GENOME EXPLORER SYSTEM TO PROCESS AND PRESENT NUCLEOTIDE VARIATIONS IN GENOME SEQUENCE DATA
1. A server system for sharing variations in complex sequences between clients, the server system comprising one or more processors coupled with at least one memory storing instructions that, when executed by the one or more processors, cause the one or more processors to:
- assemble a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample;
provide, via a network, the gene sequence map to a plurality of clients;
cause a first client to display a first user interface that receives directions to make the gene sequence map available to other clients and that receives first information about one or more of the variations made available to the other clients;
cause one or more second clients to display at least one second user interface that receives reply information from the one or more second clients about the one or more variations made available; and
provide, to the first client, the reply information for the one or more variations.
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.
- 1. A server system for sharing variations in complex sequences between clients, the server system comprising one or more processors coupled with at least one memory storing instructions that, when executed by the one or more processors, cause the one or more processors to:
assemble a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample; provide, via a network, the gene sequence map to a plurality of clients; cause a first client to display a first user interface that receives directions to make the gene sequence map available to other clients and that receives first information about one or more of the variations made available to the other clients; cause one or more second clients to display at least one second user interface that receives reply information from the one or more second clients about the one or more variations made available; and provide, to the first client, the reply information for the one or more variations.
- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
- 13. A method for sharing variations in complex sequences between clients, the method comprising performing, by a server system:
assembling a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample; providing, via a network, the gene sequence map to a plurality of clients; causing a first client to display a first user interface that receives directions to make the gene sequence map available to other clients and that receives first information about one or more of the variations made available to the other clients; causing one or more second clients to display at least one second user interface that receives reply information from the one or more second clients about the one or more variations made available; and providing, to the first client, the reply information for the one or more variations.
- View Dependent Claims (14, 15, 16)
- 17. A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to perform:
providing, via a network, the gene sequence map to a plurality of clients; providing, to the first client, the reply information for the one or more variations.
- View Dependent Claims (18, 19, 20)
This application is a divisional of U.S. patent application Ser. No. 14/062,234, filed Oct. 24, 2013, entitled “Genome Explorer System To Process And Present Nucleotide Variations In Genome Sequence Data,” which is a non-provisional of and claims the priority benefit of U.S. provisional application 61/717,773, filed Oct. 24, 2012, which are hereby incorporated herein in their entirety for all purposes.
This disclosure relates generally to the field of genome sequence analysis. More particularly, computer systems and methods are described that provide a graphical display of sequence variations and that can be integrated with a network to promote publication and community feedback.
Methods for whole genome sequencing have been described, for example in U.S. Pat. No. 7,910,354 (arrays of amplified polynucleotides), U.S. Pat. No. 8,278,039 (random array DNA analysis by hybridization); US 2009/0318304 A1 (efficient shotgun sequencing methods); and US 2011/0033854 A1 (long fragment read sequencing). Methodology for assembling DNA sequence fragments into extended genomic sequences includes but is not limited to the methodology described in U.S. Pat. No. 8,053,191 (iterative nucleic acid assembly using activation of vector-encoded traits); US 2011/0004413 A1 (calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence); US 2009/0105961 A1 (methods of nucleic acid identification in large-scale sequencing); and US 2008/0221832 A1 (methods for computing positional base probabilities).
Besides determining a genome, it is beneficial to be able to visualize the genome in an efficient and intuitive manner.
This disclosure provides a computer system and method for determining, displaying, and discussing variations that occur in genetic sequences between different individuals.
One aspect of the invention is a method for displaying variations between genomes between different individuals of the same species, and differences between other complex sequences. Sequence data is received for a test sample and a reference sample, the samples are aligned using a computer system, and variations in sequence are identified. The variations can then be displayed on a comparative gene sequence map showing where the variations are located. The user can be provided with an interface for controlling display of the comparative gene sequence map. The user can select from the interface a selection of a region within the genetic sequence map (sometimes less than half the entire comparative gene sequence map), whereupon the display is reconfigured such that the region is magnified, optionally in proportion to the size of the region: for example at least two times the original display, presented across at least about one half of the width of the display.
A display system according to the invention may be configured to display sequence and variant data in several formats. The formats may include a karyogram view, a cytogenomic view, a chromosome linkage view, a chromosome view, a linear map, or a sequence view, typically with any combination of several or all of these formats available and user selectable.
