Systems and methods for visualizing structural variation and phasing information

• US 10,650,912 B2
• Filed: 01/13/2016
• Issued: 05/12/2020
• Est. Priority Date: 01/13/2015
• Status: Active Grant

• Current Assignee: 10X Genomics Incorporated
• Original Assignee: 10X Genomics Incorporated
• Inventors: Schnall-Levin, Michael, Wong, Alexander, Stafford, David Luther Alan
• Primary Examiner(s): Zeman, Mary K
• Application Number:
  US14/995,090
• Publication Number:
  US 20160203196A1
• Time in Patent Office: 1,581 Days
• 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 30/20 Sequence assembly
• CPC Class Codes: G16B 35/10 Design of libraries
• 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 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16C 99/00 Subject matter not provided for in other groups of this subclass

Abstract

A system for providing structural variation or phasing information is provided. The system accesses a nucleic acid sequence dataset corresponding to a target nucleic acid in a sample. The dataset comprises a header, synopsis, and data section. The data section comprises a plurality of sequencing reads. Each sequencing read comprises a first portion corresponding to a subset of the target nucleic acid and a second portion that encodes an identifier for the sequencing read from a plurality of identifiers. One or more programs in the memory of the system use a microprocessor of the system to provide a haplotype visualization tool that receives a request for structural variation or phasing information from the dataset. The request is evaluated against the synopsis thereby identifying portions of the data section. Structural variation or phasing information is formatted for display in the haplotype visualization tool using the identified portions of the data section.

Claims

1. A system for providing structural variation and phasing information over a network connection to a remote client computer, the system comprising one or more microprocessors, a persistent memory and a non-persistent memory, the persistent memory and the non-persistent memory collectively storing one or more nucleic acid sequencing datasets, wherein

each respective nucleic acid sequencing dataset in the one or more nucleic acid sequencing datasets corresponds to at least one target nucleic acid in a respective sample in a plurality of samples, wherein

the respective sample is associated with a genome of at least one species,

the respective nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,

the data section comprises a plurality of sequencing reads,

each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of at least one target nucleic acid in the respective sample and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,

each respective identifier is independent of the sequence of the at least one target nucleic acid, and

the plurality of sequencing reads collectively include the plurality of identifiers, and wherein

the persistent memory and the non-persistent memory further collectively store one or more programs that use the one or more microprocessors to:

provide a visualization tool for installation on the remote client computer;

obtain a request, received from the remote client computer from a user, over a network connection, for structural variation and phasing information using a first dataset in the one or more datasets; and

responsive to obtaining the request, automatically parse the request by;

(i) loading the header and the synopsis of the first dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,

(ii) comparing the request to the synopsis of the first dataset thereby identifying one or more portions of the data section of the first dataset,

(iii) loading the one or more identified portions of the data section into non-persistent memory, wherein the loading loads less than the entirety of the data section,

(iv) formatting structural variation and phasing information for display on the client computer using the first dataset, and

(v) transmitting the formatted structural variation and phasing information over the network connection to the remote client computer for display on the remote client computer.

4. The system of claim 1, wherein the header delineates a plurality of components in the respective nucleic acid sequencing dataset.

5. The system of claim 4, wherein the plurality of components comprises two or more components selected from the group consisting of a summary, an index to variant call data, a phase block track, a refseq index track, a gene track, an exon track, an index to read data, a structural variant dataset track, an index to a target dataset, and an index to a fragment dataset.

