Method of diagnosing biological states through the use of a centralized, adaptive model, and remote sample processing

• US 20050209786A1
• Filed: 12/10/2004
• Published: 09/22/2005
• Est. Priority Date: 12/11/2003
• Status: Active Grant

• Current Assignee: Aspira Women's Health, Inc.
• Original Assignee: Correlogic Systems, Inc. (Aspira Women's Health, Inc.)
• Inventors: Chen, Tzong-Hao, Levine, Peter J., Hitt, Ben A.
• Granted Patent: US 7,761,239 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G06F 18/217 Validation; Performance evaluation; Active pattern learning techniques
• CPC Class Codes: G06F 18/2321 using statistics or function optimisation, e.g. modelling of probability density functions
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16H 50/50 for simulation or modelling of medical disorders
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

A model of a particular biological state can be developed. The model may be used to determine if an unknown biological sample exhibits a particular biological state. This can be done by receiving either a biological sample or data associated with the biological sample. After the data is received, the data may be input into the model. In one embodiment, the acquisition of the data associated with the biological sample is performed at a first location and the imputing of the data into the model is performed at a second location different than the first location. Unless the data maps identically to the model, the data would have an inherent effect on the position of the particular clusters within the discriminatory pattern, if it is allowed to affect the model. The modeling software can keep track of the net effect on the model that each sample received has on the position of the model. If the model has drifted outside of a predetermined tolerance, the model can be updated. Various business relationships may be developed to undertake various steps of the overall method for providing a diagnosis to a patient.

Claims

1. A method of determining whether a biological sample taken from a subject indicates that the subject has a disease, comprising:

transmitting a request for a set of vectors from a data stream obtained by performing an analysis of the biological sample, the data stream having a plurality of vectors, the set of vectors having at least three and less than all of the vectors of the data stream;

receiving, at a first location, the set of vectors from a second location, the second location being geographically different than the first location;

applying the set of vectors to a model to determine a diagnosis, the diagnosis including an indication of whether the biological sample is taken from a subject that has the disease; and

transmitting the diagnosis.

2. The method of claim 1, wherein the transmitting a request includes transmitting, from the first location to the second location, the request for a set of vectors from a data stream obtained by performing an analysis of the biological sample.

3. The method of claim 1, wherein the applying includes applying, at the first location, the set of vectors to a model to determine a diagnosis.

4. The method of claim 1, wherein the transmitting the diagnosis includes transmitting the diagnosis from the first location to the second location.

5. The method of claim 1, wherein the set of vectors is a first set of vectors and further comprising:

receiving, at the first location, a request from the second location, the request including an identification of at least two diseases for which the data stream should be analyzed; and

transmitting a request for a second set of vectors having at least three and less than all of the vectors of the data stream and having at least one vector not in the first set of vectors.

6. The method of claim 5, wherein the receiving a request occurs before the transmitting a request.

7. The method of claim 1, wherein the data stream is obtained by performing a mass spectral analysis on the biological sample.

8. The method of claim 1, wherein the biological sample is selected from the group consisting of serum, blood, saliva, plasma, nipple aspirant, synovial fluids, cerebrospinal fluids, sweat, urine, fecal matter, tears, bronchial lavage, swabbings, needle aspirants, semen, vaginal fluids, and pre-ejaculate.

9. The method of claim 1, wherein the disease is a cancer.

10. The method of claim 1, wherein the diagnosis is transmitted to a results database that is located at the second location.

11. The method of claim 1, wherein the set of vectors is received via an electronic means.

12. The method of claim 1, wherein the set of vectors is received via a network connection.

13. The method of claim 1, wherein the set of vectors is received via physical storage medium containing electronic data.

14. A method of determining whether a biological sample taken from a subject indicates that the subject has a disease, comprising:

providing a data stream, having a plurality of vectors, obtained by performing an analysis of a biological sample taken from a subject;

receiving an indication of at least three and less than all of the plurality of vectors are necessary for determining whether the biological sample indicates that the subject has the disease;

abstracting the data stream to obtain necessary vectors; and

transmitting the necessary vectors from a first location to a second location, the second locating being geographically different than the first location.

15. The method of claim 14, wherein the receiving includes receiving, at the first location, an indication of at least three and less than all of the plurality of vectors are necessary for determining whether the biological sample indicates that the subject has the disease from the second location.

16. The method claim 14, wherein the abstracting includes abstracting the data stream at the first location.

17. The method of claim 14, further comprising:

receiving, at the first location, a transmission from the second location, the transmission indicating whether the biological sample indicates that the subject has the disease.

18. The method of claim 14, wherein the necessary vectors are a first set of necessary vectors and further comprising:

transmitting a request from the first location to the second location, the request including an indication of a second disease for which the data stream should be analyzed; and

receiving an indication of a second set of necessary vectors being at least three and less than all of the plurality of vectors necessary for determining whether the biological sample indicates that the subject has the second disease, the second set of necessary vectors having at least one vector not included in the first set of necessary vectors.

