WO2003027236A2

WO2003027236A2 - Systems, methods and kits for remote genetic analysis and consultation

Info

Publication number: WO2003027236A2
Application number: PCT/US2002/029628
Authority: WO
Inventors: Ronald C. Mcglennen; Sabine Holmes; Timothy Johnson; Naomi M. Williamson; Aaron Franks; Robert Schuldt
Original assignee: Access Genetics, Llc
Priority date: 2001-09-21
Filing date: 2002-09-18
Publication date: 2003-04-03
Also published as: EP1578904A4; JP2005512023A; AU2002327657A8; CA2461271A1; EP1578904A2; WO2003027236A3; AU2002327657A1; MXPA04002684A

Abstract

Methods, systems and kits for genetic testing, especially for situations in which the procurement of genetic source material occurs at a different location than the testing of the material and the interpretation of the results.

Description

SYSTEMS, METHODS AND KITS FOR REMOTE GENETIC ANALYSIS AND CONSULTATION FIELD OF THE INVENTION

This invention concerns systems and methods to simplify and improve genetic testing, analysis and consultation including the capability to permit the sampling and testing of genetic source material to occur at a different location from the analysis of the results and the preparation of consultative reports based on the results.

BACKGROUND

Molecular diagnostics involves the characterization of human disease by examining nucleic acids, both DNA and RNA, which are the template for all proteins that mediate disease. Currently, molecular diagnostics involves the use of a variety of technical approaches to extract, modify, and analyze DNA for changes inherent to the nucleotide sequence that make up the genome. These changes, called mutations or polymorphisms, are the basis for determination of who we are as humans and the differences between us, some of which give rise to disease.

Generally, most genetic tests involve five primary steps or processes: 1) specimen procurement; 2) nucleic acid purification; 3) genetic chemistry; 4) interpretation of data; and 5) reporting results of the interpretation. While there are four categories of genetic testing, including (1) constitutional or inherited disorders; (2) acquired disease, such as cancer; (3) infectious disease; and (4) disease of genetic predisposition, the level of technical skill to perform the test as well as medical expertise to interpret this information into usable results are different.

While there has been a marked increase in the number of genetic tests available, the majority of existing tests are for rare and highly esoteric types of diseases. The complexity and the historic high costs of each test have driven the majority of genetic testing to be performed at a relatively small number of centralized laboratories. Other than specimen procurement, which is typically performed locally in a laboratory, hospital or physician office, these centralized laboratories perform all of the required genetic testing steps within their laboratory location. This invention aims to make cost effective, state-of-the-art genetic tests available to smaller, less sophisticated laboratories, such as those found in hospitals and physicians' offices.

SUMMARY OF THE INVENTION

To bring sophisticated genetic testing to locations previously thought to be unsuited to support such services, the invention divides the various steps in genetic tests into those performed at the site near where the sample is collected, and those related to where the test is interpreted. A telemedicine model is employed, so that the test results are transmitted to a central location where the testing expertise resides.

Specifically, the invention involves systems and methods to simplify and improve the genetic testing process to permit the secure and effective testing of genetic source material to occur at different locations from the analysis of the results and the preparation of interpretive genetic testing reports thereby permitting such tests to be performed by more clinical laboratories. The invention also involves the gathering of additional information on the patient as well as systems and methods to use such information in conjunction with the genetic testing results to provide more thorough and useful physician and patient results and feedback.

The invention may be embodied as a controlled system of computerized hardware, software, communications links, genetic and medical expertise and quality control to ensure test and report accuracy, quality and patient privacy. This could include systems and methods which employ networked, computerized equipment for all or part of the processes of: specimen procurement and nucleic acid purification; genetic chemistry; data collection; data verification; data transmission; interpretation of data; and reporting results of the interpretation. The particular selection of network hardware or software is not critical to the scope of the invention, except as specifically described below.

One aspect of the invention is a specially designed genetic testing kit (including an improvement of existing kits) that can accommodate a variety of specimen procurement types and includes components for both the nucleic acid extraction and the gene chemistry required for genetic testing. In a prefeπed embodiment, the nucleic acid extraction is enhanced to increase the likelihood of a high quantity of input DNA sample from only a minimal sample specimen. In another preferred embodiment, the nucleic acid extraction instructions are enhanced to perform the assay based on the use of a rapid extraction method. In yet another preferred embodiment, the kit simplifies the (PCR or non-PCR) genetic chemistry steps of the genetic testing protocol through better controls of the assay and simplification of the operation of the protocol. On manner of accomplishing this result is selection of equipment and configuration of the assay (e.g., aπangement of stacking racks and other kit elements) to make following the instructions easier. In another prefeπed embodiment, the kit improves upon the non-PCR genetic chemistry technology by implementing one or more of the following: (i) configuring the assembly of the various reagent mixes; (ii) prealiquoting the controls into the respective wells for the user; and (iii) improving the controls by basing the controls on the use of genomic DNA.

Another aspect of the invention is a genetic test data gathering process and system that can, either automatically or initiated by a remote site or central location, gather from a remote site database all relevant genetic data generated through genetic chemistry, such as both PCR genetic data and/or non-PCR genetic data.

Another aspect of the invention is a genetic test data gathering process or system that, based on the genetic test requested and other relevant factors, determines patient and other relevant information to gather or request regarding the patient. Such data could include, but not be limited to: patient billing information; other patient genetic data; standard medical record data; physical characterizations of the patient's state of health, past laboratory test, physical exam or specialized studies; commentary from qualified medical professionals and other information relevant to the patient's family history and genealogy; information regarding the patient's environmental context (e.g., where they live, environmental effectors such as hazardous material exposures and climatic factors); and any other information that, when coπelated with the genotype data, improve the process of genomic testing as compared to consideration of such data in isolation. In a prefeπed embodiment, the process or system can (automatically or as initiated by the remote site or central location) gather or parse from any remote site database all relevant genetic data from whatever other genetic technology data that are available (e.g., photographic or digital images data from colorimetric, fluorometric, radioisotopic or other evoked biomolecular signal outputs). In another prefeπed embodiment, the process or system can (either automatically or as initiated by the remote site or central location) automatically gather or parse relevant patient data from the remote site databases to the extent such information is available. In another prefeπed embodiment, the process or system makes requests from the test requester (e.g., physician) and/or the relevant patient data, in the form of system generated written consent forms, a form filled out on the Internet, or an email to the testing facility, or any other equivalent data gathering technique. In another prefeπed embodiment, the process or system may gather the raw or unprocessed relevant patient data when other necessary elements of data are ready to be transmitted.

