Unlock instant, AI-driven research and patent intelligence for your innovation.

Efficient base determination in sequencing reactions

A technology for sequencing and sequencing, applied in 1/026,337, 61/061 submitted on March 13, 6 fields submitted on March 12, 2008, which can solve the problems of sequencing efficiency limitation, limited signal-to-noise ratio, unsuitability, etc.

Active Publication Date: 2013-03-27
COMPLETE GENOMICS INC
View PDF50 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Conventional sequencing methods are usually limited to the determination of dozens of nucleotides before the signal is significantly degraded, so the overall sequencing efficiency is greatly limited
Conventional sequencing methods are also often limited by signal-to-noise ratios, making such methods unsuitable for single-molecule sequencing

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Efficient base determination in sequencing reactions
  • Efficient base determination in sequencing reactions
  • Efficient base determination in sequencing reactions

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0364] Embodiment 1: prepare DNBs

[0365] The following is an exemplary protocol for making DNBs (also referred to herein as "replicons") from nucleic acid templates of the invention comprising a target nucleic acid interspersed with one or more adapters. First, the single-stranded linear nucleic acid template is amplified with a phosphorylated 5' primer and a biotinylated 3' primer to obtain a biotin-labeled double-stranded linear nucleic acid template.

[0366] First, resuspend MagPrep-Streptavidin magnetic beads (Novagen Part. Prepare streptavidin magnetic beads in nuclease-free water). Place the centrifuge tubes in a magnetic centrifuge tube rack, allow the magnetic particles to settle, remove the supernatant and discard. The beads were then washed twice in 800 µl 1x Bead Binding Buffer and resuspended in 80 µl 1x Bead Binding Buffer. The amplified nucleic acid template from the PCR reaction was brought up to a volume of 60 μl, and 20 μl of 4x magnetic bead binding b...

Embodiment 2

[0372] Example 2: Single and dual c-PAL

[0373] Fully degenerate second anchor probes of different lengths were tested in a dual anchor probe detection system. The combination used was: 1) Standard one-of-a-kind anchor ligation using an anchor molecule and a 9-mer sequencing probe, wherein the anchor molecule binds the adapter adjacent to the target nucleic acid from 4 positions from the adapter. 2) use the same first anchor molecule and a double anchor molecule ligation comprising a degenerate 5-mer second anchor molecule and a 9-mer sequencing probe, starting at 9 sites from the adapter 3) using the same first anchor molecule and a second anchor molecule comprising a degenerate 6-mer and a double-anchor ligation of a 9-mer sequencing probe, starting at 10 sites from the adapter start the assay; and 4) use the same first anchor molecule and a double anchor molecule ligation comprising a degenerate 8-mer second anchor molecule and a 9-mer sequencing probe from 12 sites fro...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

The present invention relates to compositions and methods for nucleic acid identification and detection. The composition and method of the present invention include extracting target nucleic acid from a sample and performing fragmentation, using the fragmented target nucleic acid to generate target nucleic acid templates, and forming nucleic acid nanospheres through the amplification method of these target nucleic acid templates. The invention also relates to methods of detecting and identifying sequences using various sequencing applications including sequencing by ligation.

Description

[0001] Cross References to Related Applications [0002] This application claims U.S. Patent Applications 60 / 992,485 filed December 5, 2007, 61 / 026,337 filed February 5, 2008, 61 / 035,914 filed March 12, 2008, June 13, 2008 61 / 061,134, 61 / 116,193 filed November 19, 2008, 61 / 102,586 filed October 3, 2008, 12 / 265,593 filed November 5, 2008, and 12 / 11 / 08 filed November 6, 2008 266,385 priority, the aforementioned patent applications are hereby incorporated by reference in their entirety. Background of the invention [0003] Large-scale genome sequence analysis is a critical step toward understanding a variety of biological phenomena. The need for low-cost, high-throughput sequencing and resequencing has led to the development of new sequencing methods that employ parallel analysis of multiple nucleic acid targets simultaneously. [0004] Conventional sequencing methods are usually limited to determining dozens of nucleotides before the signal is significantly degraded, so the ov...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/68
CPCC12Q1/6874C12Q1/6834C12Q1/6827C12Q2531/125C12Q2525/179C12Q2521/501C12Q2525/151
Inventor 拉多杰·德玛纳克马修·卡洛安德鲁·斯帕克斯弗雷德里克·达尔克里福德·雷德
Owner COMPLETE GENOMICS INC