WO2014121128A1

WO2014121128A1 - Methods, systems, and computer readable media for exchanging genomic and/or patient information

Info

Publication number: WO2014121128A1
Application number: PCT/US2014/014276
Authority: WO
Inventors: Asim Sarosh SIDDIQU; Martin Naley; Paul Billings
Original assignee: Life Technologies Corporation
Priority date: 2013-02-01
Filing date: 2014-01-31
Publication date: 2014-08-07

Abstract

A method for exchanging genomic information includes providing or supplying a plurality of genomic sequencers at a plurality of sites, each of the plurality of genomic sequencers being configured to include or to be in connection with a genomic database, each genomic database including biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient; hosting a genomic information indexing database including indexing information associated with one or more genomic sequences; and operating a server computer in communication with the genomic information indexing database and with any genomic database included in or in connection with one of the plurality of genomic sequencers.

Description

METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR EXCHANGING GENOMIC AND/OR PATIENT INFORMATION

CROSS-REFERENCE TO RELATED APPLICATIONS

[001] This application is related to U.S. Provisional Patent Application No. 61/537,813 (Docket No. LT00563 PRO), titled "Systems and Methods for Predictive Analysis of Matched Cohorts," filed September 22, 2011; U.S. Provisional Patent Application No. 61/545,895 (Docket No. LT00595 PRO), titled "User Interface for Analysis and Interpretation of Nucleic Acid Sequence Data," filed October 11, 2011; and U.S. Provisional Patent Application No. 61/545,922 (Docket No. LT00598 PRO), titled "Systems and Methods for Analyzing and Interpreting Nucleic Acid Sequence Data," filed October 11, 2011, and the entire contents of all of which are incorporated by reference herein.

FIELD

[002] This application generally relates to methods, systems, and computer readable media for exchanging information and, more specifically, to methods, systems, and computer readable media for exchanging genomic and/or patient information.

BACKGROUND

[003] In order to help ameliorate genetic research and/or care, there is a need for new methods, systems, and computer readable media that can efficiently collect, analyze, store, transfer, retrieve, and/or distribute information across multiple sites and/or entities, including genomic and/or patient information.

EXEMPLARY EMBODIMENTS

[004] The accompanying drawings and the following description of various exemplary embodiments are exemplary and explanatory only and are not to be construed as limiting or restrictive in any way. Other embodiments, features, objects, and advantages of the present teachings will be apparent from the description and accompanying drawings, and from the claims. [005] In accordance with the teachings and principles embodied in this application, new methods, systems, and computer readable media that can efficiently collect, analyze, store, transfer, retrieve, and/or distribute information across multiple sites and/or entities, including genomic and/or patient information, are provided.

[006] According to various exemplary embodiments, there are provided methods, systems, and computer readable media for enabling various entities and/or physicians to share genetic and/or patient information. The methods, systems, and computer readable media may include enabling physicians to search for genetically similar patients or patients with genetically similar cancers/tumors. The methods, systems, and computer readable media may also include enabling physicians to identify and access clinical trials for which their patient may be a genetic match. The methods, systems, and computer readable media may advantageously be used by working seamlessly with one or more sequencing instruments, such as the Ion Personal Genome Machine (PGM™) (Life Technologies Corp. / Ion Torrent; see, e.g., U.S. Pat. No. 7,948,015 and U.S. Pat. Appl. Publ. Nos. 2010/0137143, 2009/0026082, and 2010/0282617, which are all incorporated by reference herein in their entirety), and any associated data processing and/or analysis software, including ION TORRENT SUITE and ION REPORTER.

[007] FIG. 1 illustrates, at a high level, various components and entities that may interact within methods, systems, and computer readable media according to various exemplary embodiments. These include, for example, treatment centers, consumer portals, and medical knowledge creators. Treatment centers may include locations that patients visit to get treated for their condition. The treatment centers may have access to sequencers (e.g., ION TORRENT devices) and may possess genomic and/or clinical data on their patients. In various exemplary embodiments, the genomic and/or clinical data may be interrogated to provide information that an interpreting physician can use to create a medical report that may handed to a treating physician. The consumer portals may be patient-facing interfaces. In various exemplary embodiments, the genomic and/or clinical data may be transferred to one or more patient-facing sites such as Lybba.com or patientslikeme.com, for example. These sites may represent some data and/or information to patients and be responsible for patient interaction. The medical knowledge creators may include entities that create medical knowledge using internal and/or external resources. Further, use of methods, systems, and computer readable media according to various exemplary embodiments opens up additional models for gaining revenue from other companies in the analytical or pharmaceutical spaces.

[008] FIG. 2 illustrates a variety of interactions between various components and entities according to various exemplary embodiments. In an exemplary embodiment, in a clinical trial selection (CTS) use, a physician may be enabled to identify and review clinical trials for which the patient is a genetic match. (See steps 1-6). In another exemplary embodiment, in a comparative genomic medicine (CGM) use, a physician may be enabled to evaluate data and information from multiple individuals and/or patients (based on germline or tumor genetic profiles, for example) and to review their treatment and outcome information. One beneficial aspect of this functionality may be to provide insights and useful correlations to aid the treatment of a patient. (See steps 1-6). In some embodiments, analysis and correlations provided by the system may suggest treatment options or provide indications of the expected outcomes for therapeutic regimes. In other exemplary embodiments, other uses are possible, including: (1) providing drug guidelines, (2) unknown or rare variant identification, (3) revisiting patient information over time, (4) data mining; and (5) patient-initiated data transfers. The drug guidelines use may enable a physician to review approved genetic guidelines for treating a patient in the context of that patient's genetic profile (see steps 1, 2, and 4-6). In one embodiment, the unknown or rare variant use pertains to situations where a novel variant presents in a patient that has not been seen previously in another database, in which case advanced predictive algorithms and methodologies may be invoked to suggest the impact of the novel variant on the gene function or expression (see steps 1, 2, 4, and 6). The revisit patient use may address situations in which new knowledge or information that pertains to a patient is entered in the database, which may occur passively or actively. In an exemplary passive embodiment, the patient' s data may be run through the analysis periodically and new data may be flagged or evaluated as part of the new analysis. In an exemplary active embodiment, the patient's data may undergo surveillance and monitoring such that new pertinent information is automatically routed to the interpreting physician. The data mining use may provide a valuable foundation for translational research and data mining as the databases increases in size (see step A). The patient-initiated data transfer use may enable a patient to initiate a transfer of their genetic information to one or more patient-centric services such as patientslikeme.com or Lybba.com, for example (see step C). Step B may be supported through manual curation.

[009] FIG. 3 illustrates an overall workflow for genetic analysis according to various exemplary embodiments. The steps in this workflow may include: (1) the ordering of a test, which may be done by a physician, for example; (2) the sending of a resulting test sample to a laboratory; (3) the interpretation of data from the test sample using a sequencing instrument and related data processing and/or analysis software, such as ION REPORTER, for example, which software may then present relevant medical guidelines; (4) the requesting of a list of patients or de-identified patient records that have some similarity to the test sample data, and/or of clinical trials that may be a match for a patient having presented the test sample data; (5) the receiving of a list of patients or de-identified patient records and/or matching clinical trials; (6) the preparation of a report using some or all of the relevant medical guidelines, list of patients or de- identified patient records, and/or matching clinical trials, etc., which may be prepared by a pathologist, for example; (7) the sending of the report to a treating physician; and (8) the reviewing of the report by a treating physician who may then choose an appropriate course of treatment that may take into consideration some or all of the contents of the report.

