.T not preamplified
T.sub.xS.sub.A=C.sub.T not preamplified T.sub.xS.sub.A-C.sub.T
notpreamplified endo
[0220] A second protocol can comprise running a single PCR
preamplification step on assay with, for example, a pooled primer
set. In various embodiments, the pooled primer set can contain
primers for each target DNA. Subsequently, the preamplified product
can be distributed among a plurality of wells of a microplate. PCR
gene-expression reactions can be run for each preamplified target
DNA (T.sub.x) relative to an endogenous reference (endo). These
reactions can yield cycle threshold values for each preamplified
target DNA relative to the endogenous control, as computed by:
.DELTA.C.sub.T preamplified T.sub.xS.sub.A=C.sub.T preamplified
T.sub.xS.sub.A-C.sub.T preamplified endo T.sub.xS.sub.A
[0221] A difference between these .DELTA.C.sub.T not preamplified
T.sub.xS.sub.A and .DELTA.C.sub.T preamplified T.sub.xS.sub.A can
be computed by: .DELTA..DELTA.C.sub.TT.sub.xS.sub.A=.DELTA.C.sub.T
not preamplified T.sub.xS.sub.A-.DELTA.C.sub.T preamplified
T.sub.xS.sub.A
[0222] In various embodiments, a value for
.DELTA..DELTA.C.sub.TT.sub.xS.sub.A can be zero or close to zero,
which can indicate that there is no bias in the preamplification of
target DNA T.sub.x. In various embodiments, a negative
.DELTA..DELTA.C.sub.T T.sub.xS.sub.A value can indicate the
preamplification process was less than 100% efficient for a given
target DNA (T.sub.x). For example, when using an IVT
preamplification process, a percentage of target DNA with a
.DELTA..DELTA.C.sub.T of +/-1 C.sub.T of zero can be .about.50%. In
another example, when using a multiplex preamplification process, a
percentage of target DNA with a .DELTA..DELTA.C.sub.T of +/-1
C.sub.T of zero can be .about.90%.
[0223] In various embodiments, amplification efficiency can be less
than 100% for a particular target DNA, therefore
.DELTA..DELTA.C.sub.T is less than zero for the particular target
DNA. An example can be an evaluation of .DELTA..DELTA.C.sub.T
values for a group of target DNA from a 1536-plex for the multiplex
preamplification process including four different human sample
input sources: liver, lung, brain and an universal reference tissue
composite. In this example, most .DELTA..DELTA.C.sub.T values are
near zero, however, some of the target DNA have a negative
.DELTA..DELTA.C.sub.T value but these negative values are
reproducible from one sample input source to another. In various
embodiments, a gene expression analysis system can determine if a
bias exists for target DNA analyzed for different sample inputs.
Other apparatus, compositions, and methods that may be useful
herein can be found in commonly assigned U.S. patent application
Ser. No. 11/086,261.
[0224] Some embodiments and the examples described herein are
exemplary and not intended to be limiting in describing the full
scope of compositions and methods of these teachings. Equivalent
changes, modifications, and variations of some embodiments,
materials, compositions, and methods can be made within the scope
of the present teachings, with substantially similar results.
* * * * *