Another aspect of the invention is a genetic test data verification subprocess or subsystem that determines the suitability of the genetic testing information gathered by the genetic test data gathering process or system. For example, this may involve determination if other relevant patient data gathered by the genetic test data gathering process or system is adequate, complete and otherwise ready for transmission. In another example, the system or process may generate a report at a remote site location that explains any data eπors or inconsistencies and recommendations for coπections, if the relevant patient data gathered by the genetic test data gathering process or system is not adequate, complete and otherwise ready for transmission.

Another aspect of the invention is a data transmission preparation subprocess or subsystem that prepares for electronic transmission of some or all relevant patient data that has been verified by the genetic test data verification process or system. In one prefeπed embodiment, prior to transmission, all information identifying the patient is masked and/or encrypted to prevent patient identification. In another prefeπed embodiment, prior to transmission, the subsystem or subprocess separates all data gathered into a plurality of two files. For example, one file could contain non-confidential information identifying the patient and another file could contain other confidential information but not patient identifying information. One or both of these files could be encrypted by the system. In another preferred embodiment, prior to transmission, all data gathered is simply encrypted without substantial further modification.

Another aspect of the invention is a data transmission subprocess or subsystem that transmits all data gathered to a central location. The data transmission may be initiated by the remote location or by the central location. In either case, separate files generated and/or encrypted as described above may be transmitted at different times and/or in different communication channels (e.g., one or more virtual private network(s) could be employed for separate files). It is prefeπed but not required to assemble data into batches for fast and efficient transmission to the central location.

Another aspect of the invention is, at a central location, an interpretation process or system that receives patient information electronically and performs an initial validation of the information. For example, a preliminary genetic testing diagnosis may be performed for review and validation by a qualified health professional. It is preferred that, following preliminary genetic testing diagnosis, the interpretation process or system will then include automatic review and analysis of the genetic test results (in combination with all other relevant patient information), including review and validation by a qualified health professional.

hi another prefeπed embodiment, an expert system generates natural language explanations regarding particular genetic tests. These explanations may be used for various purposes, including (without limitation): imparting the appropriate clinical application and significance of such tests; providing answers to specific queries about the use of such tests; and providing formal, context-specific interpretation of results of such tests when they have been applied to individuals.

A prefeπed (but not required) embodiment of the expert system comprises one or more of the following components:

a) An expert database containing up-to-date knowledge about relevant genetic conditions. This subjects of such knowledge could be: abnormalities arising from the human body's expression of certain genetic patterns; the underlying mechanism that causes such expression; the impact of human states such as genotype, gender and age on the likelihood and degree of expression of these abnormalities; the impact of medications, treatments, diets, and life choices on the likelihood and degree of expression of these abnormalities; recommended adjustments to standard care practices deemed or believed advisable due to such expression; recommended general health practices for those with the potential for expressing such abnormalities; recommendations for further testing to more completely characterize any genetic explanation for an abnormality; and health-related recommendations for relatives of individuals with known genotypes.

b) An interface to an electronic system that has access to requests for explanations about genetic tests, abnormalities expressed by genetic abnormalities, and the effect of life states, practices, and choices on the likely expression of these abnormalities. c) An interface to an electronic system that contains demographic information and specific state information regarding individuals being tested for genetic abnormalities and their resulting genotype determined by this testing.

d) A data storage subsystem that temporarily holds information that has been passed to the interfaces described above, and makes it available to the control mechanism described below.

e) A control mechanism that inspects the contents of the data storage subsystem and, based on the contents, assembles appropriate data from the expert database into a coherent explanation or inteφretation.

f) A display and/or reporting output module for rendering the output of the database so that is viewable or made part of a printable report.

In one prefeπed embodiment, the expert database is divided into logical compartments that coπespond to relevant elements of a genetic testing ontology for each particular genetic test, hi another prefeπed embodiment, the information stored in one or more logical compartments includes variable components that can be rendered or not rendered as output, depending on state information pertaining to the subject being tested, and under the control of the control mechanism described above. In another prefeπed embodiment, the expert database allows a content expert (such as a genetic counselor) to add information to one or more of the compartments and thus make such information available for inclusion in explanations and inteφretations, without the need of additional intervention by computer programming personnel.

Another aspect of the invention is a reporting subprocess or subsystem that, following the inteφretation of testing, automatically generates a report of the inteφretive genetic test results in medical terms. It is prefeπed but not required to additionally include a comprehensive report containing the inteφretive genetic test results that states in medical and/or genetic terms the result of the analytic test, and further comprises a comment section that may contain at least some of: a statement that recognizes the patients contextual information and what impact if any the genotype for the disease being tested has on this contextual data; a statement concerning disease risk, the modification of that risk given the genotype result, and the contextual data (given that such a risk modification is known); and a statement of the implications that may exist for therapy or prognosis. In a prefeπed embodiment, information (including the reports described above) may be entered into a database that may be accessed only at the remote testing site, using any electronic or other technique (e.g., password-type authorization, over the Internet, using direct dial-up, and so on). In another prefeπed embodiment, the central location transmits the reports to the remote location (or the patient) either by hard copy or electronic document transmission techniques (e.g., email with or without document attachments).