The gene map can provide resolution down to the level of single bases. Thus, the method comprises determining whether the region is smaller than a specified size, and if so, displaying a nucleotide sequence that spans the region, and (should at least one of the determined variations occur within the selected span at the specified size), displaying the locations of the variations with respect to the nucleotide sequence. Gene variations for display according to the method include but are not limited to copy number variations (CNVs), small nucleotide variations (SNVs), loss of heterozygosity (LOH), and other variation types listed elsewhere in this disclosure.
Richness of the display can be adapted to the liking of the provider and/or the user. For example, the display can present separate graphs across the region of interest for copy number, allele specific copy number, and protein encoding sequences. The user may be given the capacity to select 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 complex sequence occur.
To provide secure access to complex sequences of test samples, the method may comprise receiving a first identifier identifying a user and a second identifier identifying a test sample, determining whether the user has authority to access sequence data for the test sample, and if so, retrieving complex sequence for the test sample from a secure database, the secure database including genomes for a plurality of different samples. The method may also comprise doing the actual sequencing of DNA contained in the test sample, using any suitable method, such as those listed elsewhere in the disclosure. The reference sequence can optionally be selected from a database of such sequences, for example, by sourcing complex sequence for any one of a plurality of a reference samples in a reference database; comparing the complex sequence for the test sample with the reference sequence, and selecting a reference sequence if it matches the test sample according to preset criteria.
Filtering of the data can be done by receiving a selection of a filter that specifies characteristics of sequence variations to be displayed; and adapting the display to highlight variations having the characteristics and/or remove variations not having the characteristics specified by the filter. The method may comprise predicting one or more effects of sequence variations on protein expression, protein function, clinical presentation, or disease risk, and providing information about the effects with the gene sequence map. The method may also compare at least some of the variations with known variants, and providing information about the known variants with the gene sequence map, optionally from external databases. Certain variants can be highlighted or pinned by the user by receiving a selection of one or more of the variations in DNA sequence, and indicating the one or more variations on the comparative genetic map. The method may comprise receiving a selection of one or more of the variations in DNA sequence, determining the position of each of the selected variations in the human genome, obtaining information about DNA sequence variations observed for other samples at or around the position for at least some of the selected variations, and providing a display comprising the information.
Another aspect of the invention is a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to perform any aspect of the aforedescribed method.
Another aspect of the invention is a system configured to calculate and provide a display of variations in complex sequence data of a test sample relative to complex sequence data for a reference sample according to methods described herein. The system may comprise a computer processor, a database storing the reference DNA sequence data, and a DNA sequencer. The system may be configured so that the user may share information with others about one or more variations.
Another aspect of the invention is a server system for sharing variations in complex sequences between clients. The system comprises one or more processors configured to assemble a display such as a gene sequence map that shows a plurality of variations between a sample complex sequence for a test sample and a reference complex sequence for a reference sample. The processors provide the gene sequence map to a plurality of clients; provide a first user interface to a first client, wherein the user interface is configured to receive directions to make the gene sequence map available to other clients, and receive first information about one or more of the variations made available to the other client. The system is configured to provide a second user interface to one or more second clients; receive reply information from the one or more second clients about the one or more variations made available; and provide, to the first client, the reply information for the one or more variations.
The system may provide the gene sequence map to the plurality of clients with links from one or more of the variations to first information and reply information for the respective variation. The first information about the one or more variations provided by the first client user can be made available to other clients with hyperlinks that link to an indication of the one or more variations on the gene sequence map. The first information can be displayed in a feed as one or more entries, the feed being available to a plurality of users, wherein each entry corresponds to a respective variation. The first information about the one or more variations can be made available to the other users by way of an information website on the Internet. The server can be configured to compile reply information about one or more of the variations from other users into an assessment as to whether the variations are pathogenic or benign.
Other aspects of the invention will be evident from the description that follows.
The terms “complex sequence”, “sequence compilation” or “target sequence” as used in this disclosure refer to a set of nucleotide sequences for an individual or combination of individuals of any species. The sequence data may be obtained by sequencing a biological sample from a particular individual, or it may be constructed as artificial or consensus sequence data for a human individual or population. The complex sequence may be complete or partial genome sequence data, it may be cDNA sequence data from an expression library, it may be a sequence collection such as an exome or a biome, or it may be another DNA compilation of interest to the user. Unless explicitly stated otherwise, a suitable individual from which the complex sequence has been obtained may be selected from a human, other mammals, other vertebrates, other eukaryotes, prokaryotes, or combinations thereof, including but not limited to a pool of human or other biological samples from a particular source or from a particular human subclassification, single celled organisms from a particular environment, or a compilation of consensus or hypothetical sequences of an organism or component thereof.
