Genomic data analysis system and method
Embodiments relate to methods and systems for analyzing genomic data, such as genetic variants. Some embodiments relate to the efficient analysis and presentation of certain genetic variants of an individual.
1. A computer-implemented method for displaying genetic variation data, comprising using a processor for:
receiving genetic variation data from genomic sequence data of an individual;
determining annotated genetic variation data for the individual from the received genetic variation data using a plurality of variant identification tools, wherein the annotated genetic variation data comprises at least one feature selected from the group consisting of:
a type of genetic variant, a locus of a genetic variant, and a quality score for a genetic variant, and wherein genetic variants in the annotated genetic variation data comprise at least one structural variant;
creating a data structure of an index of documents for the annotated genetic variation data in a computer memory, wherein creating the index data structure comprises creating an inverted index data structure;
receiving a selection from a user for at least one filter from a plurality of filters for features of interest in the annotated genetic variation data; and
in response to receiving the selection,
searching the index data structure based upon the selected filter to generate filtered genetic variants for the individual, wherein searching the index data structure comprises searching the inverted index data structure;
identifying a genetic variant that is a translocation along with a first and second point, the first point being the location of a first breakpoint of the translocation on a first axis and the second point being the location of a second breakpoint of the translocation mapped on a second axis comprising a linear representation of a genome;
displaying on a display device a browser page that displays the filtered genetic variants of the individual, wherein the browser page comprises a first map comprising the first axis comprising a linear representation of the genome having the locations of the genetic variants mapped thereon, and wherein different types of genetic variants are identified by different icons, wherein for the translocation, the browser page displays the first and second points connected using a straight or curved line;
in response to the user further selecting an icon corresponding to the translocation, launching and displaying on the display device a second map comprising an enlarged view of the first axis and a non-enlarged view of the second axis to provide a higher resolution visualization of the first breakpoint of the translocation while maintaining a visualization of the association of the translocation with its second breakpoint at the second point within the genome; and
in response to hovering a mouse cursor over or to selecting an icon, displaying details of the translocation in a popup window.
2. The method of claim 1 , wherein the second map is reached directly from the first map.
3. The method of claim 1 , further comprising highlighting a translocation when a user hovers over or selects a corresponding icon.
4. The method of claim 1 , further comprising displaying a popup window of details of a genetic variant when a user selects the icon for the genetic variant.
5. The method of claim 1 , wherein the genetic variation data is stored at a location remote from a server that performs the search.
6. The method of claim 1 , wherein the filters selectively provide genetic variants associated with at least one feature selected from the group consisting of a whole genome, a chromosome, a type of genetic variant, a quality metric, a clinical indication, a population frequency, and an overlapping database variant.
7. The method of claim 6 , wherein the clinical indication is a phenotype associated with a genetic variant.
8. The method of claim 1 , wherein the genetic variants comprise at least one variant selected from the group consisting of an inversion, a deletion, an insertion, a duplication, a substitution, and a translocation.
9. The method of claim 1 , wherein each of the genetic variants are uniquely identified by one of the different icons.
10. The method of claim 9 , wherein the genetic variants comprise at least one variant selected from the group consisting of an inversion, a deletion, an insertion, a duplication, a substitution, and a translocation.
11. The method of claim 10 , wherein the icons are selected from the group consisting of: a semi-circular shape, a triangular shape, an inverted triangular shape, a circular shape, a cross shape, and a diamond shape.
12. The method of claim 1 , wherein the browser page further displays a Bezier curve joining an expected locus and an actual locus of the translocation.