Genome explorer system to process and present nucleotide variations in genome sequence data
First Claim
Patent Images
1. A method for displaying variations between sequences by a computer system, the method comprising performing, by the computer system:
- (a) receiving a sample complex sequence for a test sample;
(b) aligning the sample complex sequence with a reference complex sequence for a reference sample, the sample complex sequence and the reference complex sequence spanning at least one chromosome;
(c) identifying a plurality of variations between the sample complex sequence and the reference complex sequence;
(d) displaying a comparative gene sequence map at a user interface including a display screen of the computer system, the display screen showing where the plurality of variations are located within the sample complex sequence;
(e) displaying a menu of filters on the display screen of the user interface, the menu of filters for use in adapting the display of the comparative gene sequence map with respect to the plurality of variations;
(f) receiving, at the user interface via an input device of the computer system, a selection of a filter from the menu of filters, wherein the filter specifies one or more characteristics of variations to be displayed, the one or more characteristics including at least one of;
one or more regions of the reference complex sequence and one or more effects on expression;
(g) adapting the comparative gene sequence map displayed by the user interface to highlight variations having the one or more characteristics and/or remove variations not having the one or more characteristics specified by the filter, thereby providing filtered variations;
(h) receiving at the user interface an assessment of one or more of the filtered variations; and
(i) adapting the filter for subsequent use by the computer system to include or exclude one or more of the filtered variations according to the assessment.
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Abstract
This disclosure provides a technology for users to gain first-hand knowledge and experience with interpreting whole genomes. The technology graphically depicts variations in genome sequences in an expandable display, and provides a platform whereby the user may find and research the biological significance of such variants. The technology also provides a unique collaborative environment designed to capture and improve the collective knowledge of the participating community.
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Citations
21 Claims
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1. A method for displaying variations between sequences by a computer system, the method comprising performing, by the computer system:
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(a) receiving a sample complex sequence for a test sample; (b) aligning the sample complex sequence with a reference complex sequence for a reference sample, the sample complex sequence and the reference complex sequence spanning at least one chromosome; (c) identifying a plurality of variations between the sample complex sequence and the reference complex sequence; (d) displaying a comparative gene sequence map at a user interface including a display screen of the computer system, the display screen showing where the plurality of variations are located within the sample complex sequence; (e) displaying a menu of filters on the display screen of the user interface, the menu of filters for use in adapting the display of the comparative gene sequence map with respect to the plurality of variations; (f) receiving, at the user interface via an input device of the computer system, a selection of a filter from the menu of filters, wherein the filter specifies one or more characteristics of variations to be displayed, the one or more characteristics including at least one of;
one or more regions of the reference complex sequence and one or more effects on expression;(g) adapting the comparative gene sequence map displayed by the user interface to highlight variations having the one or more characteristics and/or remove variations not having the one or more characteristics specified by the filter, thereby providing filtered variations; (h) receiving at the user interface an assessment of one or more of the filtered variations; and (i) adapting the filter for subsequent use by the computer system to include or exclude one or more of the filtered variations according to the assessment. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A method for displaying variations between complex sequences by a computer system, the method comprising performing, by the computer system:
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(a) receiving a sample complex sequence for a test sample; (b) aligning the sample complex sequence with a reference complex sequence for a reference sample, the sample complex sequence and the reference complex sequence spanning at least one chromosome; (c) identifying a plurality of variations between the sample complex sequence and the reference complex sequence; (d) displaying a comparative gene sequence map at a user interface of the computer system, the display showing where the plurality of variations are located within the complex sequence; (e) receiving, at the user interface, a selection of a plurality of filters from a library of such filters provided by the computer system to obtain selected filters; (f) for each of the selected filters, adapting the comparative gene sequence map displayed by the user interface by removing variations not having characteristics specified by the respective filter, leaving filtered variations; (g) receiving, at the user interface, a selection of variations of interest from amongst the filtered variations on the comparative gene sequence map; (h) transmitting, via a network interface of the computer system in communication with a server, the variations of interest to other user interfaces of other computer systems; (i) receiving, via the network interface, comments pertaining to one or more of the variations of interest from one or more of the other user interfaces; and (j) displaying the comments from the other user interfaces on the user interface. - View Dependent Claims (17)
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18. A method for displaying variations between complex sequences by a computer system, the method comprising:
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(a) receiving a sample complex sequence for a test sample; (b) aligning, with the computer system, the sample complex sequence with a reference complex sequence for a reference sample, the sample complex sequence and the reference complex sequence spanning at least one chromosome; (c) identifying, with the computer system, a plurality of variations between the sample complex sequence and the reference complex sequence; (d) identifying, with the computer system, variations within the plurality that are sequence read errors or sequence assembly errors; (e) removing from the plurality of variations identified in step (c) the sequence read errors and sequence assembly errors identified in step (d), thereby producing a refined plurality of variations; (f) displaying a comparative gene sequence map at a user interface, the display showing where the refined plurality of variations are located within the complex sequence; (g) receiving, at the user interface, a selection of a plurality of filters from a library of such filters provided by the computer system to obtain selected filters; (h) for each of the selected filters, adapting the comparative gene sequence map displayed by the user interface by removing variations not having characteristics specified by the respective filter, leaving filtered variations; (i) receiving, at the user interface, a selection of a region within the comparative gene sequence map, the region being less than half the comparative gene sequence map and including at least one of the filtered variations; and (j) reconfiguring the display of the comparative gene sequence map such that the region is magnified, wherein the region is magnified in proportion to a size of the region, and wherein the user interface includes two graphical markers that respectively define a starting location and an ending location of the region and that move to allow a user to change the starting location and the ending location. - View Dependent Claims (19, 20, 21)
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Specification