A “reference sample” as used in this disclosure is any sample to which the user may compare a test sample, as explained below. The reference sample can have a reference complex sequence, e.g., a reference genome. A sequence of a nucleic acid molecule from the test sample (thus corresponding to the genome of the test sample) can be aligned to the reference sequence.
A “comparative gene sequence map” is a graphical depiction in which variations between two or more complex sequences are mapped between genetic position indicators (such as base count or known markers) along a DNA structure such as a chromosome. Unless otherwise specified, gene sequence maps provided for display are “expandable”, in the sense that the user may request depiction of an overview (such as an entire chromosome), or a segment thereof in increasing detail, ultimately resolving into the actual nucleotides in the sequence in the selected segment.
Nucleotide sequence “variations” include any difference between a complex sequence (e.g., a genome) of one sample and the complex sequence of another sample, as determined from sequence reads of the respective samples, which is explained and exemplified below.
A “display” is a visual depiction shown on an I/O device such as a monitor or touchpad, or within a frame or window depicted by the device. A computer system may “provide a display” of an item, for example, by causing the item to present on a suitable output device operatively connected to the system, or by sending to an external device (such as a client) a set of data that will enable the device to present the item locally.
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.
By way of illustration, each user may analyze one or more complex sequences in the following fashion. After presenting their credentials, the user calls from a client for a complex sequence obtained for a test sample and stored on a secure database accessible by the server. The system matches the test sequence to a selected reference sequence. The test and reference sequences are aligned, and sequence variations are determined. The variations are mapped on the sequence in a graphical display which is provided to the user by way of the client. The user may explore regions of interest on the map by directing the system to move about and expand the display. The user can drill down to review gene variations at the nucleotide level. The user can also request that the data be filtered for particular genes or particular types of variations.
The computer system also provides a platform by which the user may authorize other users to have access to the test sample sequence, and the genetic variations determined therefrom. Both the primary user and other users may annotate the variations and exchange comments over a social network that is integrated into the system.
Whole human genome sequencing holds great promise as a diagnostic and predictive aid in the management of human health. However, interpreting whole genome data to obtain clinically instructive information poses substantial challenges. Before development of the technology described here, expertise in analyzing and interpreting genome sequence data has been distributed across a variety of genomic databases, making it difficult to assemble different sorts of information and resolve open questions by consensus. The technology described here addresses these challenges by consolidating information from multiple sources, and providing a platform for more users to learn and share knowledge about interpreting genomic variants.
The technology described here provides a number of important advantages over what was previously available. First, the sequence analysis system described here can be integrated with a service for determining genomic sequence of a biological sample. The new sequence data can be consolidated with information from multiple sources, including prediction algorithms and cross-reference annotations from external genomic databases. Second, the technology helps users interpret genomes by providing users with important and instructive information through an easy-to-use interface.
Third, the technology allows experts to collaborate across the platform. In the tradition of modern electronic networks where people connect and share ideas in business and their personal lives, the technology described here has a collaborative function specifically focused on the interpretation of genome sequence variants This creates a vibrant knowledge base in genomics, to the benefit of clinician researchers everywhere and the patients under their care.
Each variation identified between a test sample and a reference sample may be analyzed by the server 104 with a plurality of filters or algorithms (for example, to determine if it causes a change in the encoded protein), and annotated accordingly. Each variation may be compared with previously known variations, and annotated according to the clinical or academic significance of the previously known variant. The annotations (or a selection thereof) are each provided at or near the respective sequence variation displayed on the client computer 103. In some configurations of the invention, the user has the option of making the test sequence available to one or more other users having their own client 105 connected to the server 104. Each of the other users may or may not bring their own sequence of interest from a client-specific database 106 for purpose of comparison or analysis. Information from the other clients 105 may be used by the server 104 to annotate the display presented on the first client 103. The server 104 may also provide a forum whereby the first user and the other users may exchange written commentary with regards to variations observed in the test sample.
The methods and systems described here can be used for a variety of research purposes and techniques. One such application is to assist a user in evaluating genetic variations that may be present in the genome, diseased tissue, or expression library of a particular individual. Such information may be instructive in the clinical management of the individual'"'"'s underlying condition.
Thus, the user may obtain and upload a complex sequence from test sample into the system before analysis. Another application of the technology is to integrate the analytical tools with a DNA sequencing service, whereupon sequence information obtained from a particular individual becomes the subject of the analysis.