Another aspect of the invention is a consolidated test kit for gene based testing. The consolidated test kit aids laboratories in the performance of the technical aspects of a genetic test by providing convenience, ease of use and improvements in the quality of the genetic test results. The kit may be used by itself or as part of an integrated genetic testing system that includes Internet based consultation and reporting. The integration of the respective materials and reagents, as well as with improvements in the testing procedure into a consolidated kit, enables performance of these specialized laboratory tests in a majority of clinical laboratory settings. A simplified process of specimen procurement, nucleic acid purification, genetic chemistry and other steps leading up to the inteφretation of the test to a point where no specialized training or unique laboratory skills are required, collectively provide the to perform these tests at a much larger number of laboratories, and hence at places closer to the point of care. This will improve both the availability of these healthcare services and their cost effectiveness. BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings show a particular embodiment of the invention as an example, and are not intended to limit the scope of the invention.

For example, while the invention is shown and described in schematic terms, many aspects of the invention may be performed by computer hardware or software in any combination.

Figure 1 is a schematic diagram of one embodiment of the invention.

Figure 2 is a schematic diagram of an operational scheme for genetic testing in accordance with the invention.

Figure 3 is a schematic diagram of a genetic test kit.

Figure 4 is a schematic diagram of a portion of a genetic test kit.

Figure 5 is a schematic diagram of a portion of a genetic test kit.

Figure 6 is a schematic diagram of a portion of a genetic test kit.

Figure 7 is a schematic diagram of a portion of a genetic test kit.

Figure 8 is a schematic diagram of a portion of a genetic test kit.

Figure 9 is a schematic diagram of a portion of a genetic test kit.

Figure 10 is a schematic diagram of a portion of a genetic test kit.

Figure 11 is a schematic representation of a screen shot of an embodiment of the invention.

Figure 12 is a schematic diagram of one aspect of the invention.

Figure 13 is a schematic representation of a screen shot of an embodiment of the invention. Figure 14 is a schematic diagram of one aspect of the invention.

Figure 15 is a schematic representation of a screen shot of an embodiment of the invention.

Figure 16 is a schematic representation of a screen shot of an embodiment of the invention.

Figure 17 is a schematic representation of a screen shot of an embodiment of the invention.

DETAILED DESCRIPTION

Figure 1 is a schematic view of one prefeπed embodiment of the invention. In general functional terms, the system comprises eight major components: specimen procurement; nucleic acid purification; genetic chemistry; data collection; raw data detection and verification; transmission; inteφretation; and reporting. The system may comprise discrete sub-systems, each dedicated to a single functional component, or a fully integrated system. Similarly, any or all of the individual components may be integrated into sub-systems. Thus, the following description should not necessarily be understood to define any physical or functional separation of the components, except as specifically described and required.

In general terms, Figure 1 shows a remote genetic testing system 100, comprising a clinical laboratory-based genetic testing system 200, a data collection system 300, a data transmission system 400, a computer network (shown by way of example only as the Internet) 500, a central data analysis/inteφretation system 600, an expert database 650 and report data 700. Shown schematically as lightning bolts are conventional networking hardware and software as required to connect the various components of remote genetic testing system 100 together, according to known techniques not relevant to the scope of the invention.

The remote clinical laboratory-based genetic testing system 200 schematically comprises several subsystems, specifically specimen procurement subsystem 210, nucleic acid purification subsystem 220, genetic chemistry subsystem 230, and analytic technology subsystem 240. These are described in more detail below.

Figure 2 schematically shows the genetic testing operational scheme of the invention and how the invention provides a local laboratory with the capabilities to perform genetic tests. In general terms, this involves the processes of nucleic acid extraction, gene chemistry and analysis of the test result. These steps are illustrated as separate and distinct because the invention improves upon this situation in that the collective steps can be reduced to a kit. Figure 3 illustrates one embodiment of the genetic test kit. Li general terms, the kits includes are the reagents and materials necessary to execute the technical aspects of a genetic test from a single protocol. As illustrated in Figures 3-10, one version of the genetic test kit includes the extraction rack and reagent elements for DNA extraction, the reaction rack including the components of the gene chemistry Invader in a newly organized presentation to make simpler the process of assembling the reaction components, the reaction plate and template guide and the coπesponding replacement disposable plastic supplies. The last component of the test kit is the protocol book that describes each of the steps in the technical aspects of the test, as well as for the initiation and completion of the data transmission steps of the system.

Figure 12 is a schematic of the overall architecture of the telemedicine process of the invention. The process of data collection from the analytic instrument occurs first at the computer of the remote site 400. Data is transmitted through the Internet via a process that is both secure and involves data that is encoded or dispersed in such as way as to render the patient information de-identified, 410. The transmitted analytic and patient specific demographic data is encrypted (e.g., 128- bit encryption or as otherwise desired) and unencrypted at the system firewall 420 and is collected at the central computer 430 which in turn provides the prompt to the persons inteφreting the transmitted results to work on those data files. A qualified health care professional 440 inteφrets the data with the aid of the expert database 450. The completed test result is transmitted back to the site where the test was performed and printed or in some way distributed electronically to the requestors of the tests 460.

The expert system database 650 used in the inteφretation of the genetic tests consists of electronic platform such as a software data processing program with large amounts of abstracted medical information pertaining to aspects of genetic test inteφretation. This may include subjects as the application of these tests to medical conditions, risk assessment, other contributing genes and therapeutic options for the medical condition. The initiation of a specific test and the subsequent transmission of that data registers as a need to sort the database, so that the inteφreter is presented with only a subset of the inteφreted options. The system provides the prefeπed combination of comments in an assembled natural language paragraph. Such a selection of the comment for a given analytic test result is driven from a priori knowledge provided through the Internet by the remote testing lab. The creation of the semi-automated test inteφretation is confirmed, rejected or modified by the inteφosed physician test inteφreter.

Figures 15-17 show possible reports created consequent to the transmission of the test data.

Specimen Procurement

The specimens to be tested shall be obtained from the patient in an environment most convenient to the patient, such as a hospital or physician's office. The invention may include the provision of a kit, which may use existing technologies, along with all the necessary instructions and controls, to allow laboratory technicians to expertly obtain specimen samples necessary for the relevant genetic test to be performed.

Nucleic Acid Purification

Isolation of genetic material(s) suitable for sensitive diagnostic tests requires DNA and RNA that has been separated (purified) from their cellular context and other contaminants contained in the blood, cells, tissue or body fluid samples. Ideally, such processes are performed in a clinical laboratory in or near the clinic in which procurement of the sample from the patient occurs.