[0010] FIG. 4 illustrates an exemplary information exchange workflow according to an exemplary embodiment. A genetic care database and/or server, which may be referred to as Genetic Care Interchange, may receive a query about a patient or related genetic information from a first hospital and provide in response one or more identifiers allowing identification of records for patients with similar conditions, who may have been identified or treated at other hospitals. The first hospital may then submit the one or more identifiers to the other hospitals and request some or all of the associated clinical data. The other hospitals may then provide the requested clinical data to the first hospital. Various hospitals and/or other information providers may submit queries and/or bulk quantities of genetic markers, information, and indications to the genetic care database and/or server. Submissions may be accompanied by any relevant authorization and/or compliance information and/or documents (e.g., consent or authentication information). Communications may be de-identified such that personally identifiable information is managed, restricted, or not shared along with any communicated clinical data. [0011] FIG. 5 illustrates an exemplary architecture for exchanging genetic information between various entities according to an exemplary embodiment. A querying hospital may obtain genomic information using a sequencer or other analytical instrument, which information may be processed and/or analyzed using a data analysis server (e.g., ION TORRENT SERVER). The genomic information may be submitted to a data input manager or front-end software component (e.g., ION REPORTER), which may be configured to interface (e.g., via a suitable plug-in or module) with a genetic care database and/or server. The front-end software component may be configured to submit queries and/or requests to a query and information processing engine configured to be in communication with one or more of a drug trial database, a medical guidelines database, a query repository / patient index database, and a research insights database. The query engine may be configured to return patient identifiers (which may be anonymized or de-identified so that although records may be identified by the custodian of the records with the identifiers no actual personally identifiable information is communicated), clinical trial identifiers, medical guidelines, research insights, etc. The genetic care database and/or server may receive and/or submit information regarding clinical data and patient variants to one or more consumer portals, receive medical knowledge and/or mining queries from one or more medical knowledge creators, and submit mining results to the one or more medical knowledge creators. The front-end software component may also submit received patient identifiers to a client- server, which may be under the control of a hospital, and the hospital may return relevant clinical information, which may be de-identified, corresponding to the patients, their diagnoses, and their treatment courses and outcomes. One or more transmitting hospitals may have electronic medical records and clinical data, which may be consulted to respond to inquiries from the querying hospital.

[0012] FIG. 6 illustrates an exemplary architecture for exchanging genetic information between various entities according to an exemplary embodiment. A hospital may obtain genomic information using a sequencer or other analytical instrument, which information may be processed and/or analyzed using a data analysis server (e.g., ION TORRENT SERVER). The genomic information may be submitted to a data input manager or front-end software component (e.g., ION REPORTER), which may be configured to interface (e.g., via a suitable plug-in or module) with a genetic care database and/or server. The hospital may have a client server configured to communicate with the suitable plug-in or module of the front-end software and to transfer clinical data to such plug-in or module and receive patient identifiers from such plug-in or module. The front-end software component may be configured to submit queries and/or requests to a query and information processing engine configured to be in communication with one or more of a clinical trial database, which may be updated from time to time to reflect updated trial information, and a query repository / patient index database. The query engine may be configured to return a clinical trial list and/or patient identifiers (which may be anonymized or de-identified so that although records may be identified with the identifiers by the custodian of the records no actual personally identifiable information is communicated). The client server may also be configured to transfer clinical data to other client servers hosted in other hospitals, which may have clinical data, which may be de-identified, corresponding to patients, diagnoses, and treatment courses and outcomes, as well as electronic medical records, and which may be configured to transfer patient identifiers to the hospital.

[0013] FIG. 7 illustrates an exemplary architecture for exchanging genetic information between various entities according to an exemplary embodiment. A hospital may obtain genomic information using a sequencer or other analytical instrument, which information may be processed and/or analyzed using a data analysis server (e.g., ION TORRENT SERVER). The genomic information may be submitted to a data input manager or front-end software component (e.g., ION REPORTER), which may be configured to interface (e.g., via a suitable plug-in or module) with a genetic care database and/or server. The front-end software component may be configured to submit queries and/or requests to a query and information processing engine configured to be in communication with one or more of a clinical trial database, which may be updated from time to time to reflect updated trial information, and a query repository / patient index database. The query engine may be configured to return a clinical trial list, patient identifiers (which may be anonymized or de-identified so that although records may be identified with the identifiers by the custodian of the records no actual personally identifiable information is communicated), and/or clinical data. The query engine may also be configured to transfer clinical data to client servers hosted in various other hospitals, which may have clinical data, which may be de-identified, corresponding to patients, diagnoses, and treatment courses and outcomes, as well as electronic medical records, and which may be configured to transfer patient identifiers to the query engine.

[0014] FIG. 8 illustrates an exemplary architecture for exchanging genetic information between various entities according to an exemplary embodiment. A hospital may obtain genomic information using a sequencer or other analytical instrument, which information may be processed and/or analyzed using a data analysis server (e.g., ION TORRENT SERVER). The genomic information may be submitted to a data input manager or front-end software component (e.g., ION REPORTER), which may be configured to interface (e.g., via a suitable plug-in or module) with a genetic care database and/or server. The front-end software component may be configured to submit queries and/or requests to a query and information processing engine configured to be in communication with one or more of a trial database and a query repository / patient index database. The query engine may be configured to return a clinical trial list, patient identifiers (which may be anonymized or de-identified so that although records may be identified with the identifiers by the custodian of the records no actual personally identifiable information is communicated), and/or clinical data. The hospital may have a client server configured to communicate with the suitable plug-in or module of the front-end software and to transfer clinical data to such plug-in or module and receive patient identifiers from such plug-in or module. The client server may also be configured to transfer patient identifiers to and receive clinical data from a third-party peering service client server that can communicate with other hospitals, which may have clinical data, which may be de-identified, corresponding to patients, diagnoses, and treatment courses and outcomes, as well as electronic medical records, and which may be configured to transfer patient identifiers to the hospital.

[0015] FIG. 9 illustrates a variety of interactions between various components and entities according to various exemplary embodiments. Shown are treating and interpreting physicians, treatment centers, a front-end hardware and/or software component (which may be referred to herein as ION REPORTER), a back-end hardware and/or software component (which may be referred to herein as Genetic Care Interchange Server or GCI Server), a genomic index database (which may be referred to herein as GCI Index database), medical knowledge creators, and applications (which may be referred to herein as GCI applications). The treating physician may order a test, which may be performed by a treatment center, which may submit sequence data to the front-end hardware and/or software component, which may submit patient variants to the back-end hardware and/or software component and may receive therefrom a report. The treatment centers may submit to or retrieve from the back-end hardware and/or software component medical information on similar patients. The back-end hardware and/or software component may upload patient variants to and query the genomic index database, may submit data for mining to the medical knowledge creators, which may submit applications and/or medical knowledge to the applications, which may include medical guidelines, drug trial eligibility factors, and research or emerging insights, for example. The back-end hardware and/or software component may submit or retrieve medical guidelines, drug trial eligibility factors, and research or emerging insights from the applications, and may submit patient variants to one or more consumer portals. The interpreting physician may operate the front-end hardware and/or software component and may generate and provide to the treating physician a report with findings relevant to a patient. Submissions may be accompanied by any relevant authorization and/or compliance information and/or documents (e.g., consent or authentication information). Communications may be de-identified such that personally identifiable information is managed, restricted, or not shared along with any communicated clinical data.

[0016] FIG. 10 illustrates a variety of interactions between various components and entities according to various exemplary embodiments. A querying hospital may obtain genomic information using a sequencer or other analytical instrument, which information may be processed and/or analyzed using a data analysis server (e.g., ION TORRENT SERVER) to obtain one or more reads, for example. The genomic information may be submitted to a data input manager or front-end software component (e.g., ION REPORTER), which may be configured to interface (e.g., via a suitable plug-in or module) with a core server, which interfacing may include access authentication, submission of patient identifiers and information (which may be anonymized or de-identified so that although records may be identified with the identifiers by the custodian of the records no actual personally identifiable information is communicated), hospital identifiers and information, and patient data including, for example, clinical, genetic, and other relevant or useful information such as variome-based data, and receipt of a report. The core server may include a querying engine and a report generation engine, and may submit a structure query to a uniform API for one or more applications accessible from an application store or service and receive results therefrom. The core server may submit patient identification (which may be anonymized or de-identified) and hospital identification to a clinical patient index database and associated query engine, which may both be under hospital control, and which may return clinical data to the core server. The core server may also submit a structured query to a genomic patient index and associated query engine, which may return patient identification (which may be anonymized or de-identified) to the core server. One or more transmitting hospitals may submit patient identification (which may be anonymized or de- identified), hospital identification, and/or clinical data to the clinical patient index database and associated query engine, which may be done through a uniform tool or application programming interface (API). Each transmitting hospital may have databases, which may include aggregated de-identified clinical data, medical images, research data, medical records, EMR, pathology reports, and other information along with suitable data import engines. Submissions may be accompanied by any relevant authorization and/or compliance information and/or documents (e.g., consent or authentication information). Communications may be de-identified such that personally identifiable information is managed, restricted, or not shared along with any communicated clinical data.

