U.S. patent application number 14/972715 was filed with the patent office on 2016-04-14 for computer-implemented system and method for identifying similar patients.
The applicant listed for this patent is FOUNDATION MEDICINE, INC.. Invention is credited to Mary Pat Lancelotta, Gaurav Singal.
Application Number | 20160103973 14/972715 |
Document ID | / |
Family ID | 55655628 |
Filed Date | 2016-04-14 |
United States Patent
Application |
20160103973 |
Kind Code |
A1 |
Singal; Gaurav ; et
al. |
April 14, 2016 |
COMPUTER-IMPLEMENTED SYSTEM AND METHOD FOR IDENTIFYING SIMILAR
PATIENTS
Abstract
A method, system, and database is provided that permits users
treating patients with genomic alteration to more easily and
effectively exchange information with other users treating patients
with similar genomic alterations. In one example, a user may be
permitted to assign genomic alteration tags to patients and filter
through patients based on the genomic alterations. Additional
features, such as automatically identifying, and facilitating
communication with, other users that have treated similar patients
may be provided to further enhance the user's ability to treat
genomic alterations.
Inventors: |
Singal; Gaurav; (Cambridge,
MA) ; Lancelotta; Mary Pat; (Somerville, MA) |
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Applicant: |
Name |
City |
State |
Country |
Type |
FOUNDATION MEDICINE, INC. |
Cambridge |
MA |
US |
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Family ID: |
55655628 |
Appl. No.: |
14/972715 |
Filed: |
December 17, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14463068 |
Aug 19, 2014 |
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14972715 |
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14146743 |
Jan 3, 2014 |
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14463068 |
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62093397 |
Dec 17, 2014 |
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61749291 |
Jan 5, 2013 |
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61749288 |
Jan 5, 2013 |
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61749291 |
Jan 5, 2013 |
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61749288 |
Jan 5, 2013 |
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Current U.S.
Class: |
705/3 |
Current CPC
Class: |
G16H 10/60 20180101;
G16B 50/00 20190201; G06F 19/325 20130101; G06Q 50/24 20130101;
G16H 80/00 20180101; G16H 50/70 20180101; G06F 16/9024 20190101;
G16H 50/20 20180101; G06F 16/245 20190101; G16H 70/60 20180101;
G16H 15/00 20180101 |
International
Class: |
G06F 19/00 20060101
G06F019/00; G06F 17/30 20060101 G06F017/30 |
Claims
1. A distributed computer system comprising: a database comprising
patient-specific pathology information relating to a plurality of
patients including at least one current patient; an interface for a
practitioner that provides treatment for the at least one current
patient; and a matching component adapted to identify a similar
patient among the plurality of patients based on a similarity
between the patient-specific pathology information and
patient-specific pathology information of the similar patient.
2. The system according to claim 1, wherein the patient-specific
pathology information relating to the patient includes at least one
of a group comprising disease phenotype information and genetic
alteration information.
3. The system according to claim 2, wherein the disease phenotype
information is arranged into one or more disease ontology groups,
and wherein the matching component is adapted to locate the similar
patient based on the one or more disease ontology groups.
4. The system according to claim 3, wherein the genetic alteration
information is arranged into one or more alteration groups, and
wherein the matching component is adapted to locate the similar
patient based on the one or more alteration groups.
5. The system according to claim 1, wherein the interface for a
practitioner is adapted to display an indication to the
practitioner that the similar patient is identified.
6. The system according to claim 5, wherein the system further
comprises a communication component that permits the practitioner
to communicate with a treating practitioner related to the
identified similar patient.
7. The system according to claim 5, wherein the system identifies
other practitioners that have selected to communicate about their
patients.
8. The system according to claim 5, wherein the system identifies
other practitioners that have been selected to communicate about
their patients.
9. The system according to claim 6, wherein the communication
component includes an interface that accepts structured data from
at least one of the other practitioners.
10. The system according to claim 6, wherein the communication
component includes an interface that accepts response data from at
least one of the other practitioners.
11. The system according to claim 10, wherein the response data
includes structured and unstructured data.
12. The system according to claim 6, wherein the communication
component includes an interface presents response data in a matrix
of results.
13. The system according to claim 12, wherein the matrix includes
de-identified information relating to the identified similar
patient.
14. The system according to claim 13, wherein the matrix includes
genomic data and associated response data.
15. The system according to claim 11, wherein the system includes a
component that aggregates structured data among a plurality of
identified similar patients and an interface that presents the
aggregated structured data to the practitioner.
16. The system according to claim 1, wherein the system is adapted
to collect biomarker data and is adapted to store the biomarker
data in the database.
17. The system according to claim 16, wherein the database is
adapted to store the patient-specific pathology information and
biomarker data within a graph-based data structure.
18. The system according to claim 17, wherein the database is
adapted to store information organized into a plurality of tuples
of information.
19. The system according to claim 18, wherein each of the plurality
of tuples of information include at least two elements connected by
a relation.
20. The system according to claim 17, wherein the system includes a
component adapted to determine one or more actionable items within
the graph-based data structure responsive to the biomarker data and
patient-specific pathology information.
21. The system according to claim 18, wherein the plurality of
tuples are organized by the system into a walkable graph
representation.
22. A method comprising acts of: storing, in a database,
patient-specific pathology information relating to a plurality of
patients including at least one current patient; presenting, to a
practitioner, a computer-based interface of a distributed computer
system, the practitioner providing treatment for the at least one
current patient; and identifying, by the distributed computer
system, a similar patient among the plurality of patients
responsive to an act of determining a similarity between the
patient-specific pathology information and patient-specific
pathology information of the similar patient.
23. The method according to claim 22, wherein the patient-specific
pathology information relating to the patient includes at least one
of a group comprising disease phenotype information and genetic
alteration information.
24. The method according to claim 23, wherein the disease phenotype
information is arranged into one or more disease ontology groups,
and wherein the matching component is adapted to locate the similar
patient based on the one or more disease ontology groups.
25. The method according to claim 24, wherein the method further
comprises an act of arranging genetic alteration information into
one or more alteration groups, and wherein the method further
comprises locating the similar patient based on the one or more
alteration groups.
26. The method according to claim 22, wherein the method further
comprises an act of displaying, in the interface to the
practitioner, an indication that the similar patient is
identified.
27. The method according to claim 23, wherein the method further
comprises an act of permitting the practitioner to communicate with
a treating practitioner related to the identified similar
patient.
28. The method according to claim 26, wherein the method further
comprises an act of identifying, by the computer system, other
practitioners that have selected to communicate about their
patients.
29. The method according to claim 26, wherein the method further
comprises an act of identifying, by the computer system, other
practitioners that have been selected to communicate about their
patients.
30. The method according to claim 27, wherein the method further
comprises an act of accepting, from at least one of the other
practitioners within an interface of the computer system, response
data that includes structured data.
31. The method according to claim 27, wherein the method further
comprises an act of accepting, from at least one of the other
practitioners within an interface of the computer system, response
data.
32. The method according to claim 31, wherein the response data
includes structured and unstructured data.
33. The method according to claim 27, wherein the method further
comprises an act of presenting, within an interface of the computer
system, response data in a matrix of results.
34. The method according to claim 33, wherein the matrix includes
de-identified information relating to the identified similar
patient.
35. The method according to claim 34, wherein the matrix includes
genomic data and associated response data.
36. The method according to claim 32, wherein the method further
comprises an act of aggregating, by the computer system, structured
data among a plurality of identified similar patients and
presenting, within an interface of the computer system, the
aggregated structured data to the practitioner.
37. The method according to claim 22, wherein the method further
comprises an act of collecting biomarker data and storing the
biomarker data in the database.
38. The method according to claim 37, wherein the method further
comprises an act of storing the patient-specific pathology
information and biomarker data within a graph-based data
structure.
39. The method according to claim 38, wherein the method further
comprises an act of organizing the patient-specific pathology
information and biomarker data into a plurality of tuples of
information.