Any convenient nucleic acid purification method is suitable for use with the invention, but a prefeπed method is provided by Gentra Systems, Inc. of

Minneapolis, Minnesota. Alternative nucleic acid extraction systems or methods, such as those commercialized by Qiagen N.V., Xtrana, Inc., and others are also equivalent, as are those that perform similar results but have not yet been developed or commercialized. Specific details of the Gentra Systems, Inc. technology is described in relevant portions of the following documents (the entire contents of which are incoφorated by reference), which are provided as an example of the products and processes to be used at the on site DNA extraction stage of the process:

• US Patent 5,973,137 entitled "LOW PH RNA ISOLATION REAGENTS, METHOD, AND KIT"

• International Patent Publication WO00066267A1 entitled "PREVENTING CROSS-CONTAMINATION IN A MULΉ-WELL PLATE" • International Patent Publication WO00049557A2 entitled "COMPUTER-

IMPLEMENTED NUCLEIC ACID ISOLATION METHOD AND APPARATUS"

• International Patent Publication WO09938962 A3 entitled "COMPOSITIONS AND METHODS FOR USING A LYSTNG MATRIX FOR ISOLATING DNA"

• International Patent Publication WO09939010A1 entitled "ELUTING REAGENTS, METHODS AND KITS FOR ISOLATING DNA"

• International Patent Publication WO09913976A1 entitled "APPARATUSES AND METHODS FOR ISOLATING NUCLEIC ACID" The kit included with the invention may also include existing technologies, along with all the necessary instructions and controls, to allow laboratory technicians to expertly perform the nucleic acid purification from the specimen sample.

Genetic Chemistry Doctors and patients benefit by having the genetic chemistry (manipulation and amplification) portion of the genetic testing process performed on site within a clinical laboratory in or near the health care setting where the patient sample is collected and extracted (procured). On site sample procurement, extraction, amplification or some other means of genetic manipulation reduces the risks and costs associated with shipping samples to a remote location and enhances the timeliness of the results.

Possible generic chemistry techniques suitable for use with the invention include a variety of well-known, commercially available PCR (Polymerase Chain Reaction) approaches, including: (a) those known by the tradename LIGHTCYCLER from Roche Laboratories (b) those known by the tradename LABMAP from Luminex Coφoration; and (c) those known by the tradename ESENSOR from Motorola, Inc. Other suitable approaches include the microaπay technology commercially available from a variety of sources, including the system known by the tradename INFINITI from AutoGenomics, Inc.

In one embodiment the prefeπed gene chemistry strategy employs a non- PCR approach which may be simpler for operators to use. The application of this gene chemistry to the invention involves the integration of the assembly of the reaction components, comprised of the sample control DNA admixed separately with a master reagent into a microwell incubation plate all within the confines of the kit. Additionally, the system employs the use of the analytic instrument, a fluorometer, which carries out the incubation as well as serves as the interface with the Internet based controlling software. The use of the this gene chemistry includes, but is not limited to the detection of genetic test data from a solution based reaction and/or a fluorescent reported on a solid support such as a microaπay. In each case, the data created by this gene chemistry is entered into the system and inteφreted after its transport through the Internet.

Other suitable non-PCR approaches are commercially available from Third Wave Technologies, Inc. of Madison, Wisconsin USA under the tradename INVADER^® and described in relevant portions of the following documents (the entire contents of which are incoφorated by reference):

• United States Patent 6,214,545 entitled "POLYMORPHISM ANALYSIS BY NUCLEIC ACID STRUCTURE PROBING" • United States Patent 6,210,880 entitled "POLYMORPHISM ANALYSIS BY NUCLEIC ACID STRUCTURE PROBING WITH STRUCTURE- BRIDGING OLIGONUCLEOTΓDES"

• United States Patent 6,194,149 entitled, "TARGET-DEPENDENT REACTIONS USING STRUCTURE-BRIDGING

OLIGONUCLEOTΓDES"

In addition to allowing the laboratory technicians to expertly perform the nucleic acid purification from the specimen sample, the kit provided as part of the invention also allows laboratory technicians to perform the genetic chemistry steps at their location.

Gathering of Additional Genetic Information

In addition to the typical genetic chemistry processes described above for gene amplification or some other means of genetic manipulation, the invention could also use any of a series of analytic technologies to create raw or non- inteφreted test data. These technologies may include agarose and polyacrylamide gel electrophoresis, capillary electrophoresis, fiberoptic sensor devices, planar wave guide sensing devices, DNA microaπays, micromechanical biosensors, non-aπay based chip sensors, real-time fluorescence detectors, digital image capture, fluorometers, and the like, all according to known principles.

It should be noted that the collection of components described above is only one prefeπed embodiment of the invention. The full scope of the invention includes any integrated genetic testing system 200, including (without limitation) the system disclosed in US Patent 6,054,277 entitled "INTEGRATED MICROCHIP GENETIC TESTING SYSTEM," the entire contents of which is incoφorated by reference.

Integrated Kit

As illustrated in Figures 3-10, in a prefeπed aspect of the invention an integrated genetic test kit is employed to organize and simplify the technical and operational aspect of the steps required to perform most molecular genetic assays. In general terms, the primary components of such an embodiment are a specialized package that contains the reagents and the disposable materials to perform a DNA or RNA based test. These tests could include any of a series of localized gene sequence alterations including detection of nucleotide substations through mutation, single nucleotide polymoφhisms and small nucleotide deletions or insertions. The package may include a series of devices to house the various reagents used in each of the test procedures including (without limitation): devices for the collection of specialized specimens, materials for sample labeling, forms for test requisition, and specialized "racks" for guiding the procedure for nucleic acid extraction and gene chemistry.

The component nature of the test kit enables it to be assembled from a variety of supplier sources and compiled at a single site before being shipped to the requesting laboratory, or it can be shipped directly to the performing lab and quickly assembled on-site, usually by fitting the respective components in their designated places in the kit box.

