Patents by Inventor Chunyu GENG

Chunyu GENG has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 10316356
    Abstract: Provided is a method of constructing a sequencing library using an adaptor element in a bubble shape. The bubble-shaped adaptor is ligated to a DNA fragment respectively at the 3?-terminal and the 5?-terminal i.e., two bubble-shaped adaptors with same sequences are ligated in one step. The bubble-shaped adaptor-ligated product is then amplified with a primer complementary to the 3?-terminal of the long-chain nucleic acid of the bubble-shaped adaptor, so as to replace the non-paired sequence in the short-chain nucleic acid.
    Type: Grant
    Filed: November 21, 2014
    Date of Patent: June 11, 2019
    Assignee: MGI TECH CO., LTD.
    Inventors: Yuan Jiang, Kai Tian, Xia Zhao, Wenwei Zhang, Huaiqian Xu, Hui Jiang, Radoje Drmanac, Chunyu Geng
  • Publication number: 20180291371
    Abstract: Provided are a method for constructing a nucleic acid single-stranded cyclic library and the reagents used therein. By the combination of interruption via a transposase with a restricted nick translation reaction, the method realizes a simple and rapid nucleic acid single-stranded cyclic library construction.
    Type: Application
    Filed: November 26, 2014
    Publication date: October 11, 2018
    Applicant: BGI Shenzhen Co., Ltd.
    Inventors: Chunyu Geng, Ruoying Chen, Yuan Jiang, Xia Zhao, Rongrong Guo, Lingyu He, Yaqiao Li, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Publication number: 20180282800
    Abstract: Improved single molecule sequencing methods, compositions, and devices, are provided. In a first aspect, the present invention provides a multi-pass method of sequencing a target sequence using nanopore sequencing, the method comprising: i) providing a non-naturally occurring concatemer nucleic acid molecule comprising a plurality of copies of the target sequence; ii) nanopore sequencing at least three copies of the target sequence in the concatemer, thereby obtaining a multi-pass sequence dataset, wherein the multi-pass sequence dataset comprises target sequence datasets for the at least three copies of the target sequence; and iii) using the multi-pass sequence dataset to determine the target sequence.
    Type: Application
    Filed: November 10, 2015
    Publication date: October 4, 2018
    Applicant: BGI Shenzhen Co., Ltd.
    Inventors: Handong LI, Y. Tom TANG, Jing YU, Hui JIANG, Wenwei ZHANG, Guangyi FAN, He ZHANG, Kailong MA, Chunyu GENG
  • Publication number: 20180251813
    Abstract: Disclosed are a nucleic acid fragmentation method and a sequence combination. The method comprises the following steps: subjecting a denatured nucleic acid to annealing and an extension reaction by using a single-stranded 5?-end extension primer, wherein the single-stranded 5?-end extension primer comprises a sequencing platform adaptor sequence of a 5? end and a connected random sequence, and the random sequence is subjected to annealing on a random site of the denatured nucleic acid; and directionally connecting a double-stranded 3?-end adaptor sequence to the 3? end of the nucleic acid generated in the extension reaction, and carrying out denaturalization and purification to obtain a fragmented single-stranded nucleic acid with adaptor sequences on two ends.
    Type: Application
    Filed: October 13, 2014
    Publication date: September 6, 2018
    Applicant: BGI SHENZHEN CO., LIMITED
    Inventors: Hongyan HAN, Chunyu GENG, Guanying Guo, Wenwei ZHANG, Hui JIANG, Yuan JIANG
  • Patent number: 10023906
    Abstract: Provided in the present invention are a method for constructing a nucleic acid single-stranded cyclic library and reagent kit thereof. The method comprises the steps of using a transposase embedding complex to randomly break nucleic acids and connect a first linker; connecting a second linker at a gap; performing a first PCR reaction, wherein the 5? end of one of the primers has a first affinity tag, resulting in a product with two ends connected to different linker sequences; binding the product to a solid vector having a second affinity tag; degenerating and separating single strands having no affinity tag; and cyclizing the single strands.