40. The method according to claim 39, wherein each of the plurality
of tuples of information include at least two elements connected by
a relation.
41. The method according to claim 38, wherein the method further
comprises an act of determining one or more actionable items within
the graph-based data structure responsive to the biomarker data and
patient-specific pathology information.
42. The method according to claim 39, wherein the plurality of
tuples are organized by the system into a walkable graph
representation.
Description
RELATED APPLICATIONS
[0001] This application claims priority under 35 U.S.C.
.sctn.119(e) to U.S. Provisional Application Ser. No. 62/093,397
entitled "COMPUTER-IMPLEMENTED SYSTEM AND METHOD FOR IDENTIFYING
SIMILAR PATIENTS," filed Dec. 17, 2014, which application is herein
incorporated by reference in its entirety. This application is a
continuation-in-part of U.S. patent application Ser. No. 14/463,068
entitled "SYSTEM AND METHOD FOR MANAGING GENOMIC INFORMATION" filed
Aug. 19, 2014, which claims priority under 35 U.S.C. .sctn.119(e)
to U.S. Provisional App. No. 61/749,291, entitled "SYSTEM AND
METHOD FOR MANAGING GENOMIC TESTING RESULTS," filed Jan. 5, 2013,
and U.S. Provisional App. No. 61/749,288, entitled "SYSTEM AND
METHOD FOR OUTCOME TRACKING AND ANALYSIS," filed Jan. 5, 2013. This
application is also a continuation-in-part of U.S. application Ser.
No. 14/146,743, entitled SYSTEM AND METHOD FOR MANAGING GENOMIC
TESTING RESULTS, filed Jan. 3, 2014 which is a non-provisional
application of and claims priority under 35 U.S.C. .sctn.119(e) to
U.S. Provisional App. No. 61/749,291, entitled "SYSTEM AND METHOD
FOR MANAGING GENOMIC TESTING RESULTS," filed Jan. 5, 2013, and U.S.
Provisional App. No. 61/749,288, entitled "SYSTEM AND METHOD FOR
OUTCOME TRACKING AND ANALYSIS," filed Jan. 5, 2013, of which
applications are incorporated herein by reference by their
entirety.
BACKGROUND
[0002] Genomic testing of cancer cells shows significant promise
towards developing better understanding of cancers and managing
more effective treatment approaches. Genomic testing involves the
sequencing of the genome of a patient's cancer cells and
identifying any genomic alteration in those cells. A genomic
alteration can include, for example, mutations, deleted gene
sequences, amplifications, translocation, among other options.
Understanding these genomic alterations as they are found in a
specific patient's cancer may also help develop better treatments
and help identify the best approaches for treating specific cancer
variants using genomic information.
SUMMARY
[0003] It is realized that the adoption and integration of genomic
testing into daily practice faces significant hurdles, in part,
based on the ability to access and the volume of the information
that needs to be reviewed and understood in order to facilitate
treatment decisions. Further, the complexity of the genomic
analysis has also limited its potential and in some cases limited
implementation. It is also realized that conventional approaches
for providing genomic alteration information are not readily
appreciated by the majority of practitioners (e.g., physicians,
oncologists, etc.) for their diagnostic value. Nor can the majority
of practitioners incorporate such information into actionable steps
to be taken with a given patient, or identify clinically relevant
information. Interpreting genomic data is further complicated by
the sparsity of some genomic findings and the associated scarcity
of public data regarding the efficacy of treatments targeted
against those findings, especially when stratified by tumor
type.
[0004] According to one aspect of the present invention, it is
realized that new tools that permit a practitioners such as
physicians to more easily locate other physicians that have
successfully treated similar patients would be beneficial to their
practice. Further, tools that permit identification of successful
treatments for specific genomic alterations in a particular cancer
type determined from a current patient would also increase the
likelihood that the patient could be successfully treated. To this
end, a system may be provided that permits the user to locate
similar patients using genomic information related to a patient's
cancer. For instance, information relating to genetic alterations
and the patient's tumor type may be used to identify similar
patients within a database. Preferably, such information may be
used to locate similar patients where treatment was successful or
had some other positive outcome.
[0005] According to other aspects, curated information is provided
on the system to enable physicians to make informed decisions
regarding the implications of the presence of specific genomic
alterations. Curated information includes interpretations of
available information (e.g., existing therapies, clinical trials,
journals, and publications) for genomic alterations that may be
found in a patient's tumor as a result of the genomic analysis. The
genomic analysis can identify, for example, a tumor type, an
affected gene, and an alteration type specific to a given patient
and their cancer. The available information that can be curated can
be associated with, and organized by, any of the information
provided in the genomic analysis (e.g., specific to tumor type,
gene, and alteration). Such information may be stored in a database
and accessed by physicians though one or more user interfaces.
[0006] Conventional interfaces such as databases are not generally
capable of matching patient information. For instance, much of the
data stored in such systems is generally sparse, and it is very
difficult to determine, through manual searching, all of the
information and relevant patient data that might be applicable to a
particular patient. According to one aspect of the present
invention, an ability is provided for searching a centralized
database of genomic information collected on a number of patients,
and performing a matching process by which similar patients may be
discovered. Further, tools may be provided that permit
practitioners such as physicians to contact other physicians that
have treated the identified similar patients. Because such a tool
is provided, it allows for fast identification of similar patient
scenarios, and increases the ability of the physician to solicit
information regarding treatment.
[0007] According to another aspect of the present invention, the
communication permits patients to be matched and identified without
revealing their identities to other physician users. However,
according to one aspect, physicians are provided a facility for
communicating between physicians while not revealing contact
information such that the identification of physicians with
matching patients is kept confidential. Both the initial
communication and responses to the inquiry may be stored within the
database and associated with the particular patient and/or cancer
type. After a particular communication between physicians occurs,
this information may be stored in the database and accessed for
future use (e.g., by another physician searching for a similar
patient having a similar cancer). By providing such communication
capabilities, a physician or other health care provider may more
easily locate the best treatment information in a timely
manner.
[0008] According to another aspect of the present invention, a
communication system is provided that allows physician users to
discuss cases in a semi-structured manner. For instance, some
questions are provided in a structured format where discrete
responses are provided (e.g., best response, duration, etc.). Some
questions are unstructured that permit other physician users to
convey a larger clinical narrative (e.g., via any additional
comments field, via questions such as "Why was the patient not
treated with a therapy?" among others). By providing some
structured data, responses may be aggregated from among physician
providers and reused by the system. In one example implementation,
structured data responses from multiple providers may be aggregated
and provided to a physician user within an interface. In one
embodiment, such information may be presented to a physician user
within a matrix of results. Such information may include, for
example, de-identified information regarding similar patients
identified through a matching process. The presented information
may also include genomic information as well as the response
information collected from other physician users.
[0009] According to another aspect of the present invention, is
appreciated that patient context information may be used to perform
a matching process for identifying similar patients. As used
herein, patient context information includes information that
describes a state of a particular patient with respect to his/her
disease state, along with the generic state of the disease. In one
embodiment, patient context information may include disease
phenotype and genetic alterations. According to one aspect of the
present invention, it is realized that disease subtypes can be
arranged in disease groups depending on the clinical and functional
similarity of the diseases. Such disease subtypes (e.g., tumor
types) can be grouped according to expert information, creating
disease ontology groups (DOGs). In a similar manner, alterations
may be grouped into alteration groups that are functionally
similar. Disease ontology groups (DOGs) and alteration groups (AGs)
can be used to locate similar patients. In particular, similar
patients may be defined as those having the same disease type (or
another disease type in the same DOG) and having an alteration that
falls within the same alteration group (AG).
[0010] In one aspect of the present invention, it is appreciated
that treatment data may be very sparse, such that an exact match
based on a specific information may not yield any result. However,
it is appreciated that diseases may be clinically similar such that
patients and their outcome data for similar diseases may be grouped
or pooled together, such that a search result may be determined.
Also, it is appreciated that alteration data can be generalized and
therefore patient data and associated outcome data may be grouped
together for the purpose of performing a similarity search.
