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WO2019028189A3 - Determination of str length by short read sequencing - Google Patents

Determination of str length by short read sequencing Download PDF

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Publication number
WO2019028189A3
WO2019028189A3 PCT/US2018/044889 US2018044889W WO2019028189A3 WO 2019028189 A3 WO2019028189 A3 WO 2019028189A3 US 2018044889 W US2018044889 W US 2018044889W WO 2019028189 A3 WO2019028189 A3 WO 2019028189A3
Authority
WO
WIPO (PCT)
Prior art keywords
determination
short read
read sequencing
str
str length
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/US2018/044889
Other languages
French (fr)
Other versions
WO2019028189A2 (en
Inventor
Haibao TANG
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.)
Human Longevity Inc
Original Assignee
Human Longevity Inc
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 Human Longevity Inc filed Critical Human Longevity Inc
Publication of WO2019028189A2 publication Critical patent/WO2019028189A2/en
Publication of WO2019028189A3 publication Critical patent/WO2019028189A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • 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

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Artificial Intelligence (AREA)
  • Analytical Chemistry (AREA)
  • Bioethics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Hall/Mr Elements (AREA)

Abstract

Described herein are methods, software, and systems of determining a repeat length of a short tandem repeat (STR) sequence at a given STR locus from nucleic acid sequence reads generated by short read technology.
PCT/US2018/044889 2017-08-01 2018-08-01 Determination of str length by short read sequencing Ceased WO2019028189A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762539896P 2017-08-01 2017-08-01
US62/539,896 2017-08-01

Publications (2)

Publication Number Publication Date
WO2019028189A2 WO2019028189A2 (en) 2019-02-07
WO2019028189A3 true WO2019028189A3 (en) 2019-02-28

Family

ID=65234183

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2018/044889 Ceased WO2019028189A2 (en) 2017-08-01 2018-08-01 Determination of str length by short read sequencing

Country Status (1)

Country Link
WO (1) WO2019028189A2 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112195228B (en) * 2020-09-28 2022-02-22 苏州阅微基因技术有限公司 X-STR fluorescent amplification system, kit and application

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140163900A1 (en) * 2012-06-02 2014-06-12 Whitehead Institute For Biomedical Research Analyzing short tandem repeats from high throughput sequencing data for genetic applications
US20140235456A1 (en) * 2012-12-17 2014-08-21 Virginia Tech Intellectual Properties, Inc. Methods and Compositions for Identifying Global Microsatellite Instability and for Characterizing Informative Microsatellite Loci
WO2016038220A1 (en) * 2014-09-12 2016-03-17 Illumina Cambridge Limited Detecting repeat expansions with short read sequencing data
WO2016055971A2 (en) * 2014-10-10 2016-04-14 Invitae Corporation Methods, systems and processes of de novo assembly of sequencing reads
US9708653B2 (en) * 2012-02-15 2017-07-18 Battelle Memorial Institute Methods and compositions for identifying repeating sequences in nucleic acids

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9708653B2 (en) * 2012-02-15 2017-07-18 Battelle Memorial Institute Methods and compositions for identifying repeating sequences in nucleic acids
US20140163900A1 (en) * 2012-06-02 2014-06-12 Whitehead Institute For Biomedical Research Analyzing short tandem repeats from high throughput sequencing data for genetic applications
US20140235456A1 (en) * 2012-12-17 2014-08-21 Virginia Tech Intellectual Properties, Inc. Methods and Compositions for Identifying Global Microsatellite Instability and for Characterizing Informative Microsatellite Loci
WO2016038220A1 (en) * 2014-09-12 2016-03-17 Illumina Cambridge Limited Detecting repeat expansions with short read sequencing data
WO2016055971A2 (en) * 2014-10-10 2016-04-14 Invitae Corporation Methods, systems and processes of de novo assembly of sequencing reads

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
FUNGTAMMASAN, ARKARACHAI ET AL.: "Accurate typing of short tandem repeats from genome-wide sequencing data and its applications", GENOME RESEARCH, vol. 25, no. 5, 1 May 2015 (2015-05-01), pages 736 - 749, XP055579609 *
TANG, HAIBAO ET AL.: "Profiling of short-tandem-repeat disease alleles in 12,632 human whole genomes", THE AMERICAN JOURNAL OF HUMAN GENETICS, vol. 101, 2 November 2017 (2017-11-02), pages 700 - 715, XP085274539, DOI: doi:10.1016/j.ajhg.2017.09.013 *

Also Published As

Publication number Publication date
WO2019028189A2 (en) 2019-02-07

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