[0017] FIG. 11 illustrates a variety of interactions between the various components and entities according to various exemplary embodiments, including many of the features discussed previously regarding FIG. 10. FIG. 11 additionally illustrates consumer portals, which may submit patient requests access to the core server and which may receive from the core server a patient variome, along with medical knowledge creators, which may submit mining queries to the core server and which may receive mining results from the core server.

[0018] FIG. 12 illustrates a variety of interactions between the various components and entities according to various exemplary embodiments, including many of the features discussed previously regarding FIGS. 10 and 11. FIG. 12 additionally illustrates specific applications, including a medical guidelines application, which may include a query engine and a medical guidelines database, and which may receive structure queries from the core server and may return guidelines to the core server; a drug trial application, which may include a query engine and a drug trial database, and which may receive structure queries from the core server and may return trials information to the core server; and a research or emerging insights application, which may include a query engine and a research or emerging insights database, and which may receive structure queries from the core server and may return research or emerging insights to the core server.

[0019] In various embodiments, one or more aspects of the exemplary embodiments described herein may include one or more of the features described in U.S. Provisional Patent Application No. 61/537,813, titled "Systems and Methods for Predictive Analysis of Matched Cohorts," filed September 22, 2011; U.S. Provisional Patent Application No. 61/545,895, titled "User Interface for Analysis and Interpretation of Nucleic Acid Sequence Data," filed October 11, 2011; and U.S. Provisional Patent Application No. 61/545,922, titled "Systems and Methods for Analyzing and Interpreting Nucleic Acid Sequence Data," filed October 11, 2011.

[0020] In an exemplary embodiment, a user may access a genetic care database and/or server via a graphical user interface of the data processing and/or analysis software. Once accessed, the genetic care database and/or server may allow the user to search for a de-identified patient with a certain medical or genetic condition (such as stage III lung cancer, for example) and may display for the user a list of genetic variants, which may be sorted by gene and may be selectable within the user interface. At least a portion of the variants may be described with a name or designation, a corresponding gene, a pathway indicator, and one or more variant qualifiers (e.g., synonymous or non-synonymous). The user may then be allowed to select one or more of the listed variants and to submit a query for the selected variants to the genetic care database and/or server. The query may be made by an interpreting physician. The query may be a Boolean check or comparison on whether or not each selectable variant is found in other patients or clinical trials. More complex queries are also possible. The genetic care database and/or server may or may not have access to a patient name and/or diagnosis. All communications may be anonymized or de-identified. The list of variants may be sorted by any suitable characteristic, including by gene and by pathway. A level of importance of the variants may be shown. Synonymous variants may also be shown. An impact, whether known or predicted, of the variant on the protein may be considered. Additional links or references to additional databases may be provided, including links to RefSeq and/or dbSNP, for example. Multiple variants may be selectable by gene or pathway. [0021] In an exemplary embodiment, upon submission and processing of a query, the genetic care database and/or server may return a summary of found similar patients (which may be de- identified) with corresponding location and/or pathologic (e.g., cancer) type. For example, the genetic care database and/or server may return a list of institutions showing the number of patients found at each institution and a list of cancer types showing the number of patients having such cancer types. Data relevant to such locations and cancer types may then be retrieved to show a listing of similar selectable patients with corresponding institution, diagnosis, treatment, and/or outcome. The data may be filtered according to cancer type or institution, for example. An interpreting physician may select one or more of the selectable patients for inclusion of a report.

[0022] In an exemplary embodiment, there is provided a mechanism by which a treating physician may request a genetic care database search and gain any necessary consent from any relevant patient, personnel, and/or entities. In an embodiment, all patients run through a data input manager or front-end software component (e.g., ION REPORTER) may be part of the query and contribute to the genetic care database. In an embodiment, submission by sequencing institutions of some or all of their (de-identified) data to the genetic care database may be associated with an appropriate compensation framework and/or access conditions and/or parameters to the genetic care database.

[0023] In an exemplary embodiment, which may be referred to as a Clinical Trial Selection use case, a treating physician may be enabled to receive a list of clinical trials for which a patient is a match. In this context, whether a patient is a match may be primarily based on genetic criteria, but a geographic location of the trial may also be taken into account. In an embodiment, however, other screening criteria (e.g., age, pregnancy, etc.) may be excluded from consideration. Because both a query about a patient and some or all of the patient's complete genetic data may become a permanent part of the genetic care database, any appropriate consent that may be required may be obtained and form part of an appropriate record establishing such consent.

[0024] In an exemplary embodiment, a query may include: (1) a genetic component, which may include specific variants that are being queried against a list of drugs; (2) a comprehensive or complete genetic information (variome) component for a patient; (3) information regarding treatment and diagnosis of the patient, which information may need to be retrieved at a later date from an appropriate Electronic Medical Record; and (4) a proof of payment or other information indicating that an appropriate access to the genetic care database is available for the relevant patient and/or institution and that any necessary consent has been given. The return of the query may include a list of trials and the associated variants that led to such trials being a match.

[0025] In an exemplary embodiment, which may be referred to as a Comparative Genomic Medicine use case, an interpreting physician may be enabled to receive a list of patients that are genetically similar (or have a genetically similar tumor, for example) along with associated treatment and outcome data. In an embodiment, institutions such as hospitals, for example, may be asked to deposit treatment and outcome information for patients (or links thereto or some other identifiers allowing a party aware of such identifiers to request such treatment and outcome information for patients from such institutions) in the genetic care database, as well as the genetic data. Any appropriate consent that may be required may be obtained and form part of an appropriate record establishing such consent.

[0026] In an exemplary embodiment, a query may include: (1) a genetic component, which may include specific variants that are being queried against the patients, and which may take many forms (e.g., exact match, match at a gene level, match at a functional level, match at a pathway level, etc., for example); (2) a comprehensive or complete genetic information (variome) component for a patient; (3) information regarding treatment and diagnosis of the patient, which information may be provided asynchronously; and (4) a proof of payment or other information indicating that an appropriate access to the genetic care database is available for the relevant patient and/or institution and that any necessary consent has been given. The return of the query may include a list of patients (de-identified), hospital identifiers, and normalized treatment and outcome information. That data may be presented to the interpreting physician in a manner that enables them to derive insights that may aid the treatment of a patient.

[0027] In an exemplary embodiment, the system may provide an indication of available clinical trials back to the interpreting physician, the interpreting physician may have a mechanism for selecting or reviewing trials, the system may provide a mechanism for creating reports including the results of the clinical trial queries, the system may maintain clinical trial information along with the genetic criteria for those trials and their availability and location. The system may provide a mechanism for a curator to add, remove and/or otherwise edit the list of trials. The system may provide rules for matching trials to variomes, which rules may be simple matching rules against the list of variants, genes, and/or pathways provided by the query. The query may enable query and filter criteria (e.g., AND and OR matching criteria). If specified, the query may take into account location of the trials. Any updates to the list of trials may be time- stamped such that a state of the database at any point in time can be recorded.

[0028] In an exemplary embodiment, the system may provide a list of matching patients and their hospital, diagnosis, treatment and outcome information back to an interpreting physician. The interpreting physician may have a mechanism for selecting patients from the list, either individually or by hospital. The system may provide a mechanism for creating reports including the matching patients; the system may maintain a list of de-identified patients along with their hospitals and genetic information. The system may provide rules for matching patients to variomes, which rules may be simple matching rules against the list of variants, gene, pathways provided by the query. The query may enable query and filter criteria (e.g., AND and OR matching criteria). If specified, the query may take into account hospital and diagnosis. The system may have a mechanism for retrieving a de-identified patient's diagnosis, treatment and outcome from a system under hospital control. The system may or may not store the de- identified patient's diagnosis, treatment and outcome information. Any updates to the de- identified patients may be time- stamped such that a state of the database at any point in time can be recorded. The system may supports two types of roles: an interpreting physician, who may be the main user of the system and an administrator capable of managing access to the system and managing the data.

[0029] In an exemplary embodiment, the system may receive information including: a patient identifier (which may be de-identified but which corresponds to a patient record that the hospital treating that patient could identify if provided with such patient identifier), a unique hospital identifier, some or all of the patient's complete variome, and a token representing proof-of- payment and/or compliance with any requirements (e.g., consent or authentication information) that may need to be fulfilled. The system may provide an interface enabling the interpreting physician to select a set of variants from the patient's variome. Selection may be gene-based, marker-based, or pathway-based, for example. The system may provide an interface for the interpreting physician to select diagnosis parameters. In the system, the contents of a patient's variome, diagnosis and the query may become part of the patient index of genetic care database and may be used indefinitely. The system may be configured to only store de-identified information. Treatment and outcome information may be normalized through entry. Data entry may be validated against a dictionary of terms and may be cross-validated to ensure entry of consistent information.

