Title:
METHOD FOR PERFORMING QUANTITATIVE ANALYSIS ON SUBGROUP IN SPECIFIC GROUP
Document Type and Number:
WIPO Patent Application WO/2018/086045
Kind Code:
A1
Abstract:
A method for performing quantitative analysis on a subgroup in a specific group. Specifically, the method comprises: (1) providing reference genome sequence data (a), a reference SNP matrix (b) and metagenome sequencing data of a specific group; (2) comparing the metagenome sequencing data with the reference genome sequence data of the specific group, so as to obtain the comparison result; (3) constructing a frequency matrix according to site information of the reference SNP matrix;(4) performing binarization processing on the reference SNP matrix according to the frequency matrix, so as to obtain a binarized SNP matrix; and (5) obtaining a relative abundance of each subgroup in the specific group by means of a restricted linear model and according to the frequency matrix, the binarized SNP matrix, a theoretical base frequency vector (x) and an observation base frequency vector (y), so as to obtain the quantitative analysis result of the subgroup in the specific group.
Inventors:
PENG YE (CN)
LI JUNHUA (CN)
TANG SHANMEI (CN)
ZHANG HUI (CN)
LI JUNHUA (CN)
TANG SHANMEI (CN)
ZHANG HUI (CN)
Application Number:
PCT/CN2016/105372
Publication Date:
May 17, 2018
Filing Date:
November 10, 2016
Export Citation:
Assignee:
BGI SHENZHEN (CN)
International Classes:
G06F19/20; G06F19/22
Foreign References:
| CN103955629A | 2014-07-30 | |||
| CN106055924A | 2016-10-26 |
Other References:
CHEN, BO ET AL.: "Features Extraction and Dimensions Reduction in Metagenomic Binning Problem", COMPUTER SYSTEMS & APPLICATIONS, vol. 24, no. 11, 31 December 2015 (2015-12-31), pages 31 - 37
SAHL, J.W. ET AL.: "Phylogenetically Typing Bacterial Strains from Partial SNP Genotypes Observed from Direct Sequencing of Clinical Specimen Metagenomic Data", GENOME MEDICINE, vol. 7, no. 52, 9 June 2015 (2015-06-09), pages 1 - 13, XP055503133
LUO, C.W. ET AL.: "ConStrains Identifies Microbial Strains in Metagenomic Datasets.", NAT. BIOTECHNOL., vol. 33, no. 10, October 2015 (2015-10-01), pages 1045 - 1052, XP055503134
ALEXEEV, D. ET AL.: "Bacterial Rose Garden for Metagenomic SNP-Based Phylogeny Visualization", BIODATA MINING, vol. 8, no. 10, 21 March 2015 (2015-03-21), pages 1 - 12, XP021218346
NAYFACH, S. ET AL.: "An Integrated Metagenomics Pipeline for Strain Profiling Reveals Novel Patterns of Bacterial Transmission and Biogeography", GENOME RESEARCH, vol. 26, no. 11, November 2016 (2016-11-01), pages 1612 - 1625, XP055503139
SAHL, J.W. ET AL.: "Phylogenetically Typing Bacterial Strains from Partial SNP Genotypes Observed from Direct Sequencing of Clinical Specimen Metagenomic Data", GENOME MEDICINE, vol. 7, no. 52, 9 June 2015 (2015-06-09), pages 1 - 13, XP055503133
LUO, C.W. ET AL.: "ConStrains Identifies Microbial Strains in Metagenomic Datasets.", NAT. BIOTECHNOL., vol. 33, no. 10, October 2015 (2015-10-01), pages 1045 - 1052, XP055503134
ALEXEEV, D. ET AL.: "Bacterial Rose Garden for Metagenomic SNP-Based Phylogeny Visualization", BIODATA MINING, vol. 8, no. 10, 21 March 2015 (2015-03-21), pages 1 - 12, XP021218346
NAYFACH, S. ET AL.: "An Integrated Metagenomics Pipeline for Strain Profiling Reveals Novel Patterns of Bacterial Transmission and Biogeography", GENOME RESEARCH, vol. 26, no. 11, November 2016 (2016-11-01), pages 1612 - 1625, XP055503139
Attorney, Agent or Firm:
XU & PARTNERS, LLC. (CN)
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