The kit may also include a detailed procedure manual that combines what may otherwise be separate protocols into an integrated document. This procedure manual may employ specialized instructions to communicate a complex procedure into a straightforward recipe that may be followed by relatively untrained and/or inexperienced personnel. The procedure manual may also include instructions on accessing and using several electronic tools (such as those that may be available on a website) to simplify the process of making calculations for reagent volumes, estimating time, and other aspects of the procedure. The procedure manual may also include forms for gathering patient specific information that will enhance the value of the inteφretative genetic test report.

Another prefeπed embodiment concerns the manner of labeling elemental components in the kit for the puφose of quality control and tracking of reagent lot numbers and outdates. The labeling, along with the design of the respective racks and materials, make possible the restocking of the kit through an electronically registered supply chain monitoring system. The integration of the physical kit with the labeling of the elemental components and the linkage of said elements to an electronic supply and information management monitoring system is all intended to make for a higher quality test and the subsequent medical inteφretation of the test results into a report for patient care.

The high quality of the data generated from the invention is intended to enhance the inteφretation of the genetic test data into a series of reports. One embodiment of the invention is where it is used as part of a more comprehensive genetic testing system, where the invention facilitates the extraction of the sample- derived nucleic acid and the gene chemistry steps as well as the presentation of the results through a fluorometer interfaced with a computer and connected to the Internet. The invention can be used with a fluorometer or similar bioanalytic instrument that generates results analyzed locally, i.e. on-site or as part of an integrated genetic testing system that includes transmission of various types of data to a remote computer and database, where a qualified healthcare professional provides the expert inteφretation and composition of the various reports. Through that same system, namely a secured Internet portal, the invention is used to monitor quality control of the test results being produced, to track inventory of the kit elements, and access to essential information such as material safety data, storage and outdating of the reagents. In this regard is it possible, but not required, for the kit to contain an attached or embedded device to record and store information about components of the kit. For example, in one possible embodiment an EPROM or similar data recording device may collect sensory information about the storage and or transport condition of the kit during assembly, shipment or storage, and such information may be incoφorated into the operation of the invention.

Prefeπed embodiments of the invention comprise a test kit box, made of paper or plastic, that has exterior labeling of the genetic test kit. The interior of the kit box includes a series of compartments to contain each of, but not limited to, the following test kit components. First, there is a compartment, such as a rectangular space, to contain a variety of disposable materials used in the processing of sample, extracted DNA and in the set up of the gene chemistry. Typical materials would include, but not be limited to: boxes of disposable pipet tips, transfer pipets; and a supply of additional microcentrifuge tubes. The number of prepackaged materials supplied is proportionate to the intended number of tests in each kit. The kit boxes are configurable for convenient sizes of batches of individual tests, but typically are in sizes of 24, 48 and 60 tests.

The inside cover of the kit box may have a movable flap of material, which when deployed serves as a shelf onto which the procedure manual is supported. The flap of material may be fastened to the inside cover in a number of ways, but include a flap attached by means of hook and loop fastener or reusable adhesive, or it may precut to enable it to be clipped or simply punched out of the cover material.

A second compartment in the kit box contains a variable series of specialized racks. In one embodiment, there are two separate racks, one for the operational steps of nucleic acid extraction, and one for the assembly of the gene chemistry reactions. The racks are constructed from any material (such as paper or plastic or equivalent) and in their most basic form are comprised of a rectangular support with holes on one face into which are placed tubes to hold the sample(s) at the various steps of their processing. The design of the racks is such that they can be used within the space of the larger kit box, or removed and used as a separate element. The sizes of the holes is significant in the design to hold specific types of tubes, i.e., glass vacuum tubes for blood collection, microcentrifuge tubes for sample processing, etc. The placement of the holes is significant to the use of a multichannel pipeting instrument, such that the center-to-center distance between holes coπesponds to the same between two adjacent pipet tips. The distance between adjacent holes in this dimension is related to the distance between adjacent rows of holes in a second dimension. This inter-row distance is a design feature to permit the snap tops of the tubes not to overlap and to make easier the removal of individual tubes from the rack. Other features of the general design are described in the specific racks that are part of the invention.

Another specific component is a rack designed to simplify the operational steps in extracting DNA from a sample of blood by means of a technique refeπed to a capture matrix columns. The basic design of the rack places a series of tubes in vertically oriented rows with the intent of processing individual samples horizontally across rows. Each row has holes containing the series of tubes for the capture matrix column extraction procedure, where each row is intended for a separate step in the technical procedure. The rack can be modified to accommodate various manufacturers' extraction systems. One prefeπed embodiment is that designed for the extraction system of Gentra Systems, Inc. known by the tradename GENERATION CAPTURE COLUMN SYSTEM. In this case, the first row, left side of the rack, which may be labeled as "Patient Samples," holds a set of 8 standard adult size vacuum blood tubes. The second row is designated for the column tubes of the extraction system and is labeled as "Buffy Coat." A third row also contains a set of extraction system column tubes and is labeled as "Wash." A fourth row contains another set of tubes and is labeled as "Elution and Wash." A fifth and final row contains a set of standard 1.5 mL microcentrifuge tubes and is labeled as "Elution and DNA." As described above, both the spacing between the rows of tubes and between the individual tube holes within each row is set to simplify the processing of specimens in a left to right orientation according to the instructions in the protocol book. At the top of the rack are two additional holes to place the respective "Wash" and "Elution" solutions that are added to the tubes in the respective rows.

Another component is a mixing rack. One embodiment of the mixing rack is a rectangular cardboard box of appropriate dimensions, with holes punched into the top face in a pattern that serves to fulfill the functions listed below. Another embodiment is a printed face-plate, made of paper, plastic or other printable material that overlies an insulated or non-insulated plastic or paper rack with either a matrix of coπectly spaced and sized holes or with only the specific holes needed for the function of the device.