[0011] Once one or more similar patients are identified, a
physician may be permitted (e.g., via a communication tool
presented within a user interface) to contact another physician who
treated or is treating the identified similar patient. In one
embodiment, patient data is anonymized and only the physician
contact information is provided, if offered by the responding
physician. However, the communication facility may be capable of
indicating to the responding physician which similar patient
triggered the communication so that the responding physician may
respond appropriately.
[0012] Further, after physicians are identified as having similar
patients, the physician may be contacted by the computer system to
request information about how they treated those patients and/or to
share their experiences. As these physicians respond to these
requests, the requests and associated responses may be stored
within a database. This database of communications between
physicians may be used for future treatment information that can be
presented to other physicians responsive to future queries (e.g.,
other patient matching instances).
[0013] There may be several communication instances that provide
additional functionality, such as initiating contact with another
physician based on a single patient per request, even though it may
be many similar patients that are matched. According to one aspect,
it is appreciated that a physician might be overwhelmed when
requested information regarding multiple patients. Thus, according
to one embodiment, the most relevant patient that matches the
patient currently being treated is presented to the physician.
Also, it is appreciated that if a physician has already responded
to a similar request but there are multiple matching patients,
information that has already been stored within the database may be
presented, however, the system may also prompt the physician about
other patients so that the database may be improved. In another
example patient, the physician has entered a response more than a
predetermined amount of time, is appreciated that the patient's
treatment course may have changed, and the physician may be
prompted to provide updated information. Other embodiments of the
present invention relate to the interface used to communicate with
physicians and to encourage their engagement with other physicians
and the system.
[0014] According to one aspect of the present invention, a
distributed computer system is provided comprising a database
including patient-specific pathology information relating to a
plurality of patients including at least one current patient, an
interface for a practitioner that provides treatment for the at
least one current patient, and a matching component adapted to
identify a similar patient among the plurality of patients based on
a similarity between the patient-specific pathology information and
patient-specific pathology information of the similar patient. In
one embodiment of the present invention, the patient-specific
pathology information relating to the patient includes at least one
of a group comprising disease phenotype information and genetic
alteration information.
[0015] In another embodiment, the disease phenotype information is
arranged into one or more disease ontology groups, and wherein the
matching component is adapted to locate the similar patient based
on the one or more disease ontology groups. In another embodiment,
the genetic alteration information is arranged into one or more
alteration groups, and wherein the matching component is adapted to
locate the similar patient based on the one or more alteration
groups. In another embodiment, the interface for a practitioner is
adapted to display an indication to the practitioner that the
similar patient is identified.
[0016] In another embodiment, the system further comprises a
communication component that permits the practitioner to
communicate with a treating practitioner related to the identified
similar patient. In another embodiment, the system is adapted to
identify other practitioners that have selected to communicate
about their patients. In another embodiment, the system identifies
other practitioners that have been selected to communicate about
their patients.
[0017] In another embodiment, the communication component includes
an interface that accepts structured data from at least one of the
other practitioners. In another embodiment, the communication
component includes an interface that accepts response data from at
least one of the other practitioners. In another embodiment, the
response data includes structured and unstructured data.
[0018] In another embodiment, the communication component includes
an interface presents response data in a matrix of results. In
another embodiment, the matrix includes de-identified information
relating to the identified similar patient. In another embodiment,
the matrix includes genomic data and associated response data. In
another embodiment, the system includes a component that aggregates
structured data among a plurality of identified similar patients
and an interface that presents the aggregated structured data to
the practitioner.
[0019] In another embodiment, the system is adapted to collect
biomarker data and is adapted to store the biomarker data in the
database. In another embodiment, the database is adapted to store
the patient-specific pathology information and biomarker data
within a graph-based data structure. In another embodiment, the
database is adapted to store information organized into a plurality
of tuples of information. In another embodiment, each of the
plurality of tuples of information includes at least two elements
connected by a relation. In another embodiment, the system includes
a component adapted to determine one or more actionable items
within the graph-based data structure responsive to the biomarker
data and patient-specific pathology information. In another
embodiment, the plurality of tuples is organized by the system into
a walkable graph representation.
[0020] According to another aspect of the present invention, a
method is provided comprising acts of storing, in a database,
patient-specific pathology information relating to a plurality of
patients including at least one current patient, presenting, to a
practitioner, a computer-based interface of a distributed computer
system, the practitioner providing treatment for the at least one
current patient, and identifying, by the distributed computer
system, a similar patient among the plurality of patients
responsive to an act of determining a similarity between the
patient-specific pathology information and patient-specific
pathology information of the similar patient. In one embodiment of
the present invention, the patient-specific pathology information
relating to the patient includes at least one of a group comprising
disease phenotype information and genetic alteration
information.
[0021] In another embodiment of the present invention, the disease
phenotype information is arranged into one or more disease ontology
groups, and wherein the matching component is adapted to locate the
similar patient based on the one or more disease ontology groups.
In another embodiment, the method further comprises an act of
arranging genetic alteration information into one or more
alteration groups, and wherein the method further comprises
locating the similar patient based on the one or more alteration
groups.
[0022] In another embodiment, the method further comprises an act
of displaying, in the interface to the practitioner, an indication
that the similar patient is identified. In another embodiment, the
method further comprises an act of permitting the practitioner to
communicate with a treating practitioner related to the identified
similar patient. In another embodiment, the method further
comprises an act of identifying, by the computer system, other
practitioners that have selected to communicate about their
patients. In another embodiment, the method further comprises an
act of identifying, by the computer system, other practitioners
that have been selected to communicate about their patients.
[0023] In another embodiment, the method further comprises an act
of accepting, from at least one of the other practitioners within
an interface of the computer system, response data that includes
structured data. In another embodiment, the method further
comprises an act of accepting, from at least one of the other
practitioners within an interface of the computer system, response
data. In another embodiment, the response data includes structured
and unstructured data. In another embodiment, the method further
comprises an act of presenting, within an interface of the computer
system, response data in a matrix of results. In another
embodiment, the matrix includes de-identified information relating
to the identified similar patient. In another embodiment, the
matrix includes genomic data and associated response data.
[0024] In another embodiment, the method further comprises an act
of aggregating, by the computer system, structured data among a
plurality of identified similar patients and presenting, within an
interface of the computer system, the aggregated structured data to
the practitioner. In another embodiment, method further comprises
an act of collecting biomarker data and storing the biomarker data
in the database.
[0025] In another embodiment, the method further comprises an act
of storing the patient-specific pathology information and biomarker
data within a graph-based data structure. In another embodiment,
the method further comprises an act of organizing the
patient-specific pathology information and biomarker data into a
plurality of tuples of information. In another embodiment, each of
the plurality of tuples of information includes at least two
elements connected by a relation. In another embodiment, the method
further comprises an act of determining one or more actionable
items within the graph-based data structure responsive to the
biomarker data and patient-specific pathology information. In
another embodiment, the plurality of tuples are organized by the
system into a walkable graph representation.
[0026] Still other aspects, examples, and advantages of these
exemplary aspects and examples, are discussed in detail below.
Moreover, it is to be understood that both the foregoing
information and the following detailed description are merely
illustrative examples of various aspects and examples, and are
intended to provide an overview or framework for understanding the
nature and character of the claimed aspects and examples. Any
example disclosed herein may be combined with any other example in
any manner consistent with at least one of the objects, aims, and
needs disclosed herein, and references to "an example," "some
examples," "an alternate example," "various examples," "one
example," "at least one example," "this and other examples" or the
like are not necessarily mutually exclusive and are intended to
indicate that a particular feature, structure, or characteristic
described in connection with the example may be included in at
least one example. The appearances of such terms herein are not
necessarily all referring to the same example.
