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Methods and compositions for targeted nucleic acid sequencing

a nucleic acid and composition technology, applied in combinational chemistry, biochemistry apparatus and processes, library member identification, etc., can solve the problems of increasing costs, time and labor, and high cost of genomic analysis on a whole genome level, and achieve high-accuracy sequencing reactions.

Inactive Publication Date: 2016-05-05
10X GENOMICS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

The present invention provides methods for sequencing specific parts of a genome by distributing individual nucleic acid molecules into discrete partitions and fragmenting them to create fragments with a common barcode. These fragments are then captured on a surface and sequenced using a library of probes directed to the specific parts of the genome. The methods can be used to obtain sequence information from targeted parts of the genome while keeping track of the molecular context. The technical effect of this invention is the ability to accurately sequence specific parts of the genome with high accuracy and with minimal loss of information about the surrounding molecular context.

Problems solved by technology

Such genetic analysis on a whole genome level is costly not only monetarily but also in time and labor.
These costs increase with protocols involving analyses of separate individual DNA samples.

Method used

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  • Methods and compositions for targeted nucleic acid sequencing
  • Methods and compositions for targeted nucleic acid sequencing
  • Methods and compositions for targeted nucleic acid sequencing

Examples

Experimental program
Comparison scheme
Effect test

example 1

Whole Exome Capture and Sequencing: NA12878

[0138]Genomic DNA from the NA12878 human cell line was subjected to size based separation of fragments using a Blue Pippin DNA sizing system to recover fragments that were greater than or equal to approximately 10 kb in length. The size selected sample nucleic acids were then copartitioned with barcode beads in aqueous droplets within a fluorinated oil continuous phase using a microfluidic partitioning system (See, e.g., U.S. patent application Ser. No. 14 / 682,952, filed Apr. 9, 2015, and incorporated herein by reference in its entirety for all purposes), where the aqueous droplets also included the dNTPs, thermostable DNA polymerase and other reagents for carrying out amplification within the droplets, as well as DTT for releasing the barcode oligonucleotides from the beads. This was repeated both for 1 ng of total input DNA and 2 ng of total input DNA. The barcode beads were obtained as a subset of a stock library that represented barcode...

example 2

Whole Exome Capture and Sequencing: NA19701 and NA19661

[0145]Genomic DNA from the NA19701 and NA19661 cell lines was prepared according to the methods described above in Example 1. Data, including phasing data, from those two cells lines is provided in the table below:

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Abstract

The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims the benefit of U.S. Provisional Application No. 62 / 072,164, filed Oct. 29, 2014, which is expressly incorporated herein by reference in its entirety for all purposes.BACKGROUND OF THE INVENTION[0002]The ability to sequence genomes accurately and rapidly is revolutionizing biology and medicine. The study of complex genomes, and in particular, the search for the genetic basis of disease in humans, involves genetic analysis on a massive scale. Such genetic analysis on a whole genome level is costly not only monetarily but also in time and labor. These costs increase with protocols involving analyses of separate individual DNA samples. Sequencing (and re-sequencing) of polymorphic areas in the genome that are linked to disease development will contribute greatly to the understanding of diseases, such as cancer, and therapeutic development and will help meet the pharmacogenomics challenge to identify the genes and funct...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68
CPCC12Q1/6874C12Q1/6806C12Q2535/122C12Q2537/159C12Q2565/514C12Q2563/179C12Q1/6837
Inventor JAROSZ, MIRNASCHNALL-LEVIN, MICHAELSAXONOV, SERGEHINDSON, BENJAMINZHENG, XINYING
Owner 10X GENOMICS
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