6. The system of claim 5, wherein the plurality of components comprises the summary and wherein the summary comprises two or more items in the group consisting of:

a percentage of known SNPs phased in the respective nucleic acid sequencing dataset,

a longest phase block in the respective nucleic acid sequencing dataset,

a number of unique barcodes used in the respective nucleic acid sequencing dataset,

an average fragment length in the respective nucleic acid sequencing dataset,

a mean of the average fragment length in the respective nucleic acid sequencing dataset,

a percentage of fragments greater than a lower threshold in the respective nucleic acid sequencing dataset,

a fragment length histogram in the respective nucleic acid sequencing dataset,

an N50 phase block size in the respective nucleic acid sequencing dataset,

a phase block histogram in the respective nucleic acid sequencing dataset,

a number of sequence reads represented by respective the nucleic acid sequencing dataset,

a median insert size in the respective nucleic acid sequencing dataset,

a median depth in the respective nucleic acid sequencing dataset,

a percent of the target genome with zero coverage in the respective nucleic acid sequencing dataset,

a mapped reads percentage for the respective nucleic acid sequencing dataset,

a PCR duplication percentage for the respective nucleic acid sequencing dataset,

a coverage histogram for the in the respective nucleic acid sequencing dataset,

an identity of a test nucleic acid that forms the basis for the respective nucleic acid sequencing dataset,

a genome source for the respective nucleic acid sequencing dataset,

a sex of an organism that originated the at least one test nucleic acid of the respective nucleic acid sequencing dataset,

a sex of the organism that originate the respective sample of the in the respective nucleic acid sequencing dataset,

a dataset file format version of the in the respective nucleic acid sequencing dataset, and

a pointer to a plurality of structural variant calls made for the respective nucleic acid sequencing dataset.

7. The system of claim 5, wherein the plurality of components comprises the index to variant call data that provides a correspondence between respective ranges of the genome of the species to offsets in the data section where variant call data for the respective ranges is found.

8. The system of claim 5, wherein the plurality of components comprises the phase block track and wherein the phase block track comprises (i) a dictionary and (ii) a track data section comprising phase information for one or more chromosomes in the genome of the at least one species.

9. The system of claim 5, wherein the plurality of components comprises the refseq index, wherein the refseq index comprises an index of a plurality of molecular variation identifiers that are called in the sample.

10. The system of claim 5, wherein the plurality of components comprises the gene track and wherein the gene track comprises (i) a gene track dictionary and (ii) a gene track data section.

11. The system of claim 5, wherein the plurality of components comprises the index to read data wherein the index to read data comprises a lookup table between a respective identifier in the plurality of identifiers and a shortened version of the respective identifier.

12. The system of claim 5, wherein

the plurality of components comprises the structural variant dataset track, and

the structural variant dataset track comprises (i) a dictionary and (ii) a track data section comprising structural variant call information identified in the plurality of sequencing reads.

13. The system of claim 12, wherein the dictionary comprises a plurality of names, and for each respective name in the plurality of names, an offset into the track data where records for the corresponding name are found.

14. The system of claim 13, wherein

the track data section comprises a plurality of structural variant records, and

each structural variant record in the plurality of structural variant records represents a structural variant call made in the at least one target nucleic acid in the sample.

15. The system of claim 14, wherein

each respective structural variant record in the plurality of structural variant records is represented by a node in a plurality of nodes in a respective interval tree in a plurality of interval trees, and

each interval tree in the plurality of interval trees represents a chromosome in a plurality of chromosomes for the species.

16. The system of claim 5, wherein

the plurality of components comprises the index to the target dataset,

the target dataset comprises the regions of the at least one target nucleic acid in the sample that were selected for sequencing in the respective nucleic acid sequencing dataset,

the target dataset is indexed by a target dataset index stored in the synopsis, and

the target dataset is stored in the data section.

17. The system of claim 5, wherein

the plurality of components comprises the index to the fragment dataset,

the fragment dataset comprises a length, chromosomal position, identifier, and phase of each fragment of the at least one target nucleic acid in the sample,

the fragment dataset is indexed by a fragment dataset index stored in the synopsis, and

the fragment dataset is stored in the data section.

18. The system of claim 1, wherein the request is for phasing information in a region of the genome and the formatted phasing information includes a graphic representation comprising:

a first haplotype track corresponding to a first parental haplotype of a first species in the at least one species in the region of the genome for the first dataset,

a second haplotype track, corresponding to a second parental haplotype of the first species in the region of the genome for the first dataset,

an indeterminate track corresponding to regions of the at least one nucleic acid sample that have not been assigned a parental haplotype in the region of the genome for the first dataset.