BRIEF DESCRIPTION OF THE DRAWINGS
[0027] Various aspects of at least one example are discussed below
with reference to the accompanying figures, which are not intended
to be drawn to scale. The figures are included to provide an
illustration and a further understanding of the various aspects and
examples, and are incorporated in and constitute a part of this
specification, but are not intended as a definition of the limits
of a particular example. The drawings, together with the remainder
of the specification, serve to explain principles and operations of
the described and claimed aspects and examples. In the figures,
each identical or nearly identical component that is illustrated in
various figures is represented by a like numeral. For purposes of
clarity, not every component may be labeled in every figure. In the
figures:
[0028] FIG. 1 is a block diagram showing a system for identifying
similar patients according to various aspects of the present
invention;
[0029] FIG. 2 shows an example process for identifying similar
patients according to one embodiment of the present invention;
[0030] FIG. 3 shows an example process for creating a genomic
database that may be used with various aspects of the present
invention;
[0031] FIG. 4 shows disease ontology grouping that may be performed
according to one embodiment of the present invention;
[0032] FIG. 5 shows an example process that may be performed
locating similar patients using disease ontology groups according
to one embodiment of the present invention;
[0033] FIG. 6 shows an example process for locating historical
responses and presenting them to physician users according to one
embodiment of the present invention;
[0034] FIGS. 7A-7C show an example process for conducting a
communication session between physicians according to one
embodiment of the present invention;
[0035] FIG. 8 shows an example system upon which various aspects of
the present invention may be practiced;
[0036] FIG. 9 shows yet another example system upon which various
aspects of the present invention may be practiced;
[0037] FIG. 10 shows another system there may be used to generate
data from genomic test results according to various aspects of the
present invention;
[0038] FIG. 11 illustrates one example of a user interface showing
patient and treatment information according to one embodiment of
the present invention;
[0039] FIG. 12 illustrates another example of a user interface
showing a connection user interface according to some embodiments
of the present invention; and
[0040] FIG. 13 illustrates yet another example of a user interface
displaying a feedback view according to various aspects of the
present invention.
DETAILED DESCRIPTION
[0041] As described above, genomic testing provides unique
opportunities to make more informed treatment decisions, especially
in the field of cancer diagnosis and therapy development. Some
conventional approaches can fail to provide useable information
within the volumes of information provided as results of genomic
testing. Further, it is appreciated that some conventional
approaches fail to focus practitioners on actionable information
within the genomic testing information and any associated treatment
information.
[0042] Accordingly, provided are systems and methods for managing
genomic testing information and providing a capability for
identifying similar patients for the purpose of allowing physicians
and other practitioners the ability to exchange information to
improve the quality of treatment.
[0043] One or more aspects of the present invention may be
implemented using a distributed computer system 100 is shown in
FIG. 1. System 100 may include one or more client systems (e.g.,
computer system 102A, computer system 102B) through which one or
more practitioners (e.g., physician user 102A, physician user 102B)
interface to the system. As discussed, a particular physician may
desire to determine treatment options for a particular patient
(e.g., patient 103A).
[0044] In one embodiment, a patient's tumor and is analyzed and
stored as part of a patient record (e.g., as part of patient
record(s) 107 within a database 105). The information may include,
for example, a tumor type, alteration information, outcome
information, treatment information, among other information.
Further, system 100 may store disease ontology information 108 that
describes information identifying various diseases. In one
embodiment, such diseases may include different types of cancers.
In another embodiment, it is appreciated that some types of cancers
are similar and therefore they may be grouped for the purpose of
identifying patients with similar disease states.
[0045] Further, system 100 may include a database of genomic
information 110, including, but not limited to, alteration data
including grouping information that associates related alterations.
Genomic information 110 may include other information, such as for
example, gene information, gene associations, gene states,
therapies for particular genetic states and know effects of such
therapies, among other related information.
[0046] In one embodiment, system 100 may include a matching engine
that determines one or more similar patients as compared to a
current patient being analyzed. For instance, system 100 may be
capable of communicating and receiving information regarding a
number of patients (e.g., patients 103A, 103B) as received from
multiple sources. System 100 may be adapted to communicate with
other physicians (e.g., physician 101B) that treat other patients
(e.g., patient 103B). System 100 and its matching engine may
identify other patients (e.g., patient 103B) who are similar to a
current patient (e.g., patient 103A). After identifying one or more
similar patients, system 100 may be capable of facilitating
communication between treating physicians associated with the
matched patients (e.g., patient 103A, patient 103B).
[0047] In one example implementation, patient context information
may be used to perform a matching process for identifying similar
patients. In one embodiment, patient context information may
include disease phenotype and genetic alterations. As discussed, it
is realized that disease subtypes can be arranged in disease groups
depending on the clinical and functional similarity of the
diseases. Such disease subtypes (e.g., tumor types) can be grouped
according to expert information, creating disease ontology groups
(DOGs). In a similar manner, alterations may be grouped into
alteration groups that are functionally similar. Disease ontology
groups (DOGs) and alteration groups (AGs) can be used to locate
similar patients. In particular, similar patients may be defined as
those having the same disease type (or another disease type in the
same DOG) and having an alteration that falls within the same
alteration group (AG).
[0048] FIG. 2 shows an example process 200 for identifying similar
patients according to one embodiment of the present invention. At
block 201, process 200 begins. At block 202, the patient's
particular cancer is analyzed to determine one or more generic
alterations present within that cancer. As discussed, one aspect of
the invention relates to obtaining a physical sample of a patient's
tumor and performing an analysis of the tumor with the objective of
determining a customized treatment for that particular patient.
Such alteration and tumor type information may be entered into a
database that includes patient information, and such information
may be used to perform a matching function to determine similar
patients.
[0049] At block 203, the system searches the database to locate
similar patients. In one embodiment, the system searches the
database of patients based on disease and alteration information,
and incorporating groupings of the disease and alteration
information. As discussed, in a sparse database, a direct match of
a patient may not be available and/or fully indicative of
similarity. In one implementation, disease groups of similar
disease types and alteration groups of similar alterations may be
used to locate similar patients. In one embodiment, the system may
provide an indication (e.g., at block 204) of a similar patient to
a user. This may be accomplished through a user interface, and may
be performed automatically by the system upon the receipt of one or
more signals. For instance, the system may provide the indication
upon receipt of new patient information, a change in grouping
information, an update of information, or any other triggering
activity.
[0050] In one optional embodiment, the system may provide a control
(e.g., as in block 205) that allows the physician or other
practitioner to contact another physician that is associate with
the patient identified to be similar to the current patient. As
discussed, the control may permit communication between physicians,
but in one implementation, such communication may be anonymous
without the need to identify a specific patient and/or physician.
At block 206, process 200 ends.
[0051] FIG. 3 shows an example process 300 for creating a genomic
database that may be used with various aspects of the present
invention. Shown in FIG. 3 is an example process flow 300 for
managing genomic testing information. The process 300 begins at
block 302 with access to genomic test results. According to one
embodiment, genomic test results include information specific to a
patient's tumor type, one or more genes implicated by the tumor,
and alteration type associated with the one or more gene. At block
303, the tumor type, gene, and alteration combinations for the
patient's cancer are analyzed, and relevant information items are
identified at 304.
[0052] In some embodiments, the relevant data items can include
clinical trials that match on any one or more of tumor type, gene,
and alteration. The relevant data items can also include therapies
or references that match on tumor, gene, and/or alteration. In some
example, the relevant data items are stored for analysis at block
304 based on activity of curators. In one example, human curators
can review clinical trial information (e.g., criteria,
gene/alteration target, trial therapy, trial drug) and associate
that clinical trial information with tumor types, genes, and/or
alterations. The human curators can also review and characterize
information on therapies and reference for use in, for example,
process 300.
[0053] Once relevant information is identified, for example, at
block 304, any relevant information item can be associated with the
patient having the matching tumor type, gene, and/or alteration at
305. The association(s) defined at block 305 can be used at block
306 to generate navigable data structures which can be configured
to organize gene and alteration combinations and links to any
associated relevant information (e.g., identified at block 304 and
associated at 305). In some embodiments, the navigable data
structures can be presented within a user interface display.