Sequencing methodology suitable for use with this invention includes but is not limited to the methodology described in U.S. Pat. Nos. 7,910,354; 8,278,039; US 2009/0318304 A1; and US 2011/0033854 A1. Generally, complex sequence is fully assembled before being used to identify sequence variations as described here. Methodology suitable for assembling DNA sequence fragments into extended genomic sequences includes but is not limited to what is described in U.S. Pat. No. 8,053,191; US 2011/0004413 A1; US 2009/0105961 A1; and US 2008/0221832 A1, which are here incorporated herein by reference in their entirety for all purposes.
Complex sequence from a test sample can be loaded from the sequencing apparatus into the analytic system of this technology automatically, by the system operator, or by the end user. The system can be configured with a security system so that each user may control access to complex sequences from each sample. The user may be provided with the sequence data in electronic form, and then the source data is expunged from the server. More conveniently, the server may provide a repository of data, so the user may access the data on the server by cloud computing, and thereafter apply the analytic tools of this invention to the data from each test sample at the user'"'"'s convenience.
To maintain access control, for example, the server can be programmed to receive a first identifier identifying a user and a second identifier identifying a test sample. It then compares the identifiers with stored information to determine whether the user has authority to access sequence data for the test sample. If the requesting user has such authority, the server then retrieves complex sequence for the test sample from a secure database, and permits the user to view, analyze, and optionally download the data. The user may also have authority to change permissions, such that access to the complex sequence data and/or the subsequent analysis is opened up to other specified users or class of users, other members of having access to data on the server, or the public at large.
In order to determine variations in the sequence, the system can compare the complex sequence from the test sample with complex sequence from a reference standard. After receiving complex sequence for a test sample, the system aligns the complex sequence for the test sample with complex sequence for one or more reference samples, so that substantially identical portions of sequence are compared. Differences between the test sequence and the reference standard are identified by the system as variations, which may then be filtered as described below as an aid to evaluating their biological and clinical significance.
The reference standard used for this analysis may be consistent for all test samples during a period of operation. Alternatively the reference standard may be provided or identified by the user for the analysis of a particular test sample. This may be useful, for example, in the analysis of tissue from a tumor, where normal or unaffected tissue from the same person may serve as the closest reference.
In some implementations, the server will have access to a plurality of potential reference standards, and the server will identify one or more references to be used for each test sample analyzed by the system. In this implementation, the system will source complex sequence for any one of a plurality of standard samples in a reference database. It will compare the complex sequence for the test sample with the complex sequence called from the reference base. It can then select a standard from the database if the standard sample matches the test sample according to preset criteria.
A. Identification of Sequence Variations
Methods and systems of this invention can be used to identify variations in complex sequence. These are differences between the complex sequence of one or more test samples and one or more reference samples.
Nucleotide sequence variations include any difference between a sequence determined for one sample and the genome of another sample, as determined from sequence reads of the respective samples. Apparent variations may arise from errors in sequencing and/or sequence assembly. Where a variant is known or suspected of being a sequencing error, it may be suppressed or de-emphasized in the map displayed to the user. True sequence variations between a test sample and a(those reproducible upon resequencing or otherwise suspected or confirmed) include but are not limited to the following:
- Small nucleotide variations (SNVs) and single nucleotide polymorphisms (SNPs). SNVs include the change, addition or deletion of one or more nucleotides in or around the region of variation. SNPs are a subset of SNVs wherein the variation of a single nucleotide occurs with known regularity between different individuals or different types of samples of the same species. SNPs include inheritable alleles and mutations in diseased tissue that occur with known regularity.
- Copy number variations (CNVs), where a particular gene or other functional element of a complex sequence is replicated or reduced in replicates compared with a reference sample, such as may occur through gene duplication and/or translocation.
- Loss of heterozygosity (LOH), chromosome trisomy and gene rearrangement (transposition).
Embodiments of the invention can cause any one, some or all of such types of variations to be displayed in any combination.
The reference sample may be any sample to which the user may compare a test sample. It may be a sample of another individual, but is more typically a consensus or hypothetical sequence, such as may be created by amalgamating the corresponding sequences of a plurality of individuals, and/or editing to exclude or include one or more nucleotide variations for the purpose of the comparison. The comparison can be done by aligning the test sequence with the reference sequence so as to minimize the number of variations. For example, the test sequence can be aligned to a location that results in the fewest mismatches or variations from the reference sequence.