[0030] In an exemplary embodiment, a genetic care database may partition data to prevent one hospital from directly accessing the data from another, provide access authentication, communicate with external systems through an authenticated communication protocol, operate in a multi-tenanted hosted environment, and reside in a hosted environment. Sequencing institutions (e.g., hospitals), may need to accept the provisioning of a box at their local site to provide the connection to the genetic care database and additional functionality.

[0031] According to an exemplary embodiment, there is provided a method for exchanging genomic information, comprising: (1) providing or supplying a plurality of genomic sequencers at a plurality of sites, each of the plurality of genomic sequencers being configured to comprise or to be in communication with a genomic database, each genomic database comprising biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient; (2) hosting a genomic information indexing database comprising indexing information associated with one or more genomic sequences; (3) operating a server computer in communication with the genomic information indexing database and with any genomic database comprised in or in communication with one of the plurality of genomic sequencers, comprising: (i) receiving at least some of the biological or medical data comprised in each genomic database and at least some of the sequence data comprised in each genomic database; (ii) generating indexing information corresponding to any received biological or medical data and sequence data, the indexing information being generated so as to allow identification of the genomic database and any relevant records stored in the genomic database that include the received biological or medical data and sequence data; (iii) transmitting the generated indexing information to the genomic information indexing database for storage in the genomic information indexing database; (iv) querying, upon request by a treating physician, the genomic information indexing database about a genomic sequence of interest; and (v) retrieving indexing information associated with the genomic sequence of interest from the genomic information indexing database.

[0032] According to various exemplary embodiments, the method may further comprise querying an information database about the genomic sequence of interest and retrieving information from the information database about the genomic sequence of interest. The information database may include one or more of a medical guidelines database, a database comprising information about drug trial eligibility factors, a database comprising research or medical insights, a database maintained by a government or public entity, and a database maintained by a corporate or private entity. The information retrieved from the information database may include treatment options for one or more pathological conditions associated with the genomic sequence of interest. The method may further comprise querying, via an analysis server, the genomic information indexing database about a genomic sequence of interest and mining results of the querying so as to identify a potential target for a new drug. The biological or medical data associated with the biological organism or patient may include medical data associated with a patient, and the medical data may include data regarding a cancer and treatment response. Providing or supplying the plurality of genomic sequencers may include providing or supplying semiconductor-based genomic sequencers, or may include providing or supplying genomic sequencers based on light or fluorescence detection. The received biological or medical data and sequence data may relate to a patient but not contain personal identity information of the patient, and the indexing information may also not contain personal identity information of the patient. Querying may further include querying the genomic information indexing database for one or more of an exact match between the genomic sequence of interest and one or more genomic variants at a sequence level, a match between the genomic sequence of interest and one or more genomic variants at a gene level, a match between the genomic sequence of interest and one or more genomic variants at a functional level, and a match between the genomic sequence of interest and one or more genomic variants at a pathway level. The genomic sequence of interest may be a complete genetic information (variome) of a patient. Querying may further include querying the genomic information indexing database for one or more of a patient diagnosis, a patient treatment, and a token representing proof-of-payment. Operating the server computer may further include reporting to a requesting treating physician one or more results of the querying, including a list of one or more patients, without any personal identity information of the patients but with an identification of one or more treatment centers and one or more patient identification numbers for the one or more patients that would allow the one or more treatment centers having treated the patients to identify records pertaining to the one or more patients. The one or more results may further include diagnosis information corresponding to the one or more patients, normalized treatment and outcome information corresponding to the one or more patients, and/or normalized diagnosis, treatment, and outcome information corresponding to one or more patients having a genetically similar cancer.

[0033] According to an exemplary embodiment, there is provided a system for exchanging genomic information, comprising: (1) a plurality of genomic sequencers arranged at a plurality of sites, each of the plurality of genomic sequencers comprising or being in communication with a genomic database, each genomic database comprising biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient; (2) a genomic information indexing database comprising indexing information associated with one or more genomic sequences; (3) a server computer configured to be in communication with the genomic information indexing database and with each genomic database comprised in or in communication with one of the plurality of genomic sequencers, the server computer comprising: (i) an aggregation engine configured to receive at least some of the biological or medical data comprised in each genomic database and at least some of the sequence data comprised in each genomic database; (ii) an indexing engine configured to generate indexing information corresponding to any received biological or medical data and sequence data, the indexing information being generated so as to allow identification of the genomic database and any relevant records stored in the genomic database that include the received biological or medical data and sequence data, and transmit the generated indexing information to the genomic information indexing database for storage in the genomic information indexing database; and (iii) a querying engine configured to query the genomic information indexing database about a genomic sequence of interest and retrieve indexing information associated with the genomic sequence of interest from the genomic information indexing database. [0034] According to various exemplary embodiments, the system may further comprise an information database, and the querying engine may be further configured to query the information database about the genomic sequence of interest and retrieve information from the information database about the genomic sequence of interest. The information database may include one or more of a medical guidelines database or information retrieved therefrom, a database comprising information about drug trial eligibility factors or information retrieved therefrom, a database comprising research or medical insights or information retrieved therefrom, a database maintained by a government or public entity or information retrieved therefrom, and a database maintained by a corporate or private entity or information retrieved therefrom. The information retrieved from the information database may include treatment options for one or more pathological conditions associated with the genomic sequence of interest. The system may further comprise an analysis server comprising a querying engine configured to query the genomic information indexing database about a genomic sequence of interest and to mine results of the query so as to identify a potential target for a new drug. The biological or medical data associated with the biological organism or patient may include medical data associated with a patient, and the medical data may include data regarding a patient's cancer and treatment response. The plurality of genomic sequencers may include semiconductor-based genomic sequencers, or genomic sequencers based on light or fluorescence detection. The received biological or medical data and sequence data may relate to a patient but not contain personal identity information of the patient, and the indexing information also may not contain personal identity information of the patient. The querying engine may be configured to query the genomic information indexing database for one or more of an exact match between the genomic sequence of interest and one or more genomic variants at a sequence level, a match between the genomic sequence of interest and one or more genomic variants at a gene level, a match between the genomic sequence of interest and one or more genomic variants at a functional level, and a match between the genomic sequence of interest and one or more genomic variants at a pathway level. The genomic sequence of interest may be a complete genetic information (variome) of a patient. The querying engine may be configured to query the genomic information indexing database for one or more of a patient diagnosis, a patient treatment, and a token representing proof-of-payment. The server computer may further comprise a reporting engine configured to report to a requesting treating physician one or more results of the querying performed by the querying engine, including a list of one or more patients, without any personal identity information of the patients but with an identification of one or more treatment centers and one or more patient identification numbers for the one or more patients that would allow the one or more treatment centers having treated the patients to identify records pertaining to the one or more patients. The one or more results may further include diagnosis information corresponding to the one or more patients, normalized treatment and outcome information corresponding to the one or more patients, and/or normalized diagnosis, treatment, and outcome information corresponding to one or more patients having a genetically similar cancer.

