System and method for integrating and validating genotypic, phenotypic and medical information into a database according to a standardized ontology

• US 20070178501A1
• Filed: 12/06/2006
• Published: 08/02/2007
• Est. Priority Date: 12/06/2005
• Status: Abandoned Application

• Current Assignee: Natera Incorporated (Natera)
• Original Assignee: Natera Incorporated (Natera)
• Inventors: Demko, Zachary, Rabinowitz, Matthew, Clark, Christopher, Shah, Nigam, Sheena, Jonathan
• Application Number:
  US11/634,550
• Publication Number:
  US 20070178501A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G16H 50/20 for computer-aided diagnosis, e.g. based on medical expert systems
• CPC Class Codes: G16H 70/00 ICT specially adapted for the handling or processing of medical references

Abstract

The system described herein enables clinicians and researchers to use aggregated genetic and phenotypic data from clinical trials and medical records to make the safest, most effective treatment decisions for each patient. This involves (i) the creation of a standardized ontology for genetic, phenotypic, clinical, pharmacokinetic, pharmacodynamic and other data sets, (ii) the creation of a translation engine to integrate heterogeneous data sets into a database using the standardized ontology, and (iii) the development of statistical methods to perform data validation and outcome prediction with the integrated data. The system is designed to interface with patient electronic medical records (EMRs) in hospitals and laboratories to extract a particular patient'"'"'s relevant data. The system may also be used in the context of generating phenotypic predictions and enhanced medical laboratory reports for treating clinicians. The system may also be used in the context of leveraging the huge amount of data created in medical and pharmaceutical clinical trials. The ontology and validation rules are designed to be flexible so as to accommodate a disparate set of clients. The system is also designed to be flexible so that it can change to accommodate scientific progress and remain optimally configured.

Claims

1. A method for integrating genetic, phenotypic and medical data into a database according to a standardized ontology, the method consisting of:

(i) defining and creating a standardized ontology that can accommodate all of the relevant pieces of data and data fields,

(ii) generating an interface based on the standard ontology that allows an agent to describe the data fields of the input data appropriately, and then input the data,

(iii) generating a cartridge that is capable of translating the data into a format that is compliant with the standardized ontology, and

(iv) translating and loading the input data into the database.

2. A method as in claim 1, where the integrated data undergoes validation, the validation consisting of:

(i) describing a set of expectations regarding a set of input data based on statistical models and/or expert rules,

(ii) determining the likelihood of the validity of the individual pieces of input data by checking if they conform to the expectations,

(iii) flagging any pieces of data that do not conform to the expectations, and

(iv) approving any pieces of data that do conform to the expectations.

3. A method as in claim 1, where the data is subjected to a statistical analysis that allows the calculation of the likelihood of one or more phenotypic, clinical and/or medical outcomes for a particular patient given certain possible courses of treatment, and where those predictions are formulated into a report for physicians or other agents of a subject of the data.

4. A method as in claim 1, where the integrated data is computationally comparable to other related data that was collected from other sources and assimilated into the database.

5. A method as in claim 1, where the data is subjected to a statistical analysis that allows a phenotypic prediction to be made from the data.

6. A method as in claim 1, where the data is subjected to a statistical analysis that allows a clinically relevant prediction to be made from the data.

7. A method as in claim 1, where the data is used to make a prediction, and the accuracy of the prediction is quantified with a confidence estimate.

8. A method as in claim 1, where the standardized data classes are based on a set of existing standards for clinical, laboratory and genetic data.

9. A method as in claim 1, where the data is generated in the context of a clinical trial.

10. A method as in claim 1, where the data is generated in the context of diagnostic screening.

11. A method as in claim 2, where the validation includes a step that allows a user to act upon the status of a piece of flagged data, the actions taken from a list comprising:

to override the flagging and approve the datum, to correct the datum, to remove the datum from the dataset, to resubmit the datum for validation, and combinations thereof.

12. A method as in claim 2, where the statistical model that shows the highest accuracy during a training of the model with a second set of data is selected from a plurality of statistical models in order to make the most accurate prediction.

13. A method as in claim 2, where the statistical model is trained on sparse data using one or more shrinkage functions.

14. A method as in claim 2, where an association is maintained between certain pieces of validated data and the validator of that piece of data, and where a record indicating the reliability of the validator is made available to entities who are in a position to make clinical or market decisions based on the validated data.

15. A method as in claim 2, wherein the data validation is re-examined using the latest available computer-executable rules and data, and where data managers are notified whenever the status of validation pertaining to a given datum change.

16. A method as in claim 3, where the data analyses are frequently re-examined, and where a new report is generated when one or more predictions in the report change significantly due to pertinent new information and/or data becoming available.

17. A method as in claim 3, where the report is generated automatically at periodic time intervals.

18. A computer implemented method configured to perform the method described in claim 1.