The reference sample may be selected from a database of reference samples to match the sample being analyzed. A reference sample is chosen to match a test sample if it is sufficiently similar to the test sample in terms of one or more preset criteria. By way of illustration, determining a match may include any one or more of the following criteria in any combination: degree of identity, present or absence of particular sequence variations of interest, and source information such as racial background, family relatedness, and clinical condition.
B. Display of Sequence Variations
The technology described here provides a platform by which users may visualize, filter and analyze variations in genomic sequence data in one consolidated tool. For example, small nucleotide variations (SNVs), copy number variations (CNVs) and loss of heterozygosity (LOH) events can all be viewed on the same display. A built in genome browser is provided to visualize and surf genomes with genome wide views down to base pair level views, so that the user may explore sequence variations that are relevant to their particular clinical situation.
As an introduction to results of the analysis and to orient the user, the system can provide the user with the choice of various views of the genome or expression library as a whole.
By way of illustration,
The display on the left side 220 provides a list of particular variations in a panel of genes of interest 221 which a user has selected for analysis, with a summary assessment underneath 222 as to whether it is pathogenic or benign. The gene panel is selected as described below, in reference to
One aspect of the invention is a display system for surveying and analyzing complex sequence data. Referring back to
Once the samples are aligned, the system then processes the data to determine where there are variations 153 between the test sequence(s) and the reference sequence(s). Variations include but are not limited to small nucleotide variations (SNVs), copy number variations (CNVs), loss of heterozygosity (LOH), and translocations. The variations that are identified by the system can optionally be filtered 154 to facilitate interpretation of the analysis. For example, one or more filters cam be implemented to exclude variations identified or suspected to be sequence read errors or assembly errors. As described elsewhere in this disclosure, other filters that can be implemented by choice of the use include but are not limited to filters that focus the display on particular genes or gene regions, filters that select variations depending on their effect on the function of the sequence (for example, the effect on an encoded amino acid sequence), and filters that select variations depending on previously known variants of particular interest or clinical significance. Such filters can be used singly or in any effective combination, and can be switched on and off by choice of the user during her review of the displayed data.
A display is then provided by the system 155 to a user client that show the filtered variations at their location on a map of the complex sequence: all the way from an overview map of the entire sequence (such as a karyogram view for a genomic sequence), in various degrees of detail down to the actual nucleotide sequence. The display is user controllable in the sense that (depending on how the system is configured), the user may request one or more of the following in any combination: a change in expansion or detail, the imposition or removal of filters, highlighting or annotating a particular variant identified by the system or a gene region comprising one or more variations of interest, and permitting other system users to provide their own annotations directly on the display or in a linked forum. In the configuration shown here, the user interface receives a selection of a region within a larger sequence map 156, whereupon the system reconfigures the display to magnify or focus on the region selected by the user. The user interface can also receive a request to decrease magnification or expand the scope of the region being analyzed, whereupon the system reconfigures the display to compress or scale down the previously viewed region into a smaller space so as to provide space for neighboring regions of the complex sequence to appear in the display.
Navigation between the views may be implemented in any way that is compatible with the underlying code and hardware. For example, the user may be provided with a numerical input or sliding scale to specify the degree of zoom from the original depiction. If the I/O device has a touch screen, then the view can be expanded, contracted, or moved up or downstream by touch, pinch, zoom, or tap at appropriate locations in the previous view. The interface may also be provided with links or menu choice whereby the user may specify a particular region, gene, variation, or other chromosomal feature, and be taken to a view whereby the selected feature occupies at least 10%, 20%, 40%, a majority, or substantially all of the width of the display. The system can also be configured so that the user has the option of pulling up a keyboard (
Genomes from different individuals who are not related inevitably comprise a range of sequence variations that provide a genetic basis for their individuality, but which do not necessarily portend a particular phenotype or disease susceptibility. Depending on the quality of the sequencing, there may also be sequencing errors that create noise potentially obscuring important data. To aid the clinician researcher in focusing on the variations more likely to be clinically significant, the system can provide a filtering capability to narrow the range of exploration.
- a gene alteration that results in selection of a codon synonym (hence no change on the encoded amino acid),
- in frame effects—e.g., alterations, deletions, or insertions that cause point variations but otherwise leave the encoded protein sequence intact, or
- more profound changes likely to compromise protein function, especially if they occur early in the coding sequence (for example, frame shift mutations or insertion of a stop codon).
