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WO2018037289A3 - Systems and methods for computational demultiplexing of genomic barcoded sequences - Google Patents

Systems and methods for computational demultiplexing of genomic barcoded sequences Download PDF

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Publication number
WO2018037289A3
WO2018037289A3 PCT/IB2017/001547 IB2017001547W WO2018037289A3 WO 2018037289 A3 WO2018037289 A3 WO 2018037289A3 IB 2017001547 W IB2017001547 W IB 2017001547W WO 2018037289 A3 WO2018037289 A3 WO 2018037289A3
Authority
WO
WIPO (PCT)
Prior art keywords
contig
graph
unique
raw reads
demultiplexing
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/IB2017/001547
Other languages
French (fr)
Other versions
WO2018037289A2 (en
Inventor
Gil BEN-ZVI
Omer BARAD
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
EnerginR Technologies 2009 Ltd
Original Assignee
EnerginR Technologies 2009 Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by EnerginR Technologies 2009 Ltd filed Critical EnerginR Technologies 2009 Ltd
Publication of WO2018037289A2 publication Critical patent/WO2018037289A2/en
Publication of WO2018037289A3 publication Critical patent/WO2018037289A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly

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  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

In some embodiments, the present invention is a method which includes: obtaining a whole genome of an organism, fragmenting the whole genome of the organism to produce a plurality of raw reads, tagging each raw read of the plurality of raw reads to produce a plurality of tagged raw reads, constructing a debruijn graph from the plurality of tagged raw reads, extrapolating data from the constructed debruijn graph to generate a plurality of contigs, mapping the at least one unique barcode of the plurality of unique barcodes to a corresponding unique contig or a corresponding supplementary contig, organizing each contig of the plurality of contigs according to the plurality of unique barcodes, identifying a connection weight using the Debruijn graph, filtering the connection weight in the graph with low weight, and assembling a DNA sequence order, wherein the DNA sequence order is organized from a maximum OS to a minimum OE.
PCT/IB2017/001547 2016-02-10 2017-02-10 Systems and methods for computational demultiplexing of genomic barcoded sequences Ceased WO2018037289A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662293470P 2016-02-10 2016-02-10
US62/293,470 2016-02-10

Publications (2)

Publication Number Publication Date
WO2018037289A2 WO2018037289A2 (en) 2018-03-01
WO2018037289A3 true WO2018037289A3 (en) 2018-06-07

Family

ID=61246488

Family Applications (1)

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PCT/IB2017/001547 Ceased WO2018037289A2 (en) 2016-02-10 2017-02-10 Systems and methods for computational demultiplexing of genomic barcoded sequences

Country Status (1)

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WO (1) WO2018037289A2 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023288018A2 (en) * 2021-07-14 2023-01-19 Ultima Genomics, Inc. Barcode selection
CN115331733B (en) * 2022-10-14 2023-03-24 青岛百创智能制造技术有限公司 Method and device for analyzing sequencing data of space transcriptome chip

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150111208A1 (en) * 2013-10-18 2015-04-23 Good Start Genetics, Inc. Methods for assessing a genomic region of a subject
US20150286775A1 (en) * 2013-12-18 2015-10-08 Pacific Biosciences Of California, Inc. String graph assembly for polyploid genomes
US20150363550A1 (en) * 2013-02-01 2015-12-17 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
US20150379196A1 (en) * 2014-06-26 2015-12-31 10X Technologies, Inc. Processes and systems for nucleic acid sequence assembly
WO2016061006A2 (en) * 2014-10-13 2016-04-21 Ntherma Corporation Carbon nanotubes as a thermal interface material
WO2016149261A1 (en) * 2015-03-16 2016-09-22 Personal Genome Diagnostics, Inc. Systems and methods for analyzing nucleic acid

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150363550A1 (en) * 2013-02-01 2015-12-17 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
US20150111208A1 (en) * 2013-10-18 2015-04-23 Good Start Genetics, Inc. Methods for assessing a genomic region of a subject
US20150286775A1 (en) * 2013-12-18 2015-10-08 Pacific Biosciences Of California, Inc. String graph assembly for polyploid genomes
US20150379196A1 (en) * 2014-06-26 2015-12-31 10X Technologies, Inc. Processes and systems for nucleic acid sequence assembly
WO2016061006A2 (en) * 2014-10-13 2016-04-21 Ntherma Corporation Carbon nanotubes as a thermal interface material
WO2016149261A1 (en) * 2015-03-16 2016-09-22 Personal Genome Diagnostics, Inc. Systems and methods for analyzing nucleic acid

Also Published As

Publication number Publication date
WO2018037289A2 (en) 2018-03-01

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