This rack is designed to simplify the operational steps in preparation of the master ix(es) and control DNA samples that that are essential reagents in the prefeπed non-PCR approach commercially available from Third Wave Technologies, Inc. of Madison, Wisconsin USA under the tradename INVADER. The basic design of the mixing rack places a sequence of the reagents that comprise the master mix in a series, where each sequential reagent tube, and the appropriate volume of reagent from that tube is added to the last tube in that series which is labeled as and comprises the master mix for that particular batch of tests. Each of the master mix series of tubes is oriented horizontally across the rack, where each of the tubes in that series has a color-coded cap. The color-coding of the caps coπesponds to the coloring coding and labeling on the rack. In one example, there are 5 reagents that make up the master mix. These reagents are placed in the 5 tubes labeled 1,2,3,4,5. With the calculated volumes of each reagent needed to perform a batch of tests, the assembly of the batch's master mix will involve first the addition of reagent 1 (tube 1) to the master mix tube. Second, the volume of reagent 2 (tube 2) is added to the master mix tube; then 3 (tube 3) into the master mix tube; then 4 and 5 in the same manner. The process of adding each sequential reagent to a single master mix tube is made simpler by using color-coded labels on the rack itself and on the tops of tubes with graded shading of a single color. It is prefeπed that the series of holes that hold the reagents to be combined into a common reagent are labeled with colors in a graduated pattern of shading. Thus, the combination of all lighter or darker colors are ultimately added to the lightest or darkest colored labeled in the series.

In a similar manner, the orientation of the DNA control tubes and the placement of these controls in the rack coπespond to the sequential addition of these reagents to the reaction plate in a similar orientation, and with spacing between those control tubes in the rack to accommodate the center-to-center distance between adjacent tips on a multichannel pipeting device. The design of the mixing rack, considering the placement of the respective tubes, the labeling of those tubes and their orientation within the rack as a stand alone device or in the context of the complete kit relates to a simple operational procedure in the kit procedure manual discussed in more detail below. Additionally, the determination of the appropriate volumes of reagent that are required for a particular batch of master mix for a performance of a batch of genetic tests is also linked to a web based program.

A third component of the genetic test kit is the reaction plate. The reaction plate is the point where the DNA samples, extracted as described above, and the single test volume of the prefeπed INVADER master mix, as assembled in the mixing rack, as well as other optional added materials comprise the set of individual test reactions for a given genetic test or, when multiplexed together, multiple genetic tests. The combination of the various volumes of the sample and reagents into specific reaction wells in the reaction plate can be difficult because it requires the pipeting of small volumes from the various sized tubes used in DNA extraction and INVADER master mix into very small and particularly positioned wells manually or with automated, but handheld, pipeting devices.

To this end, the invention may also includes a device in the form of a planar sheet of paper, plastic or similar material containing a series of small holes that coπespond to the underlying holes in the reaction plate, into which individual and specific reaction component samples and controls are added.

In one embodiment, a mylar laminated paper card of dimension C x D is labeled on one side with the numbers and lettering coπesponding to one type of reaction, such as the gene chemistry reaction for the wild type or normal genetic allele of a particular genetic marker. The opposite side is labeled for the mutant or alternative genetic allele for the same genetic marker. Therefore, to perform the desired gene chemistry reaction for a specific allele, the operator merely selects the appropriate side of the guide and positions that side face-up against one particular edge of the underlying reaction plate. The holes in the guide then permit the alignment of the wells for the placement of each of the respective samples for that reaction. When the opposite side of the guide is used, the holes then align to the wells designated for the alternative reactions. In this device, the operator is aided in avoiding the placement of the wrong sample or reactant into the wrong reaction well.

Another component of the invention is the procedure manual that describes and illustrates each calculated and manual operation involved in the performance for a specific genetic test beginning with sample procurement and continuing through the final step of how to activate the web portal for transmission of the results for analysis of the genetic reactions. The procedure manual is designed to make simpler the performance of the complete, as well as individual, operations required for the genetic test. The manual integrates the disparate required operations of different vendors' commercial products into a single document. The manual permits the skilled but occasional operator of these genetic tests, to achieve analytic results from the genetic testing system comparable to those obtained by an expert operator of these genetic tests.

Within the design of the complete kit, the manual may be fastened by any convenient method to the inside cover of the kit box. The kit and manual are designed so the book may be used either on a support on the inside cover or as an independent stand up display of the book, using the included paper base that holds the two covers in a triangular prop for a bench or table top use.

There will in general be various versions of the manual based on the specific genetic test to be performed and the commercial products used. The organization of each version follows a format whereby each step in the procedure is detailed on a single page, typically on the left side of the two page open book format. Each operational step also presents a single or multiplexed illustration on the opposing page. One feature of the manual is the procedure guide bar. The procedure guide bar consists of a complete listing of the operational steps across the top of the opposing two page format with an illustration of a slide bar or forward pointing set of aπows that guide the user as to what are the sequential steps in the complete protocol, along with the details of one operational step, for each two page format. The particular step that is detailed on that set of pages is highlighted in the procedure guide bar, using the illustrative technique of magnifying the text at that position on the guide bar with a larger or bolder font.

As illustrated in Figure 11, in addition to the detailed instructions for the test protocol, the manual may also describe the use of web-based tools that may complement the specific test protocol. These include a single web page display listing the respective volumes of each of the reagents that make up required mixes. The invention includes programming of the web page so that the operator needs to enter only the number of test samples intended for a particular batch run of the procedure. The program calculates the volumes of each reagent needed to assemble the master mix.

As illustrated in Figure 13, another web-based tool is a tabular display of data fields containing information about a patient, their medical history, pertinent information about the genetic history and other unique demographics that aid in the inteφretation of the genetic data created in the process of testing. This aspect of the invention makes simpler the process of entering patient demographic data, essential to the accuracy of diagnostic testing. This may be linked to a reference genetic database. In one embodiment, information entered into selected data fields will lead to a triggering of a sorting and selection function of reference information from the genetic database.

An additional component of the kit is an order pad, a convenient and simple tool by which clinicians and patients can provide information that will be subsequently entered into the web-based tools. One embodiment of this part of the invention is the listing of questions pertinent to a selection of genetic tests, which provide essential demographic and medical data about the patient to be tested. When information from the order pad is entered into the web-based tool, the genetic database is triggered. One additional feature of the order pad is fulfillment of the requirement that each genetic test used for patient care be "ordered" by a licensed physician. The order pad provides a convenient means to meet this compliance regulation.

