WO2021011990A8 - An iterative regression method for genomic prediction - Google Patents

An iterative regression method for genomic prediction Download PDF

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Publication number
WO2021011990A8
WO2021011990A8 PCT/AU2020/000072 AU2020000072W WO2021011990A8 WO 2021011990 A8 WO2021011990 A8 WO 2021011990A8 AU 2020000072 W AU2020000072 W AU 2020000072W WO 2021011990 A8 WO2021011990 A8 WO 2021011990A8
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Prior art keywords
trait
estimate
block
starting
bayesian
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PCT/AU2020/000072
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French (fr)
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WO2021011990A1 (en
Inventor
Edmond Joseph Breen
Hans Dieter Daetwyler
Michael Edward GODDARD
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Agriculture Victoria Services Pty Ltd
Dairy Australia Limited
Geoffrey Gardiner Dairy Foundation Limited
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Publication date
Priority claimed from AU2019902659A external-priority patent/AU2019902659A0/en
Application filed by Agriculture Victoria Services Pty Ltd, Dairy Australia Limited, Geoffrey Gardiner Dairy Foundation Limited filed Critical Agriculture Victoria Services Pty Ltd
Priority to AU2020318571A priority Critical patent/AU2020318571A1/en
Publication of WO2021011990A1 publication Critical patent/WO2021011990A1/en
Publication of WO2021011990A8 publication Critical patent/WO2021011990A8/en

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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
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/18—Complex mathematical operations for evaluating statistical data, e.g. average values, frequency distributions, probability functions, regression analysis
    • 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
    • G16B20/40—Population genetics; Linkage disequilibrium
    • 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
    • G16B40/20—Supervised data analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

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  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
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  • Chemical & Material Sciences (AREA)
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  • Medical Informatics (AREA)
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  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
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  • Analytical Chemistry (AREA)
  • General Physics & Mathematics (AREA)
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  • Mathematical Physics (AREA)
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  • Pure & Applied Mathematics (AREA)
  • Wood Science & Technology (AREA)
  • Computational Mathematics (AREA)
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  • Mathematical Analysis (AREA)
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Abstract

A method for improving the computational efficiency of estimation of Bayesian methods, such as Bayesian MCMC models, for performing genomic analysis of SNP data to estimate breeding values, Quantitative Trait Locus (QTLs), or genomic locations associated with a disease or trait. The method extends the BayesR method by using a blocked Gibbs sampling approach to estimate SNO effects comprising breaking the SNPS into non overlapping blocks of markers and sequentially processing each block according to a block ordering. Each regression coefficient in the block is then sequentially estimated, starting from a starting index. The method significantly reduces the computational time to estimate model parameters and can be applied to both single trait and multi-trait analyses.
PCT/AU2020/000072 2019-07-25 2020-07-23 An iterative regression method for genomic prediction WO2021011990A1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2020318571A AU2020318571A1 (en) 2019-07-25 2020-07-23 An iterative regression method for genomic prediction

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
AU2019902659 2019-07-25
AU2019902659A AU2019902659A0 (en) 2019-07-25 An iterative regression method for genomic prediction

Publications (2)

Publication Number Publication Date
WO2021011990A1 WO2021011990A1 (en) 2021-01-28
WO2021011990A8 true WO2021011990A8 (en) 2021-12-30

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Application Number Title Priority Date Filing Date
PCT/AU2020/000072 WO2021011990A1 (en) 2019-07-25 2020-07-23 An iterative regression method for genomic prediction

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AU (1) AU2020318571A1 (en)
WO (1) WO2021011990A1 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN113555063A (en) * 2021-07-28 2021-10-26 仲恺农业工程学院 Threshold character genome breeding value estimation method based on SNP chip and application
CN113808660B (en) * 2021-09-13 2024-02-13 复旦大学附属华山医院 Natural selection and database-based hereditary rare disease prevalence Bayes calculation model, construction method and application thereof

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Publication number Publication date
WO2021011990A1 (en) 2021-01-28
AU2020318571A1 (en) 2022-02-24

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