[0035] According to an exemplary embodiment, there is provided a non-transitory computer readable medium comprising instructions which, when executed by a processor, cause the processor to: operate a server computer in communication with a genomic information indexing database, the genomic information indexing database comprising indexing information associated with one or more genomic sequences, and with a plurality of genomic databases, each of the genomic databases being comprised in or in communication with one of a plurality of genomic sequencers at a plurality of sites, and each genomic database comprising biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient, the operating of the server computer comprising: (1) receiving at least some of the biological or medical data comprised in each genomic database and at least some of the sequence data comprised in each genomic database; (2) generating indexing information corresponding to any received biological or medical data and sequence data, the indexing information being generated so as to allow identification of the genomic database and any relevant records stored in the genomic database that include the received biological or medical data and sequence data; (3) transmitting the generated indexing information to the genomic information indexing database for storage in the genomic information indexing database; (4) querying the genomic information indexing database about a genomic sequence of interest; and (5) retrieving indexing information associated with the genomic sequence of interest from the genomic information indexing database. [0036] According to various exemplary embodiments, the operating of the server computer may further comprise querying an information database about the genomic sequence of interest and retrieving information from the information database about the genomic sequence of interest. The information database may include one or more of a medical guidelines database or information retrieved therefrom, a database comprising information about drug trial eligibility factors or information retrieved therefrom, a database comprising research or medical insights or information retrieved therefrom, a database maintained by a government or public entity or information retrieved therefrom, and a database maintained by a corporate or private entity or information retrieved therefrom. The information retrieved from the information database may include treatment options for one or more pathological conditions associated with the genomic sequence of interest. The non-transitory computer readable medium may further comprise querying, via an analysis server, the genomic information indexing database about a genomic sequence and mining results of the querying so as to identify a potential target for a new drug. The biological or medical data associated with the biological organism or patient may include medical data associated with a patient, and the medical data may include data regarding a cancer and treatment response. The plurality of genomic sequencers may include semiconductor-based genomic sequencers, or genomic sequencers based on light or fluorescence detection. The received biological or medical data and sequence data may relate to a patient but not contain personal identity information of the patient, and the indexing information may also not contain personal identity information of the patient. Querying may further include querying the genomic information indexing database for one or more of an exact match between the genomic sequence of interest and one or more genomic variants at a sequence level, a match between the genomic sequence of interest and one or more genomic variants at a gene level, a match between the genomic sequence of interest and one or more genomic variants at a functional level, and a match between the genomic sequence of interest and one or more genomic variants at a pathway level. The genomic sequence of interest may be a complete genetic information (variome) of a patient. Querying may further include querying the genomic information indexing database for one or more of a patient diagnosis, a patient treatment, and a token representing proof-of- payment. Operating the server computer may further include reporting to a requesting treating physician one or more results of the querying, including a list of one or more patients, without any personal identity information of the patients but with an identification of one or more treatment centers and one or more patient identification numbers for the one or more patients that would allow the one or more treatment centers having treated the patients to identify records pertaining to the one or more patients. The one or more results may further include diagnosis information corresponding to the one or more patients, normalized treatment and outcome information corresponding to the one or more patients, and/or normalized diagnosis, treatment, and outcome information corresponding to one or more patients having a genetically similar cancer.

[0037] According to an exemplary embodiment, there is provided a method for allowing physicians to share information about patients, comprising: (1) providing or supplying a plurality of sequencers to a plurality of treatment centers for use by the treatment centers to obtain patient sequencing data; (2) retrieving, from one or more databases hosted by each of the treatment centers, at least some of the obtained patient sequencing data and at least some of any corresponding patient medical information obtained by the treatment center; (3) storing indexing information in a genomic index database corresponding to the retrieved patient sequencing data and corresponding patient medical information, the indexing information being recorded against any genomic variants identified from the patient sequencing data; (4) querying, upon request by a treating physician, the genomic index database and one or more information sources about one or more characteristics of a patient; and (5) providing a report to the treating physician including findings resulting from the querying.

[0038] According to various exemplary embodiments, the plurality of sequencers may include sequencers based on semiconductor gene sequencing, or sequencers based on light or fluorescence detection gene sequencing. The at least some retrieved corresponding patient medical information may not contain identity information of the patient. The at least some retrieved corresponding patient medical information may include cancer-related clinical information including treatment and outcome information. The indexing information may not contain identity information of any patients. Querying may include querying for one or more genomic variants of the patient, for an exact match at a sequence level, for a match at a gene level, for a match at a functional level, and/or for a match at a pathway level. Querying may include querying for a complete genetic information (variome) of a patient. Querying may include querying for a diagnosis of the patient, querying for a treatment of the patient, querying asynchronously for a treatment and diagnosis of the patient, and/or submitting a token representing proof-of-payment. The findings resulting from the querying may include a list of one or more patients, without identity information of the patients, and of one or more treatment centers corresponding to the one or more patients. The findings resulting from the querying may include a list of one or more patients, without identity information of the patients, and diagnosis information corresponding to the one or more patients. The findings resulting from the querying may include a list of one or more patients, without identity information of the patients, and normalized treatment and outcome information corresponding to the one or more patients. The report to the treating physician may include a list of one or more patients having genetically similar tumors, without identity information of the patients, together with normalized diagnosis, treatment, and outcome information corresponding to the one or more patients.

[0039] According to an exemplary embodiment, there is provided a non-transitory computer readable medium comprising instructions which, when executed by a processor, cause the processor to allow physicians to share information about patients by performing steps of a method comprising: (1) retrieving, from one or more databases hosted by each of a plurality of treatment centers each having been provided or supplied one or more sequencers to obtain patient sequencing data, at least some of the patient sequencing data obtained by the treatment centers and at least some of any corresponding patient medical information obtained by the treatment center; (2) storing indexing information in a genomic index database corresponding to the retrieved patient sequencing data and corresponding patient medical information, the indexing information being recorded against any genomic variants identified from the patient sequencing data; (3) querying, upon request by a treating physician, the genomic index database and one or more information sources about one or more characteristics of a patient; and (4) providing a report to the treating physician including findings resulting from the querying.

[0040] According to various exemplary embodiments, the plurality of sequencers may include sequencers based on semiconductor gene sequencing, or sequencers based on light or fluorescence detection gene sequencing. The at least some retrieved corresponding patient medical information may not contain identity information of the patient. The at least some retrieved corresponding patient medical information may include cancer-related clinical information including treatment and outcome information. The indexing information may not contain identity information of any patients. Querying may include querying for one or more genomic variants of the patient, for an exact match at a sequence level, for a match at a gene level, for a match at a functional level, and/or for a match at a pathway level. Querying may include querying for a complete genetic information (variome) of a patient. Querying may include querying for a diagnosis of the patient, querying includes querying for a treatment of the patient, querying asynchronously for a treatment and diagnosis of the patient, and/or submitting a token representing proof-of-payment. The findings resulting from the querying may include a list of one or more patients, without identity information of the patients, and of one or more treatment centers corresponding to the one or more patients. The findings resulting from the querying may include a list of one or more patients, without identity information of the patients, and diagnosis information corresponding to the one or more patients. The findings resulting from the querying may include a list of one or more patients, without identity information of the patients, and normalized treatment and outcome information corresponding to the one or more patients. The report to the treating physician may include a list of one or more patients having genetically similar tumors, without identity information of the patients, together with normalized diagnosis, treatment, and outcome information corresponding to the one or more patients.

[0041] According to an exemplary embodiment, there is provided a method for identifying clinical trials suitable for a patient, comprising: (1) providing or supplying a plurality of sequencers to a plurality of treatment centers for use by the treatment centers to obtain patient sequencing data; (2) retrieving, from one or more databases hosted by each of the treatment centers, at least some of the obtained patient sequencing data and at least some of any corresponding patient medical information obtained by the treatment center; (3) storing indexing information in a genomic index database corresponding to the retrieved patient sequencing data and corresponding patient medical information, the indexing information being recorded against any genomic variants identified from the patient sequencing data; (4) querying, upon request by a treating physician, the genomic index database about one or more characteristics of a patient, the querying including querying a clinical trial database comprising clinical trial genomic eligibility criteria; and (5) providing a report to the treating physician including any findings resulting from the querying. [0042] According to various exemplary embodiments, the plurality of sequencers may include sequencers based on semiconductor gene sequencing, or sequencers based on light or fluorescence detection gene sequencing. The at least some retrieved corresponding patient medical information may not contain identity information of the patient. The indexing information may not contain identity information of any patients. Querying may include querying for one or more genomic variants of the patient, for a complete genetic information (variome) of a patient, and/or for a diagnosis of the patient. The findings resulting from the querying may include a list of one or more clinical trials. The list of one or more clinical trials may include related patient eligibility criteria information.

[0043] According to various exemplary embodiments, one or more of the above-discussed teachings and/or exemplary embodiments may include additional aspects pertaining to marketing and/or payment, which may include ratings of services or applications by users; information regarding payment, which may include click-use fees and various features allowing payment of such click-use fees and/or verification thereof; features providing for reduced fees for providers meeting certain criteria; etc.

[0044] According to various exemplary embodiments, one or more of the above-discussed teachings and/or exemplary embodiments may implement one or more measures for determining a similarity between genetic variants and/or sequences. Any suitable similarity metric may be used. For example, the genomic similarity measure may be computed using a variety of algorithms, such as principal components analysis, clustering, genetic algorithms, etc. The measure may include information about the similarity of two variants in their known or predicted effects on the gene function and/or expression, the pathway of the gene in which the variants reside, for example, and may incorporate additional measured information such as RNA expression level and/or epigenetic factors, etc., for example.