19. The system of claim 18, wherein the graphic representation further comprises a graphic representation of each gene that is in the region of the genome.

20. The system of claim 18, wherein the graphic representation further comprises a coverage track for the region of the genome, wherein the coverage track comprises a plurality of vertical bars, and wherein each respective vertical bar in the plurality of vertical bars indicates an average coverage-per-base in the first dataset for a corresponding portion of the genome under the bar.

21. The system of claim 1, wherein the request is converted, without human intervention, to genomic coordinates by comparison of the request against one or more lookup tables that match alphanumeric entries of genes to genomic coordinates.

22. The system of claim 1, wherein the respective sample is associated with a genome of a plurality of species and includes at least a portion of the genome of a first species and a portion of the genome of the second species.

2. A system for providing structural variation and phasing information, the system comprising one or more microprocessors, a persistent memory and a non-persistent memory, the persistent memory and the non-persistent memory collectively storing one or more nucleic acid sequencing datasets, wherein

each respective nucleic acid sequencing dataset in the one or more nucleic acid sequencing datasets corresponds to at least one target nucleic acid in a respective sample in a plurality of samples, wherein

the respective sample is associated with a genome of at least one species,

the respective nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,

the data section comprises a plurality of sequencing reads,

each respective sequencing read in the plurality of sequencing reads comprises a nucleic sequence comprising a first portion that corresponds to a subset of at least one target nucleic acid in the respective sample and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,

each respective identifier is independent of the sequence of the at least one target nucleic acid, and

the plurality of sequencing reads collectively include the plurality of identifiers, and wherein

the persistent memory and the non-persistent memory further collectively store one or more programs that use the one or more microprocessors to:

provide a visualization tool;

obtain a request from a user, through the visualization tool, for structural variation and phasing information using a first dataset in the one or more datasets,

responsive to obtaining the request, automatically parse the request by;

(i) loading the header and the synopsis of the first dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,

(ii) comparing the request for sequence information to the synopsis of the first dataset thereby identifying one or more portions of the data section of the first dataset,

(iii) loading the one or more identified portions of the data section into non-persistent memory, wherein the loading loads less than the entirety of the data section,

(iv) formatting structural variation and phasing information for display in the visualization tool using the first dataset, and

(v) displaying the formatted structural variation and phasing information in the visualization tool.

3. A system for obtaining structural variation and phasing information over a network connection from a remote computer, wherein the system comprises one or more microprocessors, and a memory that stores one or more programs, wherein the one or more programs use the one or more microprocessors to execute a method comprising:

(A) invoking a visualization tool;

(B) obtaining, through the visualization tool from a user, a request for structural variation and phasing information in a first nucleic acid sequencing dataset from among one or more nucleic acid sequencing datasets stored on the remote computer, wherein each respective nucleic acid sequencing dataset in the one or more nucleic acid sequencing datasets corresponds to at least one target nucleic acid in a respective sample in a plurality of samples, wherein

the respective sample is associated with a genome of at least one species,

the respective nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,

the data section comprises a plurality of sequencing reads,

each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of at least one target nucleic acid in the respective sample and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,

each respective identifier is independent of the sequence of the at least one target nucleic acid, and

the plurality of sequencing reads collectively include the plurality of identifiers;

(C) sending the request to the remote computer over the network connection, wherein the remote computer has persistent memory and non-persistent memory, thereby causing the remote computer to execute a method comprising;

(i) loading the header and the synopsis of the first dataset into the non-persistent memory if not already loaded into the non-persistent memory of the remote computer while retaining the data section in persistent memory,

(ii) comparing the request for sequence information to the synopsis of the first dataset thereby identifying one or more portions of the data section of the first dataset,

(iii) loading the one or more identified portions of the data section into non-persistent memory, wherein the loading loads less than the entirety of the data section, and

(iv) formatting structural variation and phasing information; and

(D) receiving the formatted structural variation and phasing information over the network connection from the remote computer for display in the visualization tool.