[0054] In other embodiments, the relevant information identified at
block 304 can be associated with patient records and/or specific
genomic tests at block 305 based on a specified data model.
Further, association of the relevant information at block 305 can
include generation and storage of the associated information a data
unit (e.g., information item) and the data unit can then be
associated with the patient, and/or a gene or alteration in the
patients genomic test results through a navigation link. The
navigation link can be used as part of a dynamic display for a
specific gene/alteration combination. Responsive to selection of
the link, the dynamic display can transition to the relevant
information.
[0055] FIG. 4 shows disease ontology grouping that may be performed
according to one embodiment of the present invention. For instance,
a disease ontology group 401 may be made and stored as part of a
database. More particularly, patient data may be grouped and
accessed by disease ontology groups that link similar diseases. For
instance, behavior and/or other characteristics of particular
diseases may allow them to be grouped together. For instance,
certain diseases may share common information such as alterations,
progression of disease state, common treatments, clinical behavior
or other information that would allow them to be grouped together.
For instance, a more general DOG may be determined called "Breast
Carcinoma" 402 which is a grouping of similar carcinomas including
breast invasive ductal carcinoma 403, breast adenocarcinoma 404,
and breast invasive lobular carcinoma 405. Such grouping may be
used as a way of grouping related patients. For instance, patient
data may include one or more disease types represented in a
database by a relation to those disease types. Upon performing a
query based on a particular defined DOG, patients having diseases
categorized within the DOG may be obtained.
[0056] FIG. 5 shows an example process 500 that may be performed
locating similar patients using disease ontology groups according
to one embodiment of the present invention. At block 501, process
500 begins. At block 502, the system (e.g., system 100) collects
patient data and stores the patient data in a data structure in
memory. As discussed, the data may include patient identification
information, the patient's tumor/disease type, detected alterations
for particular genes, treatment information, among other
patient-related information. According to one embodiment, the
information may be stored in a graph-based data structure. For
instance, information may be stored in a database as discussed in
more detail in U.S. patent application Ser. No. 14/463,068 entitled
"SYSTEM AND METHOD FOR MANAGING GENOMIC INFORMATION" filed Aug. 19,
2014, which forms an integral part of this application. It should
be appreciated that other databases may be used. However, it should
also be appreciated that such a database may be used for collecting
data from a number of sources, and may be preferable in cases where
sparse data sets are used.
[0057] At block 503, disease ontology groups may be formed. For
instance, as information is collected from various patients,
studies, articles, etc., some diseases may have characteristics
that may permit them to be grouped such as common treatments,
similar alterations, etc. Such groupings may be performed
automatically through collection of information from a number of
sources and/or curated by experts who have specific knowledge of
their relatedness.
[0058] At block 504, the system collects information regarding a
current patient. For instance, a patient's tumor may be analyzed to
determine alterations present. Such information may be stored in
the database. In one embodiment, information may be stored in the
form of tuple information including two elements connected by a
relation (e.g., patient A has a diagnosis of metastatic melanoma,
patient A has an alteration of BRAF 600E, etc.).
[0059] At block 505, the system may perform a query for a similar
patient to the current patient entered using disease ontology
groups and alteration data. For example, as discussed, data may be
sparse, and groupings of similar alterations and diseases may
permit a query to obtain results even if the disease/alteration
combination of the current client is not found. However, as more
patients are treated and their information stored, the system
becomes more useful as a tool for locating client having similar
disease structure. The query may be a two or more dimensional query
that searches for similar patients belonging to a common alteration
group and having a common disease ontology group as the current
patient. A result may include an ordered list of patients.
[0060] At block 506, the system may provide the ordered list of
patients to the physician user (e.g., within an interface of a
computer system). In one embodiment, the patient data may be
anonymized such that personally-identifiable information is masked
or omitted from the physician computer interface. The list may be
ranked such that the most relevant information is provided.
Further, information for patients having positive outcomes may be
preferred over negative outcome data, such that physicians are
connected with other physicians that have successfully treated
similar cancers. Further, information regarding a treating
physician may also be used to order results, as in one example, a
physician that has successfully treated a number of patients may be
preferred over a physician that has only treated one similar
patient. However, it should be appreciated that outcome data may
not be included with respect to identifying similar patients, as
some outcome data may be biased.
[0061] At block 507, the system may provide controls that permit
the physician user to contact other physician user(s) that treated
the identified patients. For instance, tools that captively collect
the communications between physicians may be provided such that
information is collected and saved in the database for use with
future patients. In one embodiment, once it is identified that the
database includes patients that are similar to a current patient,
the physician user caring for the current patient may be contacted.
Further aspects of the present invention relate to selecting the
patient for which a physician may be contacted.
[0062] The system may also include a number of timer and reminder
functions to facilitate the communications such that the requesting
physician is provided the information in a timely manner to support
treatment of the patient. At block 508, process 500 ends, although
it is appreciated that this process may be repeated many times,
constantly improving the database with new data including
treatments, communications and patient outcomes.
[0063] FIG. 6 shows an example process 600 for locating historical
responses and presenting them to physician users according to one
embodiment of the present invention. At block 601, process 600
begins. At block 602, a patient's cancer may be analyzed through
one or more processes, including genomic testing. It is appreciated
that through genomic testing of a patient's cancer, a targeted
treatment for the particular cancer can be created, which is more
effective and less damaging of other types of cells.
[0064] At block 603, the diagnosed tumor type and related disease
group and present alterations and related alteration group is used
to locate one or more similar patients. For example, if specific
patients identified have an identical disease and alterations,
patients are identified and returned as a result. However, if no
exact matches are found, patients belonging to the same alteration
disease groups may be returned. In another embodiment, a more
general search using the identified groups may be performed rather
than a two-step approach.
[0065] At block 604, the system may be adapted to display any
previously related historical responses to the physician user. For
instance, depending on whether a previous search was performed
using similar disease and alteration combinations, there may exist
existing response data within the database between physicians. It
may be beneficial to store such information and provided to
physicians without the necessity for contacting the treating
physician again for the same information. At block 605, process 600
ends.
[0066] FIGS. 7A-7C show an example process 700 for conducting a
communication session between physicians according to one
embodiment of the present invention. At block 715, process 700
begins. At block 701, the system identifies physicians having
matching patients, and begins a looping process through the list of
participating physicians. For example, in one embodiment,
physicians may opt in to participate in providing additional
information and communicating with other physicians about their
patients. At block 702, it is determined whether a physician within
the system (referred to herein as the Interactive Cancer Explorer
(ICE) system) has opted in to receive communications from other
physicians. If not, the physician may be removed from the result
set at block 704.
[0067] However, if the physician has opted in, it is determined at
block 703 whether the physician has matching patients for whom the
data has not been requested for this particular gene and individual
record numbers uniquely identifying a report relating to a
particular patient. Such an individual record number is referred to
hereinafter with respect to FIGS. 7A-7C as a TRF number. If the
physician has matching patients, block 706, the system chooses the
oldest TRF number in the list. If at block 708, it is determined
that the returned list includes greater than 10 practitioners (or
other predetermined number of practitioners), then only 10
practitioners (or the specified predetermined amount) are returned
at block 712. If there are less than 10 practitioners identified,
then a result page is created and displayed including the
identified doctors. Alternatively, if more than 10 doctors are
identified, then only 10 doctors are identified in the created
page.
[0068] If, at block 705, it is determined the physician has stored
responses saved within the system that meet the specified criteria,
then information is selected for particular cases to be displayed
to the user. For instance, at block 716, the system may choose the
oldest TRF number in the list and display that particular case to
the physician user. Such criteria may include, for instance, a
collection of data that relates to how stale information is within
the database, how active the cases by collected data or when the
data was last requested.