[0045] According to various exemplary embodiments, one or more of the above-discussed teachings and/or exemplary embodiments may include the use of any suitable sequencing technology, including any semiconductor-based genomic sequencers, any genomic sequencers based on light or fluorescence detection, and any nanopore-based or other sequencers.

[0046] According to various exemplary embodiments, one or more of the above-discussed teachings and/or exemplary embodiments may include the exchange of genetic information including any type of genetic information or sequences, as well as, for example, any information related to RNA signatures and/or epigenetics information.

[0047] According to various exemplary embodiments, one or more features of any one or more of the above-discussed teachings and/or exemplary embodiments may be performed or implemented using appropriately configured and/or programmed hardware and/or software elements. Determining whether an embodiment is implemented using hardware and/or software elements may be based on any number of factors, such as desired computational rate, power levels, heat tolerances, processing cycle budget, input data rates, output data rates, memory resources, data bus speeds, etc., and other design or performance constraints.

[0048] Examples of hardware elements may include processors, microprocessors, input(s) and/or output(s) (I/O) device(s) (or peripherals) that are communicatively coupled via a local interface circuit, circuit elements (e.g., transistors, resistors, capacitors, inductors, and so forth), integrated circuits, application specific integrated circuits (ASIC), programmable logic devices (PLD), digital signal processors (DSP), field programmable gate array (FPGA), logic gates, registers, semiconductor device, chips, microchips, chip sets, and so forth. The local interface may include, for example, one or more buses or other wired or wireless connections, controllers, buffers (caches), drivers, repeaters and receivers, etc., to allow appropriate communications between hardware components. A processor is a hardware device for executing software, particularly software stored in memory. The processor can be any custom made or commercially available processor, a central processing unit (CPU), an auxiliary processor among several processors associated with the computer, a semiconductor based microprocessor (e.g., in the form of a microchip or chip set), a macroprocessor, or generally any device for executing software instructions. A processor can also represent a distributed processing architecture. The I/O devices can include input devices, for example, a keyboard, a mouse, a scanner, a microphone, a touch screen, an interface for various medical devices and/or laboratory instruments, a bar code reader, a stylus, a laser reader, a radio-frequency device reader, etc. Furthermore, the I/O devices also can include output devices, for example, a printer, a bar code printer, a display, etc. Finally, the I/O devices further can include devices that communicate as both inputs and outputs, for example, a modulator/demodulator (modem; for accessing another device, system, or network), a radio frequency (RF) or other transceiver, a telephonic interface, a bridge, a router, etc.

[0049] Examples of software may include software components, programs, applications, computer programs, application programs, system programs, machine programs, operating system software, middleware, firmware, software modules, routines, subroutines, functions, methods, procedures, software interfaces, application program interfaces (API), instruction sets, computing code, computer code, code segments, computer code segments, words, values, symbols, or any combination thereof. A software in memory may include one or more separate programs, which may include ordered listings of executable instructions for implementing logical functions. The software in memory may include a system for identifying data streams in accordance with the present teachings and any suitable custom made or commercially available operating system (O/S), which may control the execution of other computer programs such as the system, and provides scheduling, input-output control, file and data management, memory management, communication control, etc.

[0050] According to various exemplary embodiments, one or more features of any one or more of the above-discussed teachings and/or exemplary embodiments may be performed or implemented using appropriately configured and/or programmed non-transitory machine- readable medium or article that may store an instruction or a set of instructions that, if executed by a machine, may cause the machine to perform a method and/or operations in accordance with the exemplary embodiments. Such a machine may include, for example, any suitable processing platform, computing platform, computing device, processing device, computing system, processing system, computer, processor, scientific or laboratory instrument, etc., and may be implemented using any suitable combination of hardware and/or software. The machine- readable medium or article may include, for example, any suitable type of memory unit, memory device, memory article, memory medium, storage device, storage article, storage medium and/or storage unit, for example, memory, removable or non-removable media, erasable or non-erasable media, writeable or re-writeable media, digital or analog media, hard disk, floppy disk, read-only memory compact disc (CD-ROM), recordable compact disc (CD-R), rewriteable compact disc (CD-RW), optical disk, magnetic media, magneto-optical media, removable memory cards or disks, various types of Digital Versatile Disc (DVD), a tape, a cassette, etc., including any medium suitable for use in a computer. Memory can include any one or a combination of volatile memory elements (e.g., random access memory (RAM, such as DRAM, SRAM, SDRAM, etc.)) and nonvolatile memory elements (e.g., ROM, EPROM, EEROM, Flash memory, hard drive, tape, CDROM, etc.). Moreover, memory can incorporate electronic, magnetic, optical, and/or other types of storage media. Memory can have a distributed architecture where various components are situated remote from one another, but are still accessed by the processor. The instructions may include any suitable type of code, such as source code, compiled code, interpreted code, executable code, static code, dynamic code, encrypted code, etc., implemented using any suitable high-level, low-level, object-oriented, visual, compiled and/or interpreted programming language.

[0051] According to various exemplary embodiments, one or more features of any one or more of the above-discussed teachings and/or exemplary embodiments may be performed or implemented at least partly using a distributed, clustered, remote, or cloud computing resource.

[0052] According to various exemplary embodiments, one or more features of any one or more of the above-discussed teachings and/or exemplary embodiments may be performed or implemented using a source program, executable program (object code), script, or any other entity comprising a set of instructions to be performed. When a source program, the program can be translated via a compiler, assembler, interpreter, etc., which may or may not be included within the memory, so as to operate properly in connection with the O/S. The instructions may be written using (a) an object oriented programming language, which has classes of data and methods, or (b) a procedural programming language, which has routines, subroutines, and/or functions, which may include, for example, C, C++, Pascal, Basic, Fortran, Cobol, Perl, Java, and Ada.

[0053] Various additional exemplary embodiments may be derived by repeating, adding, or substituting any generically or specifically described features and/or components and/or substances and/or steps and/or operating conditions set forth in one or more of the above- described exemplary embodiments. Further, it should be understood that an order of steps or order for performing certain actions is immaterial so long as the objective of the steps or action remains achievable, unless specifically stated otherwise. Furthermore, two or more steps or actions can be conducted simultaneously so long as the objective of the steps or action remains achievable, unless specifically stated otherwise. Moreover, any one or more feature, component, aspect, step, or other characteristic mentioned in one of the above-discussed exemplary embodiments may be considered to be a potential optional feature, component, aspect, step, or other characteristic of any other of the above-discussed exemplary embodiments so long as the objective of such any other of the above-discussed exemplary embodiments remains achievable, unless specifically stated otherwise.

[0054] Although the present description described in detail certain exemplary embodiments, other embodiments are also possible and within the scope of the present invention. Variations and modifications will be apparent to those skilled in the art from consideration of the specification and figures and practice of the teachings described in the specification and figures, and the claims.

Claims

1. A method for exchanging genomic information, comprising:

providing or supplying a plurality of genomic sequencers at a plurality of sites, each of the plurality of genomic sequencers being configured to comprise or to be in communication with a genomic database, each genomic database comprising biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient;

hosting a genomic information indexing database comprising indexing information associated with one or more genomic sequences;

operating a server computer in communication with the genomic information indexing database and with any genomic database comprised in or in communication with one of the plurality of genomic sequencers, comprising:

receiving at least some of the biological or medical data comprised in each genomic database and at least some of the sequence data comprised in each genomic database;

generating indexing information corresponding to any received biological or medical data and sequence data, the indexing information being generated so as to allow identification of the genomic database and any relevant records stored in the genomic database that include the received biological or medical data and sequence data;

transmitting the generated indexing information to the genomic information indexing database for storage in the genomic information indexing database;

querying, upon request by a treating physician, the genomic information indexing database about a genomic sequence of interest; and

retrieving indexing information associated with the genomic sequence of interest from the genomic information indexing database.

2. The method of claim 1, further comprising querying an information database about the genomic sequence of interest and retrieving information from the information database about the genomic sequence of interest.

3. The method of claim 2, wherein the information database includes a medical guidelines database.

4. The method of claim 2, wherein the information database includes a database comprising information about drug trial eligibility factors.

5. The method of claim 2, wherein the information database includes a database comprising research or medical insights.

6. The method of claim 2, wherein the information database includes a database maintained by a government or public entity.

