Genome explorer system to process and present nucleotide variations in genome sequence data

• US 10,347,361 B2
• Filed: 10/24/2013
• Issued: 07/09/2019
• Est. Priority Date: 10/24/2012
• Status: Active Grant

• Current Assignee: NantOmics, LLC (NantWorks, LLC)
• Original Assignee: NantOmics, LLC (NantWorks, LLC)
• Inventors: Adams, Julie, Buholzer, Mirko
• Primary Examiner(s): Woitach, Joseph
• Application Number:
  US14/062,234
• Publication Number:
  US 20140115515A1
• Time in Patent Office: 2,084 Days
• Field of Search: None
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations

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.

Claims

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.

2. The method of claim 1, wherein the plurality of variations includes copy number variations (CNVs), small nucleotide variations (SNVs), and loss of heterozygosity (LOH).

3. The method of claim 1, further comprising:

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

reconfiguring the display of the comparative gene sequence map such that the region is magnified and variations of the sample complex sequence in the region are provided in the display, wherein the display presents separate graphs across the region for copy number, allele specific copy number, and protein encoding sequences.

4. The method of claim 1, wherein the user interface is configured to provide selectable options of a karyogram view, a circular view across one or more chromosomes, or a linear view of a region of interest, any of which indicate where variations in the sample complex sequence occur, and

wherein, for the karyogram view, copy number gain and copy number loss are depicted with opposite arrows next to regions having such copy number variations.

5. The method of claim 1, wherein step (a) comprises:

(i) receiving a first identifier identifying a user and a second identifier identifying a test sample;

(ii) determining whether the user has authority to access sequence data for the test sample; and

if so, (iii) retrieving complex sequence for the test sample from a secure database, the secure database including genomes for a plurality of different samples.

6. The method of claim 1, wherein step (a) comprises sequencing DNA contained in the test sample, thereby obtaining sample complex sequence for the test sample.

7. The method of claim 1, wherein step (b) comprises iteratively:

(i) sourcing a potential reference sequence for any one of a plurality of a reference samples in a reference database;

(ii) comparing the potential reference sequence for the test sample with the sample complex sequence sourced in step (i); and

(iii) selecting the potential reference sequence sourced in step (i) as a suitable reference sequence for analyzing the sample complex sequence for the test sample if it matches the test sample according to preset criteria.

8. The method of claim 1, further comprising predicting one or more effect(s) of each of at least some of the variations identified in step (c) on protein expression, protein function, clinical presentation, and/or disease risk, and providing information about the effect(s) with the comparative gene sequence map in step (d).

9. The method of claim 1, further comprising comparing at least some of the variations identified in step (c) with known variants, and providing information about the known variants with the comparative gene sequence map in step (d).

10. The method of claim 9, wherein the information about the known variants has been obtained at least in part from external databases.

11. The method of claim 1, wherein the menu of filters includes filters for all of the following:

gene region;

type of small nucleotide variation (SNV);

CNVs greater than a given size;

zygosity;

impact on an amino acid sequence encoded at and around a variation;

number of copies of the variation;

amount of copy overlap;

occurrence of the variation in an external database of variations;

clinical presentation associated with the variation; and

quality or confidence of the sample complex sequence at and around the variation.

12. The method of claim 1, comprising automatically identifying sequencing errors in the sample complex sequence, and removing such errors from the display.

13. The method of claim 1, wherein the computer system is connected with and is configured to access all of the following:

an external database that provides a library of complex sequences for comparison with the sample complex sequence;

an external database that provides a library of previously known sequence variations for comparison with variations in the sample complex sequence; and

an external database that provides assessments of previously known sequence variations.

14. The method of claim 1, wherein the computer system is configured to provide a plurality of external user interfaces and to exchange and display assessments between the plurality of external user interfaces.

15. The method of claim 1, wherein the sample complex sequence and the reference complex sequence span a human genome.

16. A method for displaying variations between complex 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 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.

17. The method of claim 16, further comprising providing on the comparative gene sequence map displayed in step (d) at or near each of one or more of the variations identified in step (c) a hyperlink to a forum whereby a plurality of users having access to the sample complex sequence may exchange first information and reply information regarding the respective variation.

18. A method for displaying variations between complex sequences by a computer system, the method comprising:

(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.

19. The method of claim 18, wherein the refined plurality of variations has been screened to remove variations based on quality or confidence of sequencing or sequence assembly.

20. The method of claim 18, wherein the selection of the region within the comparative gene sequence map to magnify includes:

displaying a variation on a touchpad display of the computer system; and

receiving a tap on the touchpad display on the variation.

21. The method of claim 18, further comprising:

determining whether the region is smaller than a specified size; and

if the region is smaller than the specified size;

displaying a nucleotide sequence that spans the region,

displaying locations of one or more variations in the nucleotide sequence and

displaying a variant nucleotide at a location corresponding to a single nucleotide variation in the nucleotide sequence.