19. The method of claim 18, wherein the transmitting a request occurs before the receiving an indication.

20. The method of claim 14, wherein the data stream is obtained by performing a mass spectral analysis on the biological sample.

21. A method of determining whether a biological sample taken from a subject is of a first biological state or a second biological state, comprising:

abstracting a data stream, having a plurality of vectors, obtained by performing an analysis of the biological sample to obtain at least three and less than all of the plurality of vectors of the data stream;

transmitting the abstracted vectors from a first location to a second location, the second locating being geographically different than the first location; and

receiving a transmission indicating whether the biological sample is of the first state or the second state.

22. The method of claim 21, wherein the transmitting a request occurs before the receiving an indication.

23. A method of determining whether a diagnostic model is accurately applicable to a population of subjects to which the model is applied, the model being configured to determine a biological state of a subject, the model being based on a set of data streams, each of the data streams being obtained by performing an analysis of biological samples taken from subjects of known biological states, the model having at least one diagnostic cluster located in a vector space having at least three dimensions, each dimension corresponding to a vector common to the data streams in the set of data streams, the diagnostic cluster having a centroid located at an initial centroid location based on locations of vectors from the set of data streams that correspond to the diagnostic cluster, comprising:

receiving a vector set, the vector set including at least three vectors from a data stream obtained by performing an analysis of a biological sample taken from a subject of an unknown biological state;

mapping the vector set into the vector space;

if the vector set maps into the diagnostic cluster, calculating an updated location of the cluster centroid based on the location of the vectors from the vector set and the set of data streams that correspond to the diagnostic cluster;

determining the distance between the initial centroid location and the updated centroid location; and

if the distance between the initial centroid location and the updated centroid location is greater than a predetermined threshold, providing an output indicating that the threshold has been exceed.

24. The method of claim 23, further comprising;

if the distance between the initial centroid location and the updated centroid location is greater than the predetermined threshold, creating a new diagnostic model based on the vector set and the data streams that correspond to the biological samples of known biological states.

25. The method of claim 23, wherein the output is a visual output.

26. The method of claim 23, the output being a first output, further comprising:

if the distance between the initial centroid location and the updated centroid location is less than the threshold, providing a second output indicating that the threshold has not been exceeded.

27. A method of updating a model configured to determine whether a biological sample taken from a subject indicates that the subject has a disease, the model being based on a set of data streams, each of the data streams being obtained by performing an analysis of biological samples taken from subjects of known biological states, the model having at least one diagnostic cluster located within a vector space, comprising:

receiving a vector set, the vector set including at least three vectors from a data stream obtained by performing an analysis of a biological sample taken from a subject of an unknown biological state;

mapping the vector set into the vector space;

using the model to determine whether the biological sample indicates that the subject has the disease;

receiving a clinical diagnosis of the subject indicating whether the subject has the disease; and

creating another model configured to determine whether a biological sample taken from a subject indicates that the subject has the disease using the set of data streams and the vector set.

28. The method of claim 27, wherein the data stream associated with the subject of an unknown biological state is obtained by performing a mass spectral analysis on the biological sample.

29. A processor-readable medium comprising code representing instructions to cause a processor to:

transmit a request for a set of vectors from a data stream obtained by performing an analysis of the biological sample, the data stream having a plurality of vectors, the set of vectors having at least three and less than all of the vectors of the data stream;

receive, at a first location, the set of vectors from a second location, the second location being geographically different than the first location;

apply the set of vectors to a model to determine a diagnosis, the diagnosis including an indication of whether the biological sample is taken from a subject that has the disease; and

transmit the diagnosis.

30. A processor-readable medium comprising code representing instructions to cause a processor to:

receive an indication of which of a plurality of vectors are necessary for determining whether a biological sample taken from a subject indicates that the subject has the disease;

abstract a data stream, having a plurality of vectors, obtained by performing an analysis of the biological sample to obtain at least three and less than all of the plurality of vectors of the data stream; and

transmit the abstracted vectors from a first location to a second location, the second locating being geographically different than the first location.

31. A method of determining the biological state of a biological sample, comprising:

transmitting a request for a set of vectors from a data stream obtained by performing an analysis of the biological sample, the data stream having a plurality of vectors, the set of vectors having at least three and less than all of the vectors of the data stream;

receiving, at a first location, the set of vectors from a second location, the second location being geographically different than the first location;

applying the set of vectors to a model to determine a diagnosis, the diagnosis including an indication of the biological state of the biological sample; and

transmitting the diagnosis.

32. The method of claim 31, wherein the indication of the biological state is an indication that the biological sample is of a first state or a second state.

33. The method of claim 32, wherein the first state is a diseased state, the second state is a healthy state.

34. The method of claim 32, wherein the first state is the presence of a biological pathogen, the second state is the absence of the biological pathogen.