    Type: Grant
    Filed: October 14, 2014
    Date of Patent: July 17, 2018
    Assignee: MGI Tech Co., Ltd.
    Inventors: Chunyu Geng, Rongrong Guo, Ruoying Chen, Lingyu He, Wenwei Zhang, Hui Jiang
  • Publication number: 20180163251
    Abstract: Provided are a target region enrichment method based on multiplex PCR, and a reagent, the method comprising: connecting a first linker and a second linker respectively at two ends of a nucleic acid segment containing target regions to be enriched so as to obtain a linker-connected product; performing a PCR amplification on the linker-connected product using a first primer specifically bound to the first linker and a second primer specifically bound to the second linker to obtain an amplified product, the first primer or the second primer having a first affinity label; capturing a single strand having the first affinity label in the amplified product using a solid phase carrier; performing single primer linear amplification using a third primer with the captured single strand as a template; performing exponential amplification using the third primer and the first primer, with the linearly amplified product as the template, to obtain a product containing the target regions.
    Type: Application
    Filed: December 9, 2015
    Publication date: June 14, 2018
    Applicants: BGI SHENZHEN, BGI SHENZHEN CO., LIMITED
    Inventors: Jing Guo, Rongrong GUO, Meiyan LI, Chunyu GENG, Hui JIANG
  • Publication number: 20180080092
    Abstract: Disclosed are a one-stop treatment method for breaking a nucleic acid by means of a transposase, and a reagent. The method of the present invention comprises the following steps: conducting random breaking of a nucleic acid by using a transposase-embedded complex, the transposase-embedded complex comprising a transposase and a first adaptor comprising a transposase identification sequence; adding a first reagent to conduct treatment, so as to break an absorption effect of the transposase to a target sequence of the nucleic acid; adding a second reagent to conduct treatment, so as to weaken the influence of the first reagent on a follow-up enzyme-catalyzed reaction; and conducting a PCR reaction by using a product generated after the second reagent treatment as a template component, so as to obtain a PCR product of a broken nucleic acid segment whose two ends are connected to adaptors.
    Type: Application
    Filed: October 14, 2014
    Publication date: March 22, 2018
    Applicant: BGI SHENZHEN CO., LIMITED
    Inventors: Chunyu GENG, Rongrong GUO, Ruoying CHEN, Yingxin ZHANG, Andrei ALEXEEV, Hui JIANG, Wenwei ZHANG
  • Publication number: 20180044667
    Abstract: Provided in the present invention are a method for constructing a nucleic acid single-stranded cyclic library and reagents thereof. The method comprises the steps of using a transposase embedding complex to randomly break nucleic acids and connect a first linker; connecting a second linker at a gap; performing a first PCR reaction, wherein the 5? end of one of the primers has a first affinity tag, resulting in a product with two ends connected to different linker sequences; binding the product to a solid vector having a second affinity tag; degenerating and separating single strands having no affinity tag; and cyclizing the single strands.
    Type: Application
    Filed: October 14, 2014
    Publication date: February 15, 2018
    Inventors: Chunyu Geng, Rongrong Guo, Ruoying Chen, Lingyu He, Wenwei Zhang, Hui Jiang
  • Patent number: 9890375
    Abstract: Provided are an isolated oligonucleotide and a use thereof in nucleic acid sequencing, wherein the isolated oligonucleotide comprises a first strand, wherein the 5?-end nucleotide of the first strand has a phosphate group, and the 3?-end nucleotide of the first strand is a dideoxynucleotide, and a second strand, wherein the 5?-end nucleotide of the second strand does not have a phosphate group, and the 3?-end nucleotide of the second strand is a dideoxynucleotide, wherein the first strand is longer than the second strand in length, and a double-stranded structure is formed between the first strand and the second strand.