7. The method of claim 2, wherein the information database includes a database maintained by a corporate or private entity.

8. The method of claim 2, wherein the information retrieved from the information database includes treatment options for one or more pathological conditions associated with the genomic sequence of interest.

9. The method of claim 1, further comprising querying, via an analysis server, the genomic information indexing database about a genomic sequence of interest and mining results of the querying so as to identify a potential target for a new drug.

10. The method of claim 1, wherein the biological or medical data associated with the biological organism or patient includes medical data associated with a patient, and wherein the medical data include data regarding a cancer and treatment response.

11. The method of claim 1, wherein providing or supplying the plurality of genomic sequencers includes providing or supplying semiconductor-based genomic sequencers.

12. The method of claim 1, wherein providing or supplying the plurality of genomic sequencers includes providing or supplying genomic sequencers based on light or fluorescence detection.

13. The method of claim 1, wherein the received biological or medical data and sequence data relate to a patient but do not contain personal identity information of the patient, and wherein the indexing information also does not contain personal identity information of the patient.

14. The method of claim 1, wherein querying further includes querying the genomic information indexing database for one or more of an exact match between the genomic sequence of interest and one or more genomic variants at a sequence level, a match between the genomic sequence of interest and one or more genomic variants at a gene level, a match between the genomic sequence of interest and one or more genomic variants at a functional level, and a match between the genomic sequence of interest and one or more genomic variants at a pathway level.

15. The method of claim 1, wherein the genomic sequence of interest is a complete genetic information (variome) of a patient.

16. The method of claim 1, wherein querying further includes querying the genomic information indexing database for one or more of a patient diagnosis, a patient treatment, and a token representing proof-of-payment.

17. The method of claim 1, wherein operating the server computer further includes reporting to a requesting treating physician one or more results of the querying, including a list of one or more patients, without any personal identity information of the patients but with an identification of one or more treatment centers and one or more patient identification numbers for the one or more patients that would allow the one or more treatment centers having treated the patients to identify records pertaining to the one or more patients.

18. The method of claim 17, wherein the one or more results further include diagnosis information corresponding to the one or more patients.

19. The method of claim 17, wherein the one or more results further include normalized treatment and outcome information corresponding to the one or more patients.

20. The method of claim 17, wherein the one or more results further include normalized diagnosis, treatment, and outcome information corresponding to one or more patients having a genetically similar cancer.

21. A system for exchanging genomic information, comprising:

a plurality of genomic sequencers arranged at a plurality of sites, each of the plurality of genomic sequencers comprising or being in communication with a genomic database, each genomic database comprising biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient; a genomic information indexing database comprising indexing information associated with one or more genomic sequences;

a server computer configured to be in communication with the genomic information indexing database and with each genomic database comprised in or in communication with one of the plurality of genomic sequencers, the server computer comprising:

an aggregation engine configured to receive at least some of the biological or medical data comprised in each genomic database and at least some of the sequence data comprised in each genomic database;

an indexing engine configured to generate indexing information corresponding to any received biological or medical data and sequence data, the indexing information being generated so as to allow identification of the genomic database and any relevant records stored in the genomic database that include the received biological or medical data and sequence data, and transmit the generated indexing information to the genomic information indexing database for storage in the genomic information indexing database; and a querying engine configured to query the genomic information indexing database about a genomic sequence of interest and retrieve indexing information associated with the genomic sequence of interest from the genomic information indexing database.

22. The system of claim 21, further comprising an information database, wherein the querying engine is further configured to query the information database about the genomic sequence of interest and retrieve information from the information database about the genomic sequence of interest.

23. The system of claim 22, wherein the information database includes a medical guidelines database or information retrieved therefrom.

24. The system of claim 22, wherein the information database includes a database comprising information about drug trial eligibility factors or information retrieved therefrom.

25. The system of claim 22, wherein the information database includes a database comprising research or medical insights or information retrieved therefrom.

26. The system of claim 22, wherein the information database includes a database maintained by a government or public entity or information retrieved therefrom.

27. The system of claim 22, wherein the information database includes a database maintained by a corporate or private entity or information retrieved therefrom.

28. The system of claim 22, wherein the information retrieved from the information database includes treatment options for one or more pathological conditions associated with the genomic sequence of interest.

29. The system of claim 21, further comprising an analysis server comprising a querying engine configured to query the genomic information indexing database about a genomic sequence of interest and to mine results of the query so as to identify a potential target for a new drug.

30. The system of claim 21, wherein the biological or medical data associated with the biological organism or patient includes medical data associated with a patient, and wherein the medical data include data regarding a patient's cancer and treatment response.

31. The system of claim 21, wherein the plurality of genomic sequencers includes semiconductor-based genomic sequencers.

32. The system of claim 21, wherein the plurality of genomic sequencers includes genomic sequencers based on light or fluorescence detection.

33. The system of claim 21, wherein the received biological or medical data and sequence data relate to a patient but do not contain personal identity information of the patient, and wherein the indexing information also does not contain personal identity information of the patient.

34. The system of claim 21, wherein the querying engine is configured to query the genomic information indexing database for one or more of an exact match between the genomic sequence of interest and one or more genomic variants at a sequence level, a match between the genomic sequence of interest and one or more genomic variants at a gene level, a match between the genomic sequence of interest and one or more genomic variants at a functional level, and a match between the genomic sequence of interest and one or more genomic variants at a pathway level.

35. The system of claim 21, wherein the genomic sequence of interest is a complete genetic information (variome) of a patient.

36. The system of claim 21, wherein the querying engine is configured to query the genomic information indexing database for one or more of a patient diagnosis, a patient treatment, and a token representing proof-of-payment.

37. The system of claim 21, wherein the server computer further comprises a reporting engine configured to report to a requesting treating physician one or more results of the querying performed by the querying engine, including a list of one or more patients, without any personal identity information of the patients but with an identification of one or more treatment centers and one or more patient identification numbers for the one or more patients that would allow the one or more treatment centers having treated the patients to identify records pertaining to the one or more patients.

38. The system of claim 37, wherein the one or more results further include diagnosis information corresponding to the one or more patients.

39. The system of claim 37, wherein the one or more results further include normalized treatment and outcome information corresponding to the one or more patients.

40. The system of claim 37, wherein the one or more results further include normalized diagnosis, treatment, and outcome information corresponding to one or more patients having a genetically similar cancer.

41. A non-transitory computer readable storage medium comprising instructions which, when executed by a processor, cause the processor to:

operate a server computer in communication with a genomic information indexing database, the genomic information indexing database comprising indexing information associated with one or more genomic sequences, and with a plurality of genomic databases, each of the genomic databases being comprised in or in communication with one of a plurality of genomic sequencers at a plurality of sites, and each genomic database comprising biological or medical data associated with a biological organism or patient and sequence data obtained from genetic materials of the biological organism or patient, the operating of the server computer comprising:

querying the genomic information indexing database about a genomic sequence of interest; and

42. The non-transitory computer readable storage medium of claim 41, wherein the operating of the server computer further comprises querying an information database about the genomic sequence of interest and retrieving information from the information database about the genomic sequence of interest.

43. The non-transitory computer readable storage medium of claim 42, wherein the information database includes a medical guidelines database or information retrieved therefrom.

44. The non-transitory computer readable storage medium of claim 42, wherein the information database includes a database comprising information about drug trial eligibility factors or information retrieved therefrom.

45. The non-transitory computer readable storage medium of claim 42, wherein the information database includes a database comprising research or medical insights or information retrieved therefrom.

46. The non-transitory computer readable storage medium of claim 42, wherein the information database includes a database maintained by a government or public entity or information retrieved therefrom.

47. The non-transitory computer readable storage medium of claim 42, wherein the information database includes a database maintained by a corporate or private entity or information retrieved therefrom.

48. The non-transitory computer readable storage medium of claim 42, wherein the information retrieved from the information database includes treatment options for one or more pathological conditions associated with the genomic sequence of interest.

49. The non-transitory computer readable storage medium of claim 41, further comprising querying, via an analysis server, the genomic information indexing database about a genomic sequence and mining results of the querying so as to identify a potential target for a new drug.

50. The non-transitory computer readable storage medium of claim 41, wherein the biological or medical data associated with the biological organism or patient includes medical data associated with a patient, and wherein the medical data include data regarding a cancer and treatment response.