By way of further illustration, small nucleotide variations (SNV) can be filtered according to predicted pathogenicity, gene region, impact on encoded amino acid sequence, SNV type (e.g., single nucleotide polymorphisms, deletions, insertions, multi-nucleotide substitutions), zygosity (homozygous or heterozygous), whether it is found in a particular database such as dbSNP, or to exclude commonly found variants in healthy populations. Copy number variations (CNV) can be filtered according to predicted pathogenicity, gene region, number of copies, repeat category overlap, or whether it is found in a particular database such as DGV. Any quality filters, such as ploidy quality score, and CNV type quality score. Different types of variations can be screened for quality or confidence of the sequencing and/or the sequence assembly so that sequencing errors do not confound the analysis. Such filters may be selected by the user for use in any effective combination, optionally in combination with a filter of the user'"'"'s own devising that has been constructed on or loaded onto the system.
The computer system and methods of the invention can be implemented so as to provide annotations and further information to assist in drawing conclusions from the presence of genetic variations that are presented after filtering. For example, the server may provide algorithms to predict protein expression, protein function, clinical presentation, and/or disease risk in any combination. Protein expression can be predicted on the basis of the effect on the encoded amino acid sequence. Protein function can be predicted on the basis of predicted three-dimensional structure, and effects on catalytic and binding sites. Clinical presentation and disease risk can be predicted based on cumulative history of other known variations at or around the same location and their known effects. Such predictive algorithms can be programmed into the system, or sourced from external servers, for example, over the Internet.
The computer system and methods of the invention can also be implemented so as to provide comparisons with gene variations previously reported that either occur in the same genes or that have similar biological and/or clinical effects. The system can source such information from within its own records of similar analyses done on other complex sequences in the same customer and reference databases. The system can also source such information from other systems and databases that are external to the system, for example, over the Internet. Once such other known variations are identified, the system can indicate the position of each variation on the same genetic map and/or provide a nearby link to information known about each other known variant. The annotation function can be provided as both a passive and an active tool. Thus, upon receiving information on user preferences, the system may as a matter of course annotate the genetic map with information about nearby or related genetic variants using internal and/or externally obtained information, in accordance with the user preferences. Alternatively or in addition, the system may be set up with a query function. Thus, the user may select on one or more genetic variations in a test sequence, or one or more gene regions in the test or reference sequence. The system may then be prompted to run its own algorithms and/or seek external information in accordance with the request from the user.
The technology described here allows the user to take advantage of rich variant annotations. This can include (1) clinically meaningful variant names that follow HGVS standards; (2) gene annotations by transcript including functional impact and scores from prediction algorithms such as Polyphen and SIFT; (3) cross-reference annotations from several genomic databases such as dbSNP and DGV and (4) allele frequency information across several data sets such as the 1000 Genomes. The user can thereby be provided with consolidated information with smart links to additional resources. Information includes variant attributes, variant and gene annotations, technical performance summaries and context sensitive links including links to NCBI, PubMed and popular public genome browsers. Consolidated views help shorten the variant analysis and research process.
Another feature that can be implemented in the computer systems and methods of this disclosure is a platform for interacting with other users so as to improve the knowledge base, both with respect to a particular test sequence, and generally in the study of variations of a particular type or class.
This can be implemented using a server that provides information for multiple clients. In reference to
Having been granted access to the map or information from a particular test sample or particular genetic variants, other users on the system 105 (either members selected by the first user, subscribing members generally, or a member of the public who has access to the system over the Internet) can reflect on the nucleotide variations or the questions posed by the first user. Should they wish to contribute information in reply, the system provides a portal by which the reply information is transmitted to the first client user privately, or to the community of users selected by the first client user for general discussion of the topic. The portal can be implemented so as to permit the replying user to add a location marker and/or an annotation to the gene sequence map, or to append information to an annotation made by the first user. The portal can also be implemented so as to permit a discussion to occur through an exchange posting linked to the map or previous comments, or provided as a separate display whereby the first client user can receive reply information about one or more of the variations that the server obtains from one or more of the other client users.
In more general terms, the system may provide forums of various types by which users may interact about particular genetic variations, particular gene regions, particular biological effects, or particular clinical issues. Such forums may be in the style of a bulletin board or blog, optionally with links to gene maps, complex sequence data, or other discussions in any combination, optionally with various levels of controlled access depending on privacy issues or proprietary aspects of gene sequence data and/or expert interpretation thereof. Such forums may also be in the style of a news feed with links to gene maps, complex sequence data, or other discussions in any combination, optionally with various levels of controlled access. News feeds will typically be provided by subscription, whereby certain users or class of users may be given access, and may opt in or opt out to receiving the selected feeds on a periodic or as-needed basis.