Other interior space of the kit may be filled with an insulating material such as cellulose, plastic or other material for the puφose of suπounding the reagent tubes and maintain a colder, normal or heated temperature.

Data Collection

After the raw or non-inteφreted genetic data and any necessary enhancements to increase clarity is generated, it is then gathered at the remote location in any convenient manner by data collection system 300. i addition to scientific clinical data, data collection system 300 also is preferably supplied with or gathers relevant demographic data about the patient. Based on the genetic test performed, the data collection system 300 gathers from the remote location, to the extent available, patient demographic data that enhances inteφretation of the analytic data gathered at the remote site, analyzed in the central data analysis/inteφretation system 600, and/or reported in the form of report data 700. The relevant demographic data about the patient report could consist of, but is not limited to, patient identifier, gender, age, clinical history, billing infoπnation, and other coπelative information about the patient including written or numerical identifiers, cuπent and historic physical characterizations of the patient's state of health, past laboratory, physical exam or specialized studies and commentary from qualified medical professionals.

An aspect of this invention is that patient demographic data may be parsed, extracted or in some manner derived from electronic databases at or associated with the site where the patient interface occurs or at the site where the technical aspects of the test is performed. This process of deriving patient demographic information may involve information systems outside the system. Additionally, patient demographic information may be entered into the system by the physician, nurse or laboratory technologist based on the responses provided on the "Genetic Test Request Pad". The Genetic Test Request Pad is a media to convenient transcribe information pertinent to the inteφretation of the genetic tests into the system. The mformation collected varies for every test, but may include such facts as the date of birth, gender, listed medical conditions, responses to specific questions relevant to the particular test at hand, and any additional laboratory data that may precede the application of the genetic test. For a single or combination of tests offered, the genetic test request pad is customized to include questions and demographic data pertinent to the inteφretation of that selection of tests.

Within the system, the prefeπed embodiment for gathering demographic data is a simple spreadsheet with fields that permit entry of the responses to the questions on the Genetic Test Request Pad. This may involve the entry of data by any suitable technique, such as voice command, typing, touch screen, or by selection of electronic buttons or menus.

Demographic patient data may be used in any of the following ways. First, the data may be used to create a test identification number that links a certain patient with their respective analytic results. Second, the selection of demographic data may be used to sort inteφretative information in the expert database 650. Third, the data may be used to organize the placement of samples on the reaction plate.

The prefeπed embodiment for the data collection system uses computer networking techniques and systems to electronically gather data with as little human involvement as possible. The derivation of the analytic data involves the creation of a software interface to an analog data source through a connected computer which in turn is connected to a central server at a site distant to the remote laboratory through the Internet. Through this interface the system can address the remote laboratory without the aid of operator actions. One embodiment of the invention includes the warm-up of the fluorometer and the ability to address that instrument to determine if a reaction plate incubation is ongoing. This is achieved by means of a software derived "scout" that queries the instrument for a variety of its functions. The software permits the periodic cessation of the incubation and subsequent read of the reaction plate to determine if that operation is complete or incomplete. The software inteφrets the control in each reaction plate to determine if an adequate level of fluorescence signal has been created. If the reaction is complete, then the system prompts the inteφreter to read the plate, otherwise the plate is returned to the incubation mode, and the process is repeated later in time. The software is designed to control of the assay operations such as control of heating sources, mechanical movement of the plate and or plate holder, mechanical agitation of reactions and the operation of the readout functions of the machine. The interface also allows us to acquire and process the numeric results after a batch of tests are read.

The capabilities to determine what information to gather and how such information is gathered by the data collection system 300 is an important embodiment of the invention.

Verification of the Genetic Testing Data hi addition to gathering data at the remote location, depending on the preferences and capabilities of the remote location, the data collection system 300 may also include the capability to provide mathematical representations and/or transformations of raw and other data, for quality control or other puφoses, prior to transmission to the central location. Specifically, the data collection system 300 may automatically perform a preliminary review of the data gathered to determine the existence of information necessary for the central location to complete the genetic test and generate useful reports and other feedback. If such review determines insufficient or inconsistent data has been collected, the data collection system 300 generates a report for the remote location user identifying such issues along with recommendations to coπect the problem. In addition to being located at the data collection system 300, such capabilities could also be provided in central data analysis/inteφretation system 600.

The invention may include verification of the completion of the amplified genetic testing data produced on-site, with transmission of such data and specific patient demographic information through a proprietary hardware and software system to a central pool of experts in diagnosis and genetics. This enhances the quality and the value of the test results and information provided for both the doctor and the patient. One possible embodiment of this aspect of the system comprises the generation of an e-mail or voicemail prompt to the designated expert informing them that test results are available for review. This prompt may be automatically generated when a batch of test reactions is completely received from one of the connected remote sites. Another optional embodiment comprises directing the test data to one of any number of designated expert inteφreters, each of whom would be prompted to read the test results assigned to them.

Preparation of the Genetic Testing Data for Transmission

After gathering and verifying the genetic testing data, the data collection system 300 prepares the genetic testing data for transmission to the central data analysis/inteφretation system 600 for inteφretations and reports. Depending on 1) preferences or capabilities of the remote location, 2) the type of genetic testing data to be transmitted, and 3) the transmission system to be used, the preparation of the genetic testing data by the data collection system 300 for transmission could take alternative forms.

One alternative is for the data collection system 300 to mask all patient- identifying information that could be used to identify the patient, which is contrary to desired or mandated privacy requirements, from other data related to the genetic test of the patient. Under this alternative, infoπnation transmitted to the central data analysis/inteφretation system 600 does not include any information that could identify the patient. When inteφretations and reports (described below) are returned from central data analysis/inteφretation system 600, the data collection system 300 at the remote location could then coπelate the data identifying a patient data with the test result at the remote site, hi this manner, no genetic testing or demographic data positively linked to a named patient ever leaves the local clinical laboratory. This aπangement greatly increases the private nature of the entire remote genetic testing procedure.

