Interactive genome browser
Disclosed is an interactive genome browser executing within a web browser application, configured to display patient genetic data and additional genetic data tracks which are aligned by base pair. Additional tracks may include public data, community data, private data, sequence gaps, and additional genetic tests or probes which are available. Tests or probes may be ordered by selecting them from a test or probe track. Data in a genetic information database may also be searched using the interactive genome browser. Analyzed patient data may be published and made available to a community of users, which may communicate with one another.
1. One or more computing devices, comprising:
one or more processors;
memory; and
a web browser application configured to execute an interactive genome browser script, stored in the memory and executable on the one or more processors, the interactive genome browser script configured to:
receive, from a user, a set of genetic data associated with a patient undergoing analysis from one or more servers,
remove certain genetic data from the set of patient genetic data to generate filtered genetic data of the patient indicating chromosomal segment gain or loss that is associated with one or more genetic disorders that include at least one of Down syndrome, Cri du chat, Wolf-Hirschhorn syndrome, Edward's syndrome, Jacobsen syndrome or Turner syndrome, and
receive genetic data associated with multiple patients from the one or more servers, and statistically analyze the multiple patients data to determine how often the multiple patients exhibit chromosomal gain or loss across an autosomal region associated with the one or more genetic disorders, and through comparison of the filtered genetic data to the statistically analyzed multiple patients data to determine whether the chromosomal segment gain or loss of the patient undergoing analysis is clinically significant.
2. One or more computing devices as recited in claim 1 , wherein the interactive genome browser script is further configured to:
build a first genetic data track based on the filtered genetic data,
build a second genetic data track based on genetic data associated with multiple patients,
align the first genetic data track and the second genetic data track by base pairs,
display the first genetic data track and the second genetic data track, and
transmit to the one or more servers an interpretive comment of the patient undergoing analysis, the interpretive comment being accessible by a community of users when a user of the users are analyzing the set of genetic data associated with the patient undergoing analysis.
3. One or more computing devices as recited in claim 2 , wherein the interactive genome browser script is further configured to present to the user an additional track of genetic data published to the community of the users, the additional track being aligned by base pairs with the first genetic data track.
4. One or more computing devices as recited in claim 2 , wherein the interactive genome browser script is further configured to display an automatically generated International Standard Cytogenetic Nomenclature (ISCN) string describing a region designated by the user.
5. One or more computing devices as recited in claim 1 , wherein the interactive genome browser script is further configured to:
facilitate communications associated with the determining between the user and at least one of a researcher, a clinician and a doctor.
6. One or more computing devices as recited in claim 1 , wherein the interactive genome browser script is further configured to:
provide a visual representation of the chromosomal gain or loss of the patient, and the statistical results depicting how often the chromosomal gain or loss is found in the multiple patients data.
7. One or more computing devices, comprising:
one or more processors;
memory; and
a web browser application configured to execute an interactive genome browser script, stored in the memory and executable on the one or more processors, the interactive genome browser script configured to:
receive, over a network, first genetic data associated with a patient undergoing analysis and receive second genetic data associated with multiple patients from a server,
wherein the first genetic data indicating chromosomal segment gain or loss that is associated with one or more genetic disorders that include at least one of Down syndrome, Cri du chat, Wolf-Hirschhorn syndrome, Edward's syndrome, Jacobsen syndrome or Turner syndrome, and the second genetic data is a statistical analysis of the multiple patients data,
build a first genetic data track comprising the first genetic data
build a second genetic data track comprising the second genetic data associated with the multiple patients,
align the first genetic data track and the second genetic data track by base pairs,
display the first genetic data track and second genetic data track,
statistically determine how often the multiple patients exhibit chromosomal gain or loss across an autosomal region associated with the one or more genetic disorders, and through comparison of the first genetic data to the second genetic data determine whether the chromosomal segment gain or loss of the patient undergoing analysis is clinically significant, and
transmit interpretive comments of a particular patient that are derived from the first genetic data track and second genetic data track to the server.
8. One or more computing devices as recited in claim 7 , wherein the interactive genome browser script is configured to display an automatically-generated genetic information report based on clinician input during review and/or analysis of data in the interactive genome browser script.
9. One or more computing devices as recited in claim 8 , wherein the genetic information report shows benign chromosome segment gains or losses.
10. One or more computing devices as recited in claim 8 , wherein the genetic information report further comprises a template for commonly used text which may be modified.
11. One or more computing devices as recited in claim 7 , wherein the interactive genome browser script presents clinically significant data affecting patients assigned to a user, wherein the clinically significant data were added after the user analyzed the patient.
