Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection

A genome and nucleic acid technology, applied in the field of genome assembly, haplotype phasing, and target-independent nucleic acid detection, can solve problems such as difficult data sets, and achieve a highly continuous scaffolding effect

Active Publication Date: 2018-08-03
DOVETAIL GENOMICS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, high-quality de novo assembly of these highly complex datasets is generally considered intractable

Method used

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  • Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
  • Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
  • Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection

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Experimental program
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Embodiment approach 89

[0430]Numbered embodiment 89 includes a method for generating a plurality of tagged sequences from a plurality of DNA molecules, the method comprising: (a) binding the plurality of DNA molecules to a plurality of association molecules; (b) cleaving the plurality of DNA molecules; DNA molecules to generate a plurality of DNA segments; (c) labeling at least a portion of the DNA segments to form a plurality of marked DNA segments; and (d) sequencing the marked DNA segments to obtain A sequence of a plurality of tags; wherein the plurality of associated molecules are not covalently modified with an affinity tag before or during steps (a) and (b). Numbered embodiment 90 includes the method of numbered embodiment 89, wherein prior to step (b), less than 40% of the DNA segments from the DNA molecule are joined to other DNA segments that do not share a common phosphodiester bond . Numbered embodiment 91 includes the method of any one of numbered embodiments 89-90, wherein prior to st...

Embodiment approach 158

[0432]Numbered embodiment 158 ​​includes a method for generating a plurality of tagged sequences from a plurality of DNA molecules, the method comprising: (a) obtaining a plurality of DNA molecules bound to a plurality of associated molecules; (b) cleaving the DNA molecules to generate at least a plurality of DNA segments; (c) labeling at least a portion of the DNA segments to form a plurality of marked DNA segments; and (d) sequencing the marked DNA segments to obtain a plurality of A labeled sequence; wherein the total amount of said plurality of DNA molecules is less than about 5 micrograms ([mu]g). Numbered embodiment 159 includes a method for generating a plurality of tagged sequences from a plurality of DNA molecules, the method comprising: (a) obtaining a plurality of DNA molecules bound to a plurality of associated molecules; (b) cleaving the DNA molecules to generate at least a plurality of DNA segments; (c) labeling at least a portion of the DNA segments to form a pl...

Embodiment approach 229

[0434] Numbered embodiment 229 includes a method of identifying a microbial host of an antibiotic resistance gene, the method comprising: a) obtaining a stabilized sample from an individual suffering from a condition exhibiting microbial antibiotic resistance; b) processing said stabilized sample to cleavage of double-stranded DNA in the stabilized sample; c) labeling the exposed DNA ends; d) ligating the labeled exposed DNA ends to form labeled paired ends; and e) sequencing the labeled paired ends to Paired sequences are generated; where the sequence adjacent to the antibiotic resistance gene sequence indicates the microbial host of the antibiotic resistance gene. Numbered embodiment 230 includes the method of numbered embodiment 229, wherein the stabilized sample has been crosslinked. Numbered embodiment 231 includes the method of any one of numbered embodiments 229-230, wherein the stabilized sample has been contacted with formaldehyde. Numbered embodiment 232 includes th...

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Abstract

The disclosure provides methods to assemble genomes of eukaryotic or prokaryotic organisms. The disclosure provides methods for haplotype phasing and meta-genomics assemblies. The disclosure providesa streamlined method for accomplishing these tasks, such that intermediates need not be labeled by an affinity label to facilitate binding to a solid surface. The disclosure also provides methods andcompositions for the de novo generation of scaffold information, linkage information, and genome information for unknown organisms in heterogeneous metagenomic samples or samples obtained from multiple individuals. Practice of the methods can allow de novo sequencing of entire genomes of uncultured or unidentified organisms in heterogeneous samples, or the determination of linkage information fornucleic acid molecules in samples comprising nucleic acids obtained from multiple individuals.

Description

[0001] cross reference [0002] This application claims U.S. Provisional Patent Application No. 62 / 243,576, filed October 19, 2015 (herein incorporated by reference in its entirety), U.S. Provisional Application No. 62 / 243,591, filed October 19, 2015 (incorporated by reference incorporated herein in its entirety), U.S. Provisional Application No. 62 / 255,953, filed November 16, 2015 (incorporated herein by reference in its entirety), and U.S. Provisional Patent Application No. 62, filed February 11, 2016 / 294,198 (incorporated herein by reference in its entirety). [0003] Statement Regarding Federally Funded Research [0004] This invention was made with US Government support under Contract No. 5R44HG008719-02 from the National Human Genome Research Institute. Background technique [0005] In theory and in practice, it is still difficult to generate high-quality, highly contiguous genome sequences. High-throughput sequencing allows the genetic analysis of organisms that ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6806C12Q1/6809C12Q1/6869G16B30/10G16B30/20G16B50/00
CPCC12Q1/6806C12Q1/6809C12Q1/6869G16B30/00G16B50/00G16B30/10G16B30/20Y02A90/10C12Q2521/301C12Q2523/101C12Q2535/122C12N15/11C12Q1/68C12N15/1065C12Q1/6874
Inventor 理查德·E·格林保罗·哈特利克里斯多佛·特罗尔闵艾艾
Owner DOVETAIL GENOMICS
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