[0069] If, at block 705 it is determined that there is no data for
particular physician, is determined at block 707 whether the
physician includes matching patients for whom data was requested
greater than a predetermined time but yet has not returned any
results. If not, the physician may be removed from the result set
at block 704. However, if the physician has not yet been contacted
more than a predetermined number of times (e.g., three times)
regarding this TRF, the next TRF may be chosen at block 711 with
the oldest last requested date. If the physician has not been
contacted more than the predetermined number of times, the TRF with
the oldest last requested date for the particular TRF may be chosen
at block 710. As a result of identifying the most current
information, responsive physicians, and relevant patient
information, a page output may be constructed and displayed to the
physician user at block 713. At block 714, process 700 ends.
[0070] FIG. 8 shows an example system upon which various aspects of
the present invention may be practiced. FIG. 8 shows a system 800
which may include one or more computer-based systems that receive
and collect biomarker data 801 and patient specific pathology
information 802. System 800 includes an inference engine 803 that
interprets a graph-based data model 804 to determine one or more
actionable items 805. Such actionable items may be presented to a
user 806 (e.g. a physician, oncologists, or other user type). Such
actionable items may include recommending a patient for clinical
trial, a recommendation of a particular form of treatment, or other
recommendation.
[0071] Such a model may be a learning model in that information is
being added to the system in real time, and the recommendations
made by the system may also change over time. For instance,
information may be added, deprecated, deleted, or updated, such as
adding information relating to patients, studies, journal articles
or other information. Additional information may be added as tuples
to the graph-based data model. The inference engine may use such
additional information to make one or more inferences regarding the
data model.
Example Genomic System
[0072] FIG. 9 shows yet another example system upon which various
aspects of the present invention may be practiced. In particular,
FIG. 9 shows an example embodiment of a system 900 for managing
genomic testing information. The system 900 can be configured to
provide a single reporting source for accessing and applying
available information on a patient's cancer. According to some
embodiments, genomic testing on the patient's cancer provides
specific information the tumor, one or more genes implicated by the
tumor, and one or more alterations within the genes which can be
displayed by the system 900 through a web interface 901. In some
embodiments, the web interface 901 can include an alteration engine
(e.g., element 902) that performs any of the operations discussed
below with respect to the alteration engine 1001. For example, the
web interface and/or alteration engine can be configured to use the
testing information on tumor, gene, and alteration for a patient to
manage delivery of curated information to end users (e.g.,
technicians, physicians, medical personal, etc.) over a
communication network (e.g., 918). In one embodiment, the
alteration engine can include a UI or navigation component 911
configured to generate displays that focus users (e.g., physicians)
on actionable information within the genomic test results and
associated information. For example, the UI component 911 can
display navigable data structures including information on genes
and alterations identified in a genomic test coupled with
indicators informing the user of available actionable information
associated with a patient's cancer.
[0073] According to some embodiments, the alteration engine can
include specific component for provide specific functionality on
the web interface 901. For example, the alteration engine 902 also
can include a report generator component 903 configured to generate
physical and/or static report for downloading through the web
interface. The alteration engine can also include an analytic
subsystem 904 an analytic subsystem configured to identify matches
information between a current patient's tumor type, gene, and/or
alteration and include or identify the matching information items
for display in the patient's test results.
[0074] According another embodiment, the alteration engine 902 can
also include a curation component 910 configured to generated
curated information for use on the system. The curated information
can include interpreted statements regarding any one or more of
genomic alterations, an implicated gene, a patient's tumor type,
and/or potentially applicable therapies for a patient's cancer. In
some examples, the curation component can be accessed by human
operators "curators" who generate and/or approve system generated
interpreted statement regarding genomic alterations, an implicated
gene, a patient's tumor type, and/or potentially applicable
therapies.
[0075] As discussed, the alteration engine can also include the UI
component 911 configured to generate and display navigable data
structures which include information on genes and alterations
identified in a genomic test, which can be coupled with indicators
for actionable information associated with a patient's cancer. The
UI component 911 can transition the system to the actionable
information (e.g., therapy information items, trial information
items, reference information items) responsive to selection in the
user interface. Further, the UI component may be modified to allow
physicians to communicate information responsive to identifying
similar patients.
[0076] In further embodiments, the alteration engine can include an
update component 912 configured to track any updates to genomic
alterations and any information associated with the genomic
alterations. In one embodiment, the update component 912 can
identify updates information for display by the UI component 911.
Various embodiments, of the alteration engine components are
configured to perform the function and operations discussed above
with respect to the alteration engine and associated
components.
[0077] According to some embodiments, the web interface 901 can be
accessed by users (e.g., 905) over the internet. The user can
access the web interface from a variety of location (e.g.,
laboratory 915, hospital 914, and treatment facility 913). In
various embodiments, the users at any one or more of 913-915 can
share genomic test reports with each other. For example, the web
interface 901 can be configured to provide social functions between
users. In some embodiments, the web interface can limit sharing to
practice groups, within treatment facilities, or within medical
institutions (e.g., hospitals). According to one aspect, sharing of
test results and associated genomic information on patients can
create a strong community of physicians, and foster discussion
about treatment. Further, as discussed above, the interface may
permit identification of similar patients and foster collaboration
about similar patients.
[0078] According to some embodiments, the web interface 901 is
adapted to store genomic test information in database 921. Database
921 is illustrated as a single database, but in other embodiments,
database 921 can include any storage medium or organizational unit
for storing and accessing genomic test results and associated
information. Further embodiments can include a plurality of
databases and can also include distributed data architectures.
According to one embodiment, database 921 can include a variety of
data records accessed by the web interface 901 to manage delivery
of genomic test results and associated information.
[0079] For example, the database can include information on genomic
testing. In one example, genomic test results are stored and
associated with patient records. The genomic test results can
include information on genomic alterations. Specific genomic
alterations can be stored in database 217 and access for presenting
information within a display of a patient's test report. The
database can include curation records stored and associated with
any one or more of a tumor type, gene, and/or genomic alteration.
Other information may be stored, such as disease ontology groups,
alteration groups, communications between physicians, outcome
information, and/or any other type of information. Information on
clinical trials can likewise be stored as information items
associated with any one or more of a tumor type, gene, and/or
genomic alteration. The database 921 can also store therapy
information and references information and provide associated for
either to any one or more of a tumor type, gene, and/or genomic
alteration.
[0080] The database 921 can also be configured to track and store
information on updates to any information within the database. In
one example, updates can be flagged by other system components and
the flags resolved or remove once viewed.
[0081] In further embodiments, the database can store information
on data views for used by web interface and/or the UI component
911. Each one of the views can be accessed and used by the web
interface to present information on genomic testing and associated
information to a user. In some examples, the system and/or web
interface can be configured to capture information from external
information sources for storage in database 921. In one example,
external data source 916 can contain information related to a
patient's tumor type, gene, and/or alteration. The information from
the external information can be captured and stored as records in
database 921 accessible via the relationship to the tumor type,
gene, and/or alteration.
[0082] According to some embodiments, the information stored in
database 921 can include reference to the external information
source. For example, clinical trial information items can include
links to clinicaltrials.gov 917, reference information items can
include links to PubMed.gov (e.g., 228). In further embodiments,
the web interface 202 can be configured to access genomic
alteration information for cancer diagnoses made at a hospital or
laboratory (e.g., 919). For example, the web interface can capture
genomic information from EMR (electronic medical records) data to
retrieve tumor type, implicated gene, and/or alteration type for
storage in database 921. In some implementations, references or
links to the specific medical records can also be stored in the
database. In one example, the links to the medical records can be
presented in a dynamic display generated on system 900.
[0083] According to one aspect, the database 921 and all associated
information can be organized or accessed based on one or more of
tumor type, gene, and alteration. In one embodiment, the tumor
type, gene, and alteration data is stored as a data unit (e.g., a
tuple). The data unit can be used by the system to identify or
display related information based on matching any one or more of
the tumor type, gene, and alteration. In further embodiments, each
data unit can be linked to actionable information (where it
exists). For example, each data unit can be linked to a matching
therapy (e.g., a therapy information item describing a specific
therapy, application, etc.). In another example, data units can be
linked to a matching clinical trial (e.g., stored as a clinical
trial information item).