12. One or more computing devices as recited in claim 7 , wherein the interactive genome browser script is further configured to:
provide a visual representation of the chromosomal gain or loss of the patient, and the statistical results depicting how often the chromosomal gain or loss is found in the multiple patients data.
13. One or more computing devices as recited in claim 7 , wherein the interactive genome browser script is further configured to:
enable anonymous exchange of patient information associated with the interpretive comments among users.
14. One or more computing devices, comprising:
one or more processors;
memory; and
a web browser application configured to execute an interactive genome browser script, stored in the memory and executable on the one or more processors, the interactive genome browser script configured to:
receive, over a network, first genetic data associated with a patient undergoing analysis and second genetic data associated with multiple patients from a server, the first genetic data indicating chromosomal segment gain or loss that is associated with one or more genetic abnormalities,
build a first genetic data track based on the first genetic data associated with the patient undergoing analysis,
build a second genetic data track based on the second genetic data associated with the multiple patients,
calculate a frequency of occurrence of the chromosomal segment gain or loss associated with a chromosomal region of the patient using the second genetic data associated with multiple patients,
analyze the genetic data associated with the patient for the chromosomal region using the frequency of the occurrence of the chromosomal segment gain or loss to enable a user to determine a degree that the patient has the one or more genetic abnormalities, and
display the first genetic track and the second genetic track by indicating the chromosomal segment gain or loss associated with the chromosomal region of the patient undergoing analysis, and one or more corresponding frequencies associated with the chromosomal region of the multiple patients.
15. One or more computing devices as recited in claim 14 , wherein the interactive genome browser script is further configured to initiate a search of genetic data.
16. One or more computing devices as recited in claim 15 , wherein the search is configured to filter on a range of base pairs selected within the interactive genome browser script.
17. One or more computing devices as recited in claim 15 , wherein the search is configured to filter by chromosomal location.
18. One or more computing devices as recited in claim 15 , wherein the search is configured to filter by a search term.
19. One or more computing devices as recited in claim 18 , wherein the search term is a symptom.
20. One or more computing devices as recited in claim 18 , wherein the search term is a clinical sign.
21. One or more computing devices as recited in claim 15 , wherein the search is configured to filter to display patients assigned to a user.
22. One or more computing devices as recited in claim 15 , wherein the search is configured to display a summarized set of search results.
23. One or more computing devices as recited in claim 22 , wherein selection of the summarized set of search results displays a detailed version of the search results.
24. One or more computing devices as recited in claim 14 , wherein the interactive genome browser script is further configured to search genetic data published to a community of users.
25. A system comprising:
one or more processors;
memory; and
an application, stored in the memory and executable on the one or more processors, configured to:
retrieve and display a patient genetic data track comprising genetic data associated with a patient,
load an additional genetic data track comprising genetic data associated with multiple other patients, the patient genetic data track and the additional genetic data track including indications of chromosomal segment gain or loss for at least one of the patient or a particular patient of the multiple other patients, the chromosomal segment gain or loss being associated with one or more genetic disorders that include at least one of Down syndrome, Cri du chat, Wolf-Hirschhorn syndrome, Edward's syndrome, Jacobsen syndrome or Turner syndrome,
display the additional genetic data track in alignment with the patient genetic data track,
calculate a frequency of occurrence of the chromosomal segment gain or loss associated with a chromosomal region among the multiple other patients; and
analyze the genetic data associated with the patient for the chromosomal region using the frequency of the occurrence of the chromosomal segment gain or loss to enable a user to determine a degree that the patient has the one or more genetic disorders.
26. The system as recited in claim 25 , wherein the application is further configured to:
allow a user to annotate the genetic data, and
publish the annotations or clinical patient information to a community of the user.
27. The system as recited in claim 25 , wherein the displaying the additional genetic data track in alignment with the patient genetic data track comprises display the additional genetic data track in alignment with the patient genetic data track for comparison, and the application is further configured to facilitate a physician to order one or more additional genetic tests based on the comparison.
28. The system as recited in claim 25 , wherein the application is further configured to compare chromosomal segment gain or loss of one patient against one or more relatives of the one patient to determine whether the chromosomal segment gain or loss of the one patient is clinically significant, wherein the relative(s) is selected from the group consisting of parent, child, sibling, maternal half sibling, maternal uncle, maternal aunt, maternal grandparent, paternal half sibling, paternal uncle, paternal aunt, paternal grandparent, spouse or partner, sperm donor, egg donor, and surrogate.