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Next Generation Sequencing Libraries

A sequencing library, next-generation technology, applied in the field of preparing next-generation sequencing libraries containing overlapping DNA fragments and sequencing one or more target nucleic acids, can solve problems such as performance and quality degradation, saturated output capacity, etc., to achieve reduced sequencing time, effect of time reduction

Inactive Publication Date: 2019-08-06
ABBOTT MOLECULAR INC A CORP ORGANISED & EXISTING UNDER THE LAWS OF THE STATE OF DELAWARE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Additionally, the performance and quality of most cycle sequencing technologies degrades substantially after ~100 bases have been determined, introducing a degree of uncertainty associated with individual sequence reads longer than ~100 bases and the longer sequence assemblies in which they are used
Due to these quality and time constraints of current NGS platforms, the increasing demand for long, high-quality nucleotide sequences saturates the output capacity of the installed base of sequencing devices

Method used

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Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0257] Example 1 - Comparison to Illumina MiSeq

[0258] During the development of the technology presented herein, calculations were performed to compare the technology presented here (Tables 1 and 2, "SOD Libraries") with the conventional technology provided by Illumina in the MiSeq platform (Tables 1 and 2, "Illumina Amplicon Libraries") ”) performance. Data were collected from two scripts that differed, for example, in the number of samples per run, the standard used to measure throughput, etc. (see Tables 1 and 2).

[0259] As shown in Tables 1 and 2, the technology described herein reduces instrument run time, has higher throughput and produces a higher percentage of reads with a mass score greater than Q30 relative to NGS library construction using Illumina technology.

[0260] Table 1 - Comparison to Illumina MiSeq (Targeted Sequencing: Amplicon Panel)

[0261]

[0262] a) MiSeq Reagent Kit v2: duplex scanning, 12–15 million cluster-pass filters

[0263] b) To co...

example 2

[0276] Example 2 – Comparison to Ion Torrent PGM (Targeted Sequencing: Amplicon Panel)

[0277] During the development of the technology presented herein, calculations were performed to compare the technology presented here (Tables 3 and 4, "SOD Libraries") with the conventional technology provided by Ion Torrent in the PGM platform (Tables 3 and 4, "Ion Amplicon library") performance. Data were collected from two scripts that differed, for example, in the number of samples per run, the standard used to measure throughput, etc. (see Tables 3 and 4).

[0278] As shown in Tables 3 and 4, the techniques described herein reduce instrument run time and generate a higher percentage of reads with quality scores greater than Q20 relative to NGS library construction using Ion Torrent technology.

[0279] Table 3 - Comparison with Ion Torrent PGM

[0280]

[0281] a) PGM 400 bp Sequencing Kit v2

[0282] b) To cover the entire 400 bp amplicon, perform 1 × 400 bp bidirectional sequ...

example 3

[0295] Example 3 - Comparison of Long Read Techniques

[0296] Tables 5 and 6 compare the performance of the techniques presented herein with conventional techniques for sequencing long amplicons of approximately 1000 bp (Table 5) and 2000 bp (Table 6). Run time for this technique does not increase with amplicon size, as the read size is always ~30–50 bases regardless of the size of the target nucleic acid being sequenced. In some embodiments, the techniques provided herein generate 2000-bp sequences in an order of magnitude less time than conventional techniques (see, eg, Table 6). In some embodiments, the techniques provided herein provide longer sequence reads in the same runtime as conventional techniques.

[0297] Table 5 - Comparison of long amplicon sequencing 1000 bp

[0298] SOD library a

Illumina TruSeq Libraries Ion gDNA library Number of samples / run 8 8 1 Number of amplicons / sample 50 50 50 Average size of amplicons (bp) ...

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Abstract

Provided herein are technologies related to next generation sequencing and in particular, but not exclusively, to methods and compositions for preparing next generation sequencing libraries comprising short overlapping DNA fragments and using the libraries to sequence one or more target nucleic acids.

Description

[0001] This application claims priority to US Provisional Patent Application Serial No. 61 / 867,224, filed August 19, 2013, which is hereby incorporated by reference in its entirety. [0002] field of invention [0003] Provided herein are technologies related to next-generation sequencing and in particular, but not exclusively, to methods, compositions, kits, and methods for preparing a next-generation sequencing library comprising overlapping DNA fragments and using the library to sequence one or more target nucleic acids. System technology. [0004] Background of the invention [0005] Nucleic acid sequences encode information necessary for an organism to function and reproduce. Determining such sequences is therefore a useful tool in the pure study of how and where an organism lives, as well as in applied sciences such as drug development. In medicine, sequencing tools are used to diagnose and develop treatments for a variety of pathologies, including cancer, infectious di...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C40B40/06
CPCC12Q1/6806C12Q2525/161C12Q2525/186C12Q2525/191C12Q2525/204C12Q2525/307C12Q2535/122C12Q2563/179C12N15/10C40B40/06C12Q1/68C12N15/1086C40B50/06
Inventor D.H.金
Owner ABBOTT MOLECULAR INC A CORP ORGANISED & EXISTING UNDER THE LAWS OF THE STATE OF DELAWARE