[0084] According to one embodiment, associated of all the
information in the database according to tumor, gene, or alteration
provides insight into prescribed uses of therapies (on-label) and
off-label applications for such therapies. In one example,
off-label used can be identified based on alteration (e.g.,
different tumors but same alteration--provides relation information
on a potentially effective therapy the current patient's
cancer.
[0085] According to another embodiment, each record can be
associated with a data space for an update flag. Responsive to any
update to information on the database 921, the system can enter
information in the data space for the update flag. Tracking updates
to genomic alteration and associated information facilitates user
awareness of potential significant changes in a patient report.
Further, tracking of update information in the database 921 enables
the system to deliver notification regarding any updates.
[0086] In some further embodiment, social functions can have
associated records in the database. For example, permission
information (e.g., who can share a report and/or who can receive a
shared report) can be associated with test reports stored in
database 921. Further, communication sessions between physicians
may be stored as records within the database.
[0087] FIG. 10 shows another system that may be used to generate
data from genomic test results according to various aspects of the
present invention. As described above, genomic testing provides
unique opportunities to make more informed treatment decisions,
especially in the field of cancer diagnosis and therapy
development. Some conventional approaches can fail to provide
useable information within the volumes of information provided as
results of genomic testing. Further, it is appreciated that some
conventional approaches fail to focus practitioners on actionable
information within the genomic testing information and any
associated treatment information.
[0088] Accordingly, provided are systems and methods for managing
genomic testing information that provide a single reporting source
for accessing and applying available information on a patient's
cancer. According to some embodiments, genomic testing on the
patient's cancer provides specific information on the tumor, one or
more genes implicated by the tumor, and one or more alterations
within the genes. The testing information on tumor, gene, and
alteration can be used by the system to manage delivery of curated
information that focuses users (e.g., physicians) on actionable
information within the genomic test results and associated
information. For example, publically available data (e.g., therapy
data, clinical trial data, and journal publications) can be
interpreted to provide the curated information based on its
relationship to one or more of the tumor, gene, and alteration for
a patient. The publically available information can be processed on
the system to provide navigable data structures informing the user
of available actionable information associated with a patient's
cancer.
[0089] According to one embodiment, by providing users an indicator
of actionable information, information within genomic testing
reports can be provided succinctly and enable the users to select
the indicator to access more detailed information as needed.
Further, genomic test results (e.g., listings of alterations) can
be ordered based on the presence or absence of actionable
information items. In one example, actionability of the navigable
data structures can be defined on available information for an FDA
approved agent in the patient's tumor type, available information
for an FDA approved agent in another tumor type, and/or available
information for a mechanistically driven or biologically relevant
clinical trial based on the alteration(s) found.
[0090] The ordering can be configured to focus the user on the
actionable information to facilitate review of a plurality of
alterations and their associated information. Indicators of
actionable items can be displayed based on an information source
(e.g., a therapy indicator/tag references available therapy
information items related to a genomic alteration, a trial tag
references available clinical trial information items, and a
reference tag for reference information items). The indicator can
be associated with a respective alteration in the plurality of
alterations resulting from genomic testing.
[0091] In some embodiments, the system facilitates successive
selection of alterations and associated information within the
plurality of alteration results, for example, using the indicators.
By enabling successive selections, the system facilitates better
understanding of a patient's cancer and enables more informed
treatment decisions.
[0092] According to some embodiments, the actionable information
includes identification of FDA approved therapies for a tumor,
gene, and alteration combination. Actionable information can also
include identification of related therapies that are implicated by
any one or more of the tumor, gene, and alteration characteristic
of a patient's cancer. According to some embodiments, related
therapies can be determined by the system and displayed to users to
facilitate treatment decisions. For example, indicators regarding
the related therapies can be displayed as part of the navigable
data structures within user interface displays generated by the
system.
[0093] Referring to FIG. 10, there is illustrated an example of a
system 1000 for managing genomic testing information using an
alteration engine 1001. Elements of the system 1000 can be provided
using a computing system such as a computer system such as that
described above with reference to FIG. 9. For example, the
alteration engine 1001 can be executed on the computer system to
provide the functions and operations discussed herein. In other
embodiments, the alteration engine 1001 can include additional
components executed on the computer system to perform specific
operations.
[0094] As shown in FIG. 10, various embodiments of the alteration
engine 1001 are configured to accept genomic test results 1002 and
associate the genomic test results with curated information. The
curated informing can include detailed analysis or additional
information tailored to the characteristic of the test results. For
example, the test results generated for a specific patient can
specify a plurality of genes and alterations found within the
patient's cancer. The alteration engine 1001 can be configured to
associate curated information tailored to the specific
genes/alteration identified for the patient.
[0095] In some embodiments, the alteration engine 1001 can be
configured to generate a single source display of the test results,
curated information, and any additional information (e.g.,
identified similar patient data) as a dynamic display 1003. The
dynamic display 1003 can include and organize the test results, the
curated information, and the additional information to minimize the
volume of data displayed to the user at any one time. According to
one embodiment, the dynamic display 1003 can include a plurality of
views of the test results, the curated information, and the
additional information. In one example, the test, curated, and
additional information can be organized into categories for display
in a user interface. In some embodiments, the user interface can be
specially configured for navigation with mobile devices.
[0096] The user interfaces generated by the system can also be
configured to include gene and alteration information specific to a
current patient being viewed. The user interfaces are configured to
present categorized information to facilitate understanding of the
gene and alteration information for the current patient. In one
example, the dynamic display is presented for a specific patient
selected by the user from a patient listing. Once selected, the
current patient's information (e.g., name, date of birth, height,
weight, sex, patient id, case id, etc.) can be provided along with
information regarding the genetic testing conducted (e.g., specimen
receipt date, report generation date, diagnosis (type of tumor),
collection date for specimen, collection method, specimen type,
etc.) as a first portion of a dynamic display 1003. If anonymized
(e.g., the patient is not the user's patient) some or all of this
identifying information may be masked or removed.
[0097] A second portion of the dynamic display 1003 generated by
the system and/or alteration engine 1001 can include the results of
the genetic testing organized by gene and alteration. In some
embodiments, the alteration engine 1001 can include a user
interface ("UI") component configured to generate and to provide
for navigation within the dynamic display 1003. For example, each
gene and alteration result generated from genomic testing of the
current patient's cancer can be displayed as its own data
structure. The data structure can contain selectable indicators of
actionable information specific to each of the gene/alteration
results. In one embodiment, the UI component is configured to
transition the dynamic display 1003 to the actionable information
in response to selection of the indicators.
[0098] In some embodiments, the alteration engine 1001 can be
configured to generate a single source display of the test results,
curated information, and any additional information (e.g.,
identified similar patient data) using a dynamic display 1003. The
dynamic display 1003 can include and organize the test results, the
curated information, and the additional information to minimize the
volume of data displayed to the user at any one time. According to
one embodiment, the dynamic display 1003 can include a plurality of
views of the test results, the curated information, and the
additional information. In on example, the test, curated and
additional information can be organized into categories for display
in a user interface. In some embodiments, the user interface can be
specially configured for navigation with mobile devices.
[0099] The user interfaces generated by the system can also be
configured to include gene and alteration information specific to a
current patient being viewed. The user interfaces are configured to
present categorized information to facilitate understanding of the
gene and alteration information for the current patient. In one
example, the user interfaces are presented for a specific patient
selected by the user from a patient listing. Once selected, the
current patient's information (e.g., name, date of birth, height,
weight, sex, patient id, case id, etc.) can be provided along with
information regarding the genetic testing conducted (e.g., specimen
receipt date, report generation date, diagnosis (type of tumor),
collection date for specimen, collection method, specimen type,
etc.) as a first portion of a user interface. If anonymized (e.g.,
the patient is not the user's patient) some or all of this
identifying information may be masked or removed.