Another alternative is for the data collection system 300 to separate the data into two separate files that can be transmitted separated. One of the files can include information on the patient that is not generally viewed as confidential, such as the patient's name, address, job, age sex, weight and third party payer information, while the other file can include patient data that is confidential such as genetic testing data and medical history. The file containing the confidential information does not include any information that identifies the patient. After the data is separated, the two files of information can be transmitted separately, including the transmission of information through different transmission modalities and at different times. Upon receipt of the two files, the central data analysis/mteφretation system 600 can then coπelate the two files to perform the required inteφretations and analysis necessary to generate the reports (described below). Under this alternative, the central data analysis/inteφretation system 600 has all of the pertinent information on the patient, yet no genetic testing or other confidential data on a patient that could identify the patient is ever transmitted.

Another alternative is for the data collection system 300 to encrypt, using any convenient encryption technology, any portion of the information to be transmitted. The encrypted transmission is deciphered by the analysis/inteφretation system 600 upon receipt.

Any or all of these data preparation alternatives may be used in any desired combination to ensure the safe, secure and confidential transmission of the genetic testing data and other infoπnation from the remote location to the analysis/inteφretation system 600. Transmission of the Genetic Testing Data

The raw and non-inteφreted, and possibly encrypted, data is then transmitted, either automatically or initiated by an operator, to a central data analysis/inteφretation system 600, which may be in a location different from the clinical laboratory that performs the testing processes described above. This transmission may be accomplished using any convenient data transmission scheme. In a prefeπed embodiment, a remote, secure Internet portal 400 is provided and accessed from the clinic location. In another prefeπed embodiment, conventional application service provider architecture is used by the central data analysis/inteφretation system 600 to service an application 400 running on the clinic data collection system 300.

Regardless of the data transmission scheme chosen, the functions of this component of the system include the distinct capture of the raw and non-inteφreted analytic data and the pertinent patient demographic data. The transmission, processing inteφretation and report of these data, including the maintenance of each type of data in a secured and confidential form is an important embodiment of the invention. Figure 12 shows one embodiment of the invention, in which genetic testing information is transmitted over the Internet as a non-limiting example of a computer network.

Data Interpretation

Medical and genetic experts resident at a cential location read and inteφret the genetic data transmitted from the remote locations and determine the genetic profile of the patient. In addition, the demographic information on the patient provided with the genetic data greatly enhances the ability of the medical and genetic experts resident at a central location to provide additional useful advice in the reports to clinical professional (physician) and the patient as discussed below.

Once the data has been inteφreted, a series of reports 700 are generated and securely transmitted back to the source clinic. While any secondary data transmission scheme may be used, the prefeπed approach is to use the same data transmission scheme as used to transmit the data from the source clinical laboratory to the central data inteφretation facility, i.e., a two-way communications scheme.

Typical contents of the reports include the analytic measurements of the genetic tests themselves; insurance reimbursement data (e.g., recommended CPT coding for the procedures that have been performed); and genetic counseling. In a prefeπed embodiment, both a technical report directed to the clinical professional (physician), arid a separate non-technical report directed to the patient, are included. The system may identify technical problems in the performance of the test steps done at the remote location that require added samples or steps to ensure a quality test result. Such problems may then be identified to a remote location so that coπective actions may be taken.

Another aspect of the invention is the manner is which additional information derived from the medical and scientific literature is incoφorated into the construction of customized inteφretations and comments. The expert inteφreter of these tests relies in whole or in part on an integral expert system database, which contains large amounts of prewritten information pertaining to various clinical and pathologic aspects of the condition being tested. The expert system is part of the invention and is described in detail below.

The expert system is integral to the genetic testing system. In general terms, the expert system is a electronic database constructed from one or more of a variety of commercially available software products. The database is derived from the manual and automated review of the medical and scientific literature made available from the variety of the public and subscription based information search sources. The database collates information from the various sources based on prescribed key words that a are specific the disease, test and clinical condition. The database sort is modified according to the results obtained from a particular patients test, and in combination with the provided demographic information. Hence the expert system contains information in excess of what is needed for any one patient sample, and uses the specific results, transmitted from the remote lab to initiate a sort of pertinent references and comments which in turn is presented to the expert inteφreter.

The expert system integrates with other aspects of the system at the points involving the sorting of patient demographic and analytic data. The interface involves the initiation of a primary sort of pertinent comments based on the specific analytic result from one patient. The primary sorting derives, from a large data set, a subset of information such as risk and therapeutic options that is based on the specific gene test results. When provided, the demographic data, including information such as gender, age, medications and pre-existing medical conditions, initiates subsequent sorts of the database. The subsequent sorts further reduce the set of selected comments and references to those pertinent to all of the provided demographic and analytic data conditions. The result is a markedly reduced set of prewritten inteφretations and comments that the expert can then use in the creation of the customized genetic test report.

The expert system 650, which is a subsystem to the complete system, contains entries from the medical literature derived from public and commercial sources (such as Medline, PubMed, Compendex, GeneBank, www.genetest.com and www.webmd.com). From searches performed within these sources, the expert system abstracts selected information about a particular disease or genetic condition. The expert system involves the assignment of various categories of the derived data that are used in the sort function. Such categories include, but are not limited to disease association with a particular genetic result, risk calculations about a diseases given a certain demographic or analytic test result, and options for therapy.

Claims

We claim:

1. A method of performing genetic testing in a telemedicine model, in which test results are transmitted to a central location at which expertise in inteφretation of genetic testing resides.

2. A method of genetic testing in which genetic source material is tested at a location different than a location at which analysis of results of the testing and preparation of inteφretive genetic testing reports occurs.

3. A genetic testing kit for multiple specimen types, comprising both components for nucleic acid extraction and components required for genetic testing of each of the multiple specimen types.

4. A genetic test data gathering process that, automatically or as initiated by a remote site or central location, gathers from a remote site database genetic data relevant to a desired genetic test to be performed at the remote site and subsequently inteφreted at the central location.