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Systems and methods for determining structural variation and phasing using variant call data

a variant call and variant naming technology, applied in the field of haplotype phasing and structural variant detection using nucleic acid sequencing data, can solve the problems of np-hard problem, existing algorithms not applicable to targeted sequencing data,

Pending Publication Date: 2021-09-23
10X GENOMICS
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  • Summary
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  • Claims
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AI Technical Summary

Benefits of technology

This approach enables efficient detection of structural variations and haplotype phasing in sequencing data, overcoming the limitations of existing methods and improving the ability to diagnose and treat genetic disorders with reduced computational complexity.

Problems solved by technology

This limitation makes existing algorithms not applicable to targeted sequencing data, such as whole exome sequencing (WES) data.
Such a problem has been shown to be NP-hard.

Method used

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  • Systems and methods for determining structural variation and phasing using variant call data
  • Systems and methods for determining structural variation and phasing using variant call data
  • Systems and methods for determining structural variation and phasing using variant call data

Examples

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example 1

[0333]Sample preparation. FIG. 8 provides an example of sample preparation in accordance with an exemplary embodiment of the present disclosure. The GemCode Platform massively partitions and barcodes DNA, producing sequencing-ready libraries with >100,000 unique barcodes. Custom algorithms use this barcode information to map reads back to original, long molecules of DNA, creating linked reads that span many tens of kilobases. Long template molecules from ˜1 ng of gDNA are randomly distributed across >100,000 barcoded partitions, giving <10 fg (<0.3% of the genome) per partition. Each partition carries primers with barcodes that are constant within a partition, but distinct across partitions. An amplification reaction creates barcoded short read library fragments within each partition. The resulting library is compatible with standard exome capture, while preserving long range linkage information. In particular, the resulting libraries are sample-indexed and can be whole genome seque...

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Abstract

Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.

Description

CROSS REFERENCE TO RELATED APPLICATIONS[0001]This application is a continuation of U.S. patent application Ser. No. 15 / 019,928, entitled “Systems and Methods for Determining Structural Variation and Phasing Using Variant Call Data,” filed Feb. 9, 2016, now U.S. Pat. No. 10,854,315, which is hereby incorporated by reference in its entirety.[0002]This application claims priority to U.S. Provisional Patent Application 62 / 238,077, entitled “Systems and Methods for Determining Structural Variation Using Probabilistic Models,” filed Oct. 6, 2015, which is hereby incorporated by reference in its entirety.[0003]This application also claims priority to U.S. Provisional Patent Application 62 / 113,693, entitled “Systems and Methods for Determining Structural Variation,” filed Feb. 9, 2015, which is hereby incorporated by reference in its entirety.[0004]This application also claims priority to U.S. Provisional Patent Application 62 / 120,247, entitled “Systems and Methods for Implementing Linked R...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): G16B20/20G16B30/00G16B20/00G16B30/10
CPCG16B20/20G16B30/10G16B20/00G16B30/00C12Q1/6837C12Q1/6869A61P3/00A61P43/00C12Q2537/165C12Q2525/161
Inventor KYRIAZOPOULOU-PANAGIOTOPOULOU, SOFIAMARKS, PATRICKSCHNALL-LEVIN, MICHAELZHENG, XINYINGJAROSZ, MIRNASAXONOV, SERGEGIORDA, KRISTINAMUDIVARTI, PATRICEORDONEZ, HEATHERTERRY, JESSICAHEATON, WILLIAM HAYNES
Owner 10X GENOMICS
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