51. The non-transitory computer readable storage medium of claim 41, wherein the plurality of genomic sequencers includes semiconductor-based genomic sequencers.

52. The non-transitory computer readable storage medium of claim 41, wherein the plurality of genomic sequencers includes genomic sequencers based on light or fluorescence detection.

53. The non-transitory computer readable storage medium of claim 41, wherein the received biological or medical data and sequence data relate to a patient but do not contain personal identity information of the patient, and wherein the indexing information also does not contain personal identity information of the patient.

54. The non-transitory computer readable storage medium of claim 41, wherein querying further includes querying the genomic information indexing database for one or more of an exact match between the genomic sequence of interest and one or more genomic variants at a sequence level, a match between the genomic sequence of interest and one or more genomic variants at a gene level, a match between the genomic sequence of interest and one or more genomic variants at a functional level, and a match between the genomic sequence of interest and one or more genomic variants at a pathway level.

55. The non-transitory computer readable storage medium of claim 41, wherein the genomic sequence of interest is a complete genetic information (variome) of a patient.

56. The non-transitory computer readable storage medium of claim 41, wherein querying further includes querying the genomic information indexing database for one or more of a patient diagnosis, a patient treatment, and a token representing proof-of-payment.

57. The non-transitory computer readable storage medium of claim 41, wherein operating the server computer further includes reporting to a requesting treating physician one or more results of the querying, including a list of one or more patients, without any personal identity information of the patients but with an identification of one or more treatment centers and one or more patient identification numbers for the one or more patients that would allow the one or more treatment centers having treated the patients to identify records pertaining to the one or more patients.

58. The non-transitory computer readable storage medium of claim 57, wherein the one or more results further include diagnosis information corresponding to the one or more patients.

59. The non-transitory computer readable storage medium of claim 57, wherein the one or more results further include normalized treatment and outcome information corresponding to the one or more patients.

60. The non-transitory computer readable storage medium of claim 57, wherein the one or more results further include normalized diagnosis, treatment, and outcome information corresponding to one or more patients having a genetically similar cancer.

61. A method for allowing physicians to share information about patients, comprising: providing or supplying a plurality of sequencers to a plurality of treatment centers for use by the treatment centers to obtain patient sequencing data;

retrieving, from one or more databases hosted by each of the treatment centers, at least some of the obtained patient sequencing data and at least some of any corresponding patient medical information obtained by the treatment center;

storing indexing information in a genomic index database corresponding to the retrieved patient sequencing data and corresponding patient medical information, the indexing information being recorded against any genomic variants identified from the patient sequencing data;

querying, upon request by a treating physician, the genomic index database and one or more information sources about one or more characteristics of a patient; and

providing a report to the treating physician including findings resulting from the querying.

62. The method of claim 61, wherein the plurality of sequencers includes sequencers based on semiconductor gene sequencing.

63. The method of claim 61, wherein the plurality of sequencers includes sequencers based on light or fluorescence detection gene sequencing.

64. The method of claim 61, wherein the at least some retrieved corresponding patient medical information does not contain identity information of the patient.

65. The method of claim 61, wherein the at least some retrieved corresponding patient medical information includes cancer-related clinical information including treatment and outcome information.

66. The method of claim 61, wherein the indexing information does not contain identity information of any patients.

67. The method of claim 61, wherein querying includes querying for one or more genomic variants of the patient.

68. The method of claim 61, wherein querying includes querying for an exact match at a sequence level.

69. The method of claim 61, wherein querying includes querying for a match at a gene level.

70. The method of claim 61, wherein querying includes querying for a match at a functional level.

71. The method of claim 61, wherein querying includes querying for a match at a pathway level.

72. The method of claim 61, wherein querying includes querying for a complete genetic information (variome) of a patient.

73. The method of claim 61, wherein querying includes querying for a diagnosis of the patient.

74. The method of claim 61, wherein querying includes querying for a treatment of the patient.

75. The method of claim 61, wherein querying includes querying asynchronously for a treatment and diagnosis of the patient.

76. The method of claim 61, wherein querying includes submitting a token representing proof-of-payment.

77. The method of claim 61, wherein the findings resulting from the querying include a list of one or more patients, without identity information of the patients, and of one or more treatment centers corresponding to the one or more patients.

78. The method of claim 61, wherein the findings resulting from the querying include a list of one or more patients, without identity information of the patients, and diagnosis information corresponding to the one or more patients.

79. The method of claim 61, wherein the findings resulting from the querying include a list of one or more patients, without identity information of the patients, and normalized treatment and outcome information corresponding to the one or more patients.

80. The method of claim 61, wherein the report to the treating physician includes a list of one or more patients having genetically similar tumors, without identity information of the patients, together with normalized diagnosis, treatment, and outcome information corresponding to the one or more patients.

81. A non-transitory computer readable storage medium comprising instructions which, when executed by a processor, cause the processor to allow physicians to share information about patients by performing steps of a method comprising:

retrieving, from one or more databases hosted by each of a plurality of treatment centers each having been provided or supplied one or more sequencers to obtain patient sequencing data, at least some of the patient sequencing data obtained by the treatment centers and at least some of any corresponding patient medical information obtained by the treatment center;

82. The non-transitory computer readable storage medium of claim 81, wherein the plurality of sequencers includes sequencers based on semiconductor gene sequencing.

83. The non-transitory computer readable storage medium of claim 81, wherein the plurality of sequencers includes sequencers based on light or fluorescence detection gene sequencing.

84. The non-transitory computer readable storage medium of claim 81, wherein the at least some retrieved corresponding patient medical information does not contain identity information of the patient.

85. The non-transitory computer readable storage medium of claim 81, wherein the at least some retrieved corresponding patient medical information includes cancer-related clinical information including treatment and outcome information.

86. The non-transitory computer readable storage medium of claim 81, wherein the indexing information does not contain identity information of any patients.

87. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for one or more genomic variants of the patient.

88. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for an exact match at a sequence level.

89. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for a match at a gene level.

90. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for a match at a functional level.

91. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for a match at a pathway level.

92. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for a complete genetic information (variome) of a patient.

93. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for a diagnosis of the patient.

94. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying for a treatment of the patient.

95. The non-transitory computer readable storage medium of claim 81, wherein querying includes querying asynchronously for a treatment and diagnosis of the patient.

96. The non-transitory computer readable storage medium of claim 81, wherein querying includes submitting a token representing proof-of-payment.

97. The non-transitory computer readable storage medium of claim 81, wherein the findings resulting from the querying include a list of one or more patients, without identity information of the patients, and of one or more treatment centers corresponding to the one or more patients.

98. The non-transitory computer readable storage medium of claim 81, wherein the findings resulting from the querying include a list of one or more patients, without identity information of the patients, and diagnosis information corresponding to the one or more patients.

99. The non-transitory computer readable storage medium of claim 81, wherein the findings resulting from the querying include a list of one or more patients, without identity information of the patients, and normalized treatment and outcome information corresponding to the one or more patients.

100. The non-transitory computer readable storage medium of claim 81, wherein the report to the treating physician includes a list of one or more patients having genetically similar tumors, without identity information of the patients, together with normalized diagnosis, treatment, and outcome information corresponding to the one or more patients.

101. A method for identifying clinical trials suitable for a patient, comprising:

providing or supplying a plurality of sequencers to a plurality of treatment centers for use by the treatment centers to obtain patient sequencing data;

querying, upon request by a treating physician, the genomic index database about one or more characteristics of a patient, the querying including querying a clinical trial database comprising clinical trial genomic eligibility criteria; and

providing a report to the treating physician including any findings resulting from the querying.

102. The method of claim 101, wherein the plurality of sequencers includes sequencers based on semiconductor gene sequencing.

103. The method of claim 101, wherein the plurality of sequencers includes sequencers based on light or fluorescence detection gene sequencing.

104. The method of claim 101, wherein the at least some retrieved corresponding patient medical information does not contain identity information of the patient.

105. The method of claim 101, wherein the indexing information does not contain identity information of any patients.

106. The method of claim 101, wherein querying includes querying for one or more genomic variants of the patient.

107. The method of claim 101, wherein querying includes querying for a complete genetic information (variome) of a patient.

108. The method of claim 101, wherein querying includes querying for a diagnosis of the patient.

109. The method of claim 101, wherein the findings resulting from the querying include a list of one or more clinical trials.

110. The method of claim 109, wherein the list of one or more clinical trials includes related patient eligibility criteria information.