クロマチン相互作用データの分析用の方法および装置 - THE REGENTS OF THE UNIVERSITY OF MICHIGAN

Title:

クロマチン相互作用データの分析用の方法および装置

Document Type and Number:

Japanese Patent JP7350002

Kind Code:

B2

Abstract:

To analyze spatial organization of chromatin a computing device may compile genomic element contacts or reads into variable size bins using a binary search tree. The bins may be selected to each represent a different cutsite increment or functional element within a genome, such as a gene, TAD, chromatin state segment, loop domain, chromatin domain, etc. Two sets of bins are selected to generate a squared genome matrix of bin pairs, where each set represent an axis of the matrix. Then a normalization method is applied to the interaction frequencies for the bin pairs having variable size and/or shape to generate normalized interaction frequencies for each bin pair. The normalized interaction frequencies may be used to identify bin pairs having enriched and depleted contacts for a variety of analyses, including the detection of target genes of genomic variants, as well as genome wide analysis of contacts.

Inventors:

Ali, Arin-Foyer
Brian, Dee Athi
Gerald A. Higgins
Alex, Aid

Application Number:

JP2020551384A

Publication Date:

September 25, 2023

Filing Date:

March 21, 2019

Export Citation:

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Assignee:

THE REGENTS OF THE UNIVERSITY OF MICHIGAN

International Classes:

G16B20/00

Foreign References:

WO2009155443A2

Other References:

Jesse R. Dixon, et al.,Topological domains in mammalian genomes identified by analysis of chromatin interactions,Nature [online],2012年04月11日,Vol.485,Pages 376-380,[検索日:2023年4月21日],
Boyan Bonev, et al.,Multiscale 3D Genome Rewiring during Mouse Neural Development,Cell [online],2017年10月19日,Vol.171,Pages 557-572, e1-8,[検索日:2023年4月21日],
John C. Stansfield,HiCcompare: an R-package for joint normalization of Hi-C datasets,BMC Bioinformatics [online],Vol.19 No.279,2018年07月31日,Pages 1-10,[検索日:2023年4月21日],
William Stafford Noble, et al.,Software tools for visualizing Hi-C data,Genome Biology [online],2017年02月03日,Vol.18, No.26,Pages 1-9,[検索日:2023年4月21日],
Adriana Miele, et al.,Mapping cis- and trans- chromatin interaction networks using chronosome conformation capture (3C),Method in Molecular Biology [online],2013年12月30日,Vol.464,Pages 1-17,[検索日:2023年4月21日],

Attorney, Agent or Firm:

Yukitaka Nakamura
Satoru Asakura
Takeshi Sekine
Akira Akaoka
Tomoya Deguchi

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