[0100] A second portion of a user interface generated by the system
and/or displayed by the dynamic display 1003 can include the
results of the genetic testing organized by gene and alteration. In
some embodiments, the alteration engine 1001 can include a user
interface ("UI") component configured to generate and to provide
for navigation within the user interfaces displayed by the dynamic
display 1003. For example, each gene and alteration result
generated from genomic testing of the current patient's cancer can
be displayed as its own data structure. The data structure can
contain selectable indicators of actionable information specific to
each of the gene/alteration results. In one embodiment, the UI
component is configured to transition the user interfaces displayed
by the dynamic display 1003 to the actionable information in
response to selection of the indicators.
[0101] For example, FIG. 11 illustrates a user interface 1100 that
may be used to display patient information and potential therapies
for one or more genomic alterations. In at least one embodiment,
the user interface 1100 is configured to provide patient
information 1102, genomic alteration information 1104, therapy
information 1106, and/or an on call button 1108.
[0102] In certain embodiments, a patient list button 1109 is also
provided. Responsive to selection of the patient list button 1109,
a patient list user interface is displayed comprising a list of
patients in the system. Selection of a patient from the list of
patients is operable to display a patient information user
interface similar to that of FIG. 11. In some embodiments, the user
interface can include one or more filters (e.g., a diagnosis, a
physician, a facility, etc.) to sort a list of patients.
[0103] The patient information 1102 includes general information
1110 about a patient, such as a patient name, a patient diagnosis,
an attending physician, a diagnosis location, a date of report
creation, and so forth. Furthermore, a patient details button 1112
is provided in some embodiments that can be expanded to display
additional information about a patient, such as a patient's height,
weight, date of birth, gender, and so forth.
[0104] According to some embodiments, a genomic alteration
information 1104 section is provided to display genomic alteration
information associated with a patient. For example, the genomic
alteration information can include information identifying an
abnormal gene associated with a patient, and how the abnormal gene
has been altered (e.g., mutations, amplification, etc.). In one
embodiment, the genomic alteration information 1104 section
displays each genomic alteration 1114 in a list format and,
responsive to selection of a specific genomic alteration, the
system is operable to display therapy information 1106 pertaining
to the selected genomic alteration.
[0105] In at least one embodiment, the therapy information 1106
section includes one or more selectable therapies 1116, displayed
in a list format, that are associated with the selected genomic
alteration. Selection of one of the one or more therapies 1116
provides expanded details 1118 about the selected therapy. For
example, the expanded details 1118 can include target and rationale
for the selected therapy, FDA-approved uses, clinical trial
information, references pertaining to the selected therapy, and so
forth.
[0106] In one embodiment, an on call button 1108 is provided,
operable to connect a user with other users. For example, the other
users can be physicians that have patients with genomic alterations
similar or substantially identical to one or more of the listed
genomic alterations 1114. In at least one example, selection of the
on call button 1108 is operable to display a connection user
interface illustrated by FIG. 12 below.
[0107] FIG. 12 illustrates one example of a user interface 1200
that is operable to connect a user with other physicians. For
example, the user interface 1200 can include a list of each genomic
alteration 1202 associated with a patient and, operable to
selection of a genomic alteration 1202 from the list, navigate to a
connection user interface configured to connect the user with
physicians that have treated, or are treating, patients with the
selected genomic alteration 1202. The system may include a matching
engine that identifies similar patients within the database based
on genomic alterations 1202, amongst other information. For
example, in one embodiment, the connection user interface includes
contact information for one or more other physicians and allows the
user to send a message (e.g., an email message, a prerecorded voice
message, etc.) to the other physicians. The message may be
automatically generated by the system in some examples, while in
other examples, the user may generate the message. In yet other
embodiments, the system may pre-populate a message with a generic
request, but allow the user to further modify or customize the
message. Responsive to a user input, the message can be sent to any
of the one or more physicians.
[0108] According to one embodiment, a user can receive a message
indicating a request for information from one or more other users.
For example, the user may have treated a patient with a specific
genomic alteration, and a second user may request information about
the treatment identified in the message. In some embodiments, the
request is displayed by a user interface comprising a series of
questions about the treatment for the specific genomic alteration.
For example, the series of questions can include questions
pertaining to a name of the treatment, a duration of the treatment,
a patient response to the treatment, comments about the treatment,
clinical trial notes about the treatment, and so forth. In at least
one embodiment, a set of responses to the series of questions is
accepted by the system in response to input from the user. The
system compiles one or more responses to a request from one or more
users and, in some examples, sends the compilation to the user that
sent the request.
[0109] FIG. 13 illustrates one example of a user interface 1300
displaying a compilation of responses to a request. In one
embodiment, the compilation includes one or more responses 1302
categorized by a therapy administered by a physician. For example,
a first category 1304 can include responses involving therapies
targeting a genomic alteration, a second category 1306 can include
responses involving abstinence from administering a therapy
targeting the genomic alteration, and a third category (not
pictured) can include responses involving a clinical trial for the
genomic alteration. Each of the first category 1304 and the second
category 1306 can be further organized by one or more genomic
alteration parameters 1308.
[0110] For example, the genomic alteration parameters 1308 can
include a name of a respondent, patient demographic information
(e.g., a patient's age, gender, etc.), a tumor type (e.g., a type
of tumor associated with a patient), a genomic profile (e.g.,
information about one or more patient genomes), contact information
(e.g., contact information for the respondent), update history
information (e.g., the last date at which a response's genomic
alteration parameters 1308 were modified), and/or a comments
section.
[0111] According to one embodiment, the first category 1304 further
includes therapy information 1310. For example, the therapy
information 1310 can include a therapy name, a therapy duration
(e.g., a length of time over which a patient underwent the
therapy), and/or best response information (e.g., no response, some
response, stable disease, etc.).
[0112] Furthermore, the second category 1306 can include abstinence
information 1312. In some examples, the abstinence information 1312
includes a reason for abstaining from administering a therapy to a
patient (e.g., a patient had already become stable from
chemotherapy, etc.).
[0113] Returning to FIG. 12, in some embodiments, one or more of
the genomic alterations 1202 may not have been previously addressed
by a physician, or a physician may not respond to a request for
information about an indicated genomic alteration 1202.
Accordingly, the system notes that a request has not been
satisfactorily fulfilled, and in some examples, the system is
automatically prompted to send a notification to an originator of
the request after a time period (e.g., 24 hours, 48 hours, 72
hours, one week, etc.) has elapsed. The notification can include,
for example, additional resource information to address the
request, and can include one or more suggested courses of action
for the originator of the request to pursue.
[0114] Other embodiments of the invention may relate to
implementations disclosed and discussed in U.S. application Ser.
No. 14/146,743, entitled SYSTEM AND METHOD FOR MANAGING GENOMIC
TESTING RESULTS, filed Jan. 3, 2014, which forms an integral part
of this specification.
[0115] Also, the phraseology and terminology used herein is for the
purpose of description and should not be regarded as limiting. Any
references to embodiments or elements or acts of the systems and
methods herein referred to in the singular may also embrace
embodiments including a plurality of these elements, and any
references in plural to any embodiment or element or act herein may
also embrace embodiments including only a single element.
References in the singular or plural form are not intended to limit
the presently disclosed systems or methods, their components, acts,
or elements. The use herein of "including," "comprising," "having,"
"containing," "involving," and variations thereof is meant to
encompass the items listed thereafter and equivalents thereof as
well as additional items. References to "or" may be construed as
inclusive so that any terms described using "or" may indicate any
of a single, more than one, and all of the described terms. Any
references to front and back, left and right, top and bottom, upper
and lower, and vertical and horizontal are intended for convenience
of description, not to limit the present systems and methods or
their components to any one positional or spatial orientation.
[0116] Having thus described several aspects of at least one
embodiment of this invention, it is to be appreciated that various
alterations, modifications, and improvements will readily occur to
those skilled in the art. Such alterations, modifications, and
improvements are intended to be part of this disclosure, and are
intended to be within the spirit and scope of the invention.
Accordingly, the foregoing description and drawings are by way of
example only.
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