Such forums may also be in the style of a passive knowledge base or wiki, where the system provides a repository of information available for research into particular topics or genetic variants. The knowledge base may have links to gene maps, complex sequence data, or other discussions in any combination, optionally with various levels of controlled access, and optionally also provides a means by which the initiating user of each entry or other users may have authority to update, depending on their level of access.
Thus, the social networking aspect of the invention can be implemented so that as users filter and search for variants, they can mark variants of interest by highlighting or annotating them to get back to them easily. Community assessments allow users to contribute to and leverage community knowledge about the pathogenicity of variants. As users use the technology to create variant assessments, they can opt to share them with the community. Users can then comment on each other'"'"'s assessments. The next time that variant is seen in the context of a case, users see a summary of all shared assessment as well as the detail of each assessment including who made the assessment, when and all the supporting notes, evidence and comments. Newsfeeds provide a way for users to stay on top of the latest activities and collaborate with other users. Colleagues can comment and collaborate with each other directly through the newsfeed to exchange information, solve cases and assess the pathogenicity of variants.
The figures accompanying this description show a non-limiting illustration of certain aspects of the invention. The system for analyzing genetic variants shown in this illustration has been developed by Complete Genomics Inc. for use in commerce under the service mark Voyager™ or Voyager Genome Explorer™.
Voyager provides an application platform for use on a computer station, personal data assistant, touch pad, or other client configured for interaction with a server that provides sequence information and display. The platform may be implemented on standard operating systems such as iPad™, iOS™, Android™, and Windows™. The user opens up the application, logs in, and gets access to cases from the server to which the logged in user is permitted access. Voyager is integrated seamlessly with Complete Genomics'"'"' gene sequencing service. Thus, the credentialed user will have access to sequence data from samples they provided, sequence data that has been made generally available to Voyager subscribers and/or the general public.
A user having a complex sequence they want analyzed logs into the system once the sequence is available from the gene sequencing service. The sequence is labeled with information about the test sample: for example, nature of the sample (such as peripheral blood), the sampling date, and an identifier (ID) for the particular sample. The sequence is given its own Internal Accession Number that is unique to the sample and the sequencing run. Thus, samples from different patients, multiple samples from the same patient on different days, and different sequence runs for the same sequence are identified separately.
Upon launching or enquiring about complex sequence from a particular patient, the user is first presented with clinical context: differential diagnosis, phenotypes (collected at time of order using standard ontology from SNOmed); additional clinical information as available; pedigree information; identity of the treating and/or interpreting clinician. There are also areas to attach additional information (for example, laboratory results, and/or clinical or family history). The user may also look at technical summary to see quality of the sequence data: for example, information about the subject, a quality control report, and more detailed statistics about the data, such as genome vs. exome coverage, or summary of variants by various dimensions.
In this implementation, the user has an option to apply the filters to either single nucleotide variations (SNVs), copy number variations (CNVs), or both. For SNVs, the user may restrict the analysis to variants where there is some information in the system which indicates its pathogenicity. Other SNV filters include gene region (what region the variant falls in, e.g. CDS, 5′UTR, 3′UTR), the functional impact (e.g. synonymous, missense, nonsense, or frameshift), SNV type (e.g., insertion, deletion, or substitution), zygosity (homozygous or heterozygous), dbSNP (whether it'"'"'s found in dbSNP or not), minor Allele Freq for 1000 genomes to potentially filter out commonly found variants in healthy populations, and filters for sequence quality and minimum count. For CNVs, the user may select filters for CNV: whether they should be included (for example, CNVs greater than a given size), pathogenicity, copy number state, repeat category overlap (e.g. DNA, LINE, Low_Complexity, SINE, Satellite, SegDup, Self-chain, Simple_Repeats, scRNA, tRNA, snRNA), whether it appears in the Database of Genetic Variants (DGV), and quality filters (e.g., Ploidy Quality Score, CNV Type Quality Score). The Voyager system allows the user may create their own filter having filtering characteristics they desire.
The system also provides links to external databases and browsers such as UCSC or Ensembl so that the user can investigate more details on gene structure or conservation information in a gene region of interest, look up information in GeneReviews or do a more global NCBI Search.