    Type: Grant
    Filed: September 12, 2014
    Date of Patent: February 13, 2018
    Assignee: BGI SHENZHEN CO., LIMITED
    Inventors: Chunyu Geng, Dennis G. Ballinger, Yanyan Zhang, Shujin Fu, Lingyu He, Wenwei Zhang, Hui Jiang
  • Publication number: 20170356039
    Abstract: Provided are a vesicular linker and a single-chain cyclic library constructed by using the linker. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantages of high throughput sequencing, high accuracy and simple operations.
    Type: Application
    Filed: November 21, 2014
    Publication date: December 14, 2017
    Inventors: Yuan Jiang, Jing Guo, Xiaojun Ji, Chunyu Geng, Kai Tian, Xia Zhao, Huaiqian Xu, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Publication number: 20170292153
    Abstract: Provided are a method for breaking a nucleic acid and adding an adaptor by means of a transposase, and a reagent.
    Type: Application
    Filed: October 14, 2014
    Publication date: October 12, 2017
    Applicant: BGI SHENZHEN CO., LIMITED
    Inventors: Chunyu GENG, Ruoying CHEN, Rongrong GUO, Andrei ALEXEEV, Yingxin ZHANG, Hui JIANG, Wenwei ZHANG
  • Publication number: 20170275616
    Abstract: The present invention provides a primer for nucleic acid random fragmentation and a nucleic acid random fragmentation method. The primer consists of a plurality of upstream random primers and downstream random primers. The sequence composition of the upstream random primers is 5?-X-Y-3?, and the sequence composition of the downstream random primers is 5?-P-Y?-X?-close-3?, wherein Y and Y? are random sequences, X is all or part of sequences of a sequencing platform 5? end adaptor, X? is all or part of sequences of a sequencing platform 3? end adaptor, P is phosphorylation modification, and close is close modification. The primer of the present invention adopts double random anchoring of both the upstream random primers and the downstream random primers, and a DNA sample can be randomly broken.
    Type: Application
    Filed: October 17, 2014
    Publication date: September 28, 2017
    Applicant: BGI SHENZHEN
    Inventors: Chunyu GENG, Hongyan HAN, Guangying GUO, Wenwei ZHANG, Hui JIANG, Yuan JIANG
  • Publication number: 20170275609
    Abstract: Provided are an isolated oligonucleotide and a use thereof in nucleic acid sequencing, wherein the isolated oligonucleotide comprises a first strand, wherein the 5?-end nucleotide of the first strand has a phosphate group, and the 3?-end nucleotide of the first strand is a dideoxynucleotide, and a second strand, wherein the 5?-end nucleotide of the second strand does not have a phosphate group, and the 3?-end nucleotide of the second strand is a dideoxynucleotide, wherein the first strand is longer than the second strand in length, and a double-stranded structure is formed between the first strand and the second strand.
    Type: Application
    Filed: September 12, 2014
    Publication date: September 28, 2017
    Inventors: Chunyu Geng, Dennis G. Ballinger, Yanyan Zhang, Shujin Fu, Lingyu He, Wenwei Zhang, Hui Jiang
  • Publication number: 20170233728
    Abstract: Provided is a linker element and a method of using the linker element to construct a sequencing library, wherein the linker element consists of a linker A and a linker B, the linker A is obtained through the complementary pairing of a long nucleic acid strand and a short nucleic acid strand, the 5? end of the long strand has a phosphoric acid modification, and the 3? end of the short strand has an enclosed modification, with enzyme sites in the short strand; and the linker B is a nucleic acid single strand, and the 3? end thereof can be in a complementary pairing with the 5? end of the long strand of the linker A. Using the linker element of the present invention for constructing a sequencing library ensures the linking directionality of the linkers while solving the problems of fragment interlinking, linker self-linking and low linking efficiency, and reducing the purification reaction between steps, shortening the linking time and reducing costs.
    Type: Application
    Filed: October 14, 2014
    Publication date: August 17, 2017
    Inventors: Yuan JIANG, Chunyu GENG, Xia ZHAO, Shujin FU, Lingyu HE, Yaqiao LI, Xiaoshan SU, Fanzi WU, Wenwei ZHANG, Hui JIANG, Andrei ALEXEEV, Radoje DRMANAC