The bar chart 701 shows the distribution of community assessments by rating. Underneath the chart, the user may access written comments 702 from each of the contributors to the assessment. As new assessments are created or comments are posted on assessments, other members of community get notifications that there is new activity. In the case when the user is not already logged into Voyager, they would see iPad notifications. If users is already in Voyager, they would see an indicator on a newsfeed icon presented as part of the display. Where the user is in the context of a specific case, the newsfeed is automatically filtered to community activity for the given case. There is also a newsfeed on the home page which shows activity across all cases.
The server then creates a map of variations 931, in which differences between the test and reference sample(s) are located in relation to known chromosomal markers. The server then compiles a graphical display 932 of the variations, which is then presented to the client 933. The display may be presented in a certain preselected chromosomal region of interest. Alternatively, as described in more detail below, the differences can be presented according to the scope of the test sequence (for example, a karyogram or chromosome view), from which the user may zoom in to focus on the details of a particular region 934, or zoom back out. The display is adjusted 935, and presented to the client 933 according to the request. As described below, the user may also request one or more filters 936 which are used to select variations between the test and reference samples 937 which are significant or of particular interest. The variations remaining after the filters are then used to create a map 931 and a graphical display 932 for display to the client 933. The user may provide their own annotation 941 for each variation which is incorporated 942 into the display 932. In a multi-user system, other users may reply 943 to the first user'"'"'s annotation. The reply information is then incorporated into the display 942 either as a direct annotation or as a linked comment.
As a general matter, computer systems referred to in the context of this invention, their design, manufacture, control, and programming may be conducted according to any suitable technology. Any of the computer systems referred to in this disclosure can use any suitable number of subsystems. A computer system may include a single computer apparatus, where the subsystems can be the components of the computer apparatus. Alternatively, a computer system can include multiple computer apparatuses, each being a subsystem, with internal components.
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A computer system can include a plurality of the same components or subsystems connected together by external interface 1011 or by an internal interface. Optionally, computer systems, subsystem, or apparatuses can communicate over a network. In such instances, one computer can be considered a client and another computer a server, where each can be part of a same computer system. A client and a server can each include multiple systems, subsystems, or components.
Any of the embodiments of the invention can be implemented in the form of control logic using hardware and/or using computer software in a modular or integrated manner. Any of the software components or functions in this disclosure may be implemented as software code to be executed by a processor using any suitable computer language such as, for example, Java, C++ or Perl using, for example, conventional or object-oriented techniques. The software code may be stored as a series of instructions or commands on a computer readable medium for storage and/or transmission, suitable media include random access memory (RAM), a read only memory (ROM), a magnetic medium such as a hard-drive or a floppy disk, or an optical medium such as a compact disk (CD) or DVD (digital versatile disk), or flash memory. The computer readable medium may be any combination of such storage or transmission devices.
Computer programs may also be encoded and transmitted using carrier signals adapted for transmission via wired, optical, and/or wireless networks conforming to a variety of protocols, including the Internet. As such, a computer readable medium may be created using a data signal encoded with such programs. Computer readable media encoded with the program code may be packaged with a compatible device or provided separately from other devices (for example, via Internet download). Any such computer readable medium may reside on or within a single computer program product (such as a hard drive, a CD, or an entire computer system), and may be present on or within different computer program products within a system or network. A computer system may include a monitor, printer, or other suitable display for providing interaction and display with the user.
Any of the methods referred to in this disclosure may be totally or partially performed with a computer system including a processor, which can be configured to perform the steps. Thus, embodiments can be directed to computer systems configured to perform the steps of any of the methods described here, potentially with different components performing a respective steps or a respective group of steps. Although presented as numbered steps, steps of methods herein can be performed at a same time or in a different order. Portions of these steps may be used with portions of other steps from other methods. Also, all or portions of a step may be optional. Additionally, any of the steps of any of the methods can be performed with modules, circuits, or other means for performing these steps.
The invention has been described and illustrated in this disclosure with reference to particular embodiments for the benefit and convenience of the reader. Discussion of various aspects of products and methods does not limit manufacture or use of the claimed invention except where expressly indicated.
The devices and methods of the invention may be substituted and adapted for use in different contexts for different objectives using different materials, elements, and steps without undue experimentation, thus achieving any or all of the benefits of the invention without departing from the scope of what is claimed.
In the United States of America and elsewhere as permitted by law, each publication and patent document cited in this disclosure is incorporated into the disclosure by reference in its entirety for all purposes.