A heterozygote advantage analysis for tuberculosis resistance in dairy cattle
|
|
|
- Kelley McCormick
- 7 years ago
- Views:
Transcription
1 A heterozygote advantage analysis for tuberculosis resistance in dairy cattle Smaragda Tsairidou Tsairidou S. 1, Woolliams J.A. 1, Allen A.R. 2, Skuce R.A. 2,3, McBride S.H. 2, Wright D.M. 3, Bermingham M.L. 1, Pong-Wong R. 1, Matika O. 1, Pooley C.M. 1, McDowell S.W.J. 2, Glass E.J. 1, Bishop S.C. 1 (1) The Roslin Institute and RDVS, University of Edinburgh (2) Agri-Food and Biosciences Institute, Belfast (3) Queen s University of Belfast, Belfast
2 btb status: it s complicated
3 btb status: it s complicated Genetic Resistance
4 Part 1: Genomic Selection using Genetic Markers
5 Genomic Selection Genomic Selection» selection of animals based on their genotypes» genotyping using dense SNP chip data Genetic Markers» SNPs (Single Nucleotide Polymorphisms) across the genome, likely to be linked with QTLs (Quantitative Trait Loci)
6 Genomic Selection Genomic Selection» selection of animals based on their genotypes» genotyping using dense SNP chip data Genetic Markers» SNPs (Single Nucleotide Polymorphisms) across the genome, likely to be linked with QTLs (Quantitative Trait Loci) We can identify more resistant individuals using markers» Marker Assisted Selection (MAS)
7 Genomic Selection Genomic Selection» selection of animals based on their genotypes» genotyping using dense SNP chip data Genetic Markers» SNPs (Single Nucleotide Polymorphisms) across the genome, likely to be linked with QTLs (Quantitative Trait Loci) We can identify more resistant individuals using markers» Marker Assisted Selection (MAS)» genetic selection of btb resistant individuals may offer a complementary control strategy for btb
8 Marker Based Selection: previous examples MAS for Infectious Pancreatic Necrosis (IPN) in Atlantic Salmon Selection for Scrapie resistance in sheep based on the PrP genotype
9 btb infection: a complex trait Susceptibility to btb is a complex trait:» environment + many genetic variants
10 btb infection: a complex trait Susceptibility to btb is a complex trait:» environment + many genetic variants The principles of genetic selection apply in disease control» requirement: presence of heritable genetic variation in host susceptibility
11 btb infection: a complex trait Susceptibility to btb is a complex trait:» environment + many genetic variants The principles of genetic selection apply in disease control» requirement: presence of heritable genetic variation in host susceptibility Different loci have different properties and all loci do NOT affect the trait in the same way» additive and non-additive genetic variation
12 Genetic variation Additive: (AA BB) / 2
13 Genetic variation Dominance: AB - (AA + BB) / 2
14 Genetic variation Complete dominance: AB - (AA + BB) / 2
15 Genetic variation - The heterozygote advantage hypothesis Heterozygote advantage and hybrid vigour Disease resistance: both alleles present more options to respond to infection Overdominance: AB - (AA + BB) / 2
16 Genetic variation Heterozygote dis-advantage Underdominance: AB - (AA + BB) / 2
17 Part 2: Genome Wide Association Studies (GWAS) and Heterozygote (dis)advantage Analysis
18 Aims of the study Study the genetic architecture of resistance to btb: is it a single QTL affecting btb resistance? Investigate the hypothesis that loci showing heterozygote (dis)advantage are associated with resistance to btb Compare such loci to those obtained from standard GWAS
19 Phenotypes and Genotypes Holstein-Friesian cows (n = 1,151) Commercial herds in Northern Ireland Age, Year, Season, Reason, Breed Illumina BovineHD BeadChip (617,885 SNPs)
20 Phenotypes and Genotypes Holstein-Friesian cows (n = 1,151) Commercial herds in Northern Ireland Age, Year, Season, Reason, Breed Illumina BovineHD BeadChip (617,885 SNPs) CASES: positive SICCT i.e. >4mm than reaction to M. avium after 72 h + confirmed lesions by post-mortem examination CONTROLS: multiple negative test results (higher prevalence herds)
21 Datasets» Dataset 1: all animals included» Dataset 2: animals clustering separately in CMDS removed Classical Multidimensional Scaling» Dataset 3: herds contributing no controls removed (n = 222) Quality Control: MAF>0.05, call rate>95%, HWE p< Dataset n animals n SNPs n animals after QC n SNPs after QC
22 Standard Genome Scans Genome Wide Association Study (GWAS)» method for identifying SNPs across the genome having an effect on the trait under study based on their p-values» assumption: they reside within or are linked to a QTL SNP Chr Additive model p-value rs x rs x rs x rs x rs x rs x rs x (Bermingham et al. 2014)
23 GWAS for Heterozygote Advantage Heterozygote advantage GWAS» assumption: underlying non-additive genetic variation» genotypes recoded into heterozygotes (A 1 A 2 ) and homozygotes (A 1 A 1 & A 2 A 2 )» GWAS repeated for each of the three datasets (GenABEL package, R/2.15.2) Accounting for relatedness» genomic kinship (K) matrix calculated using SNP information
24 GWAS for Heterozygote Advantage Heterozygote advantage GWAS» assumption: underlying non-additive genetic variation» genotypes recoded into heterozygotes (A 1 A 2 ) and homozygotes (A 1 A 1 & A 2 A 2 )» GWAS repeated for each of the three datasets (GenABEL package, R/2.15.2) Accounting for relatedness» genomic kinship (K) matrix calculated using SNP information Binary phenotype (btb status): case = 1, control = 0 Reason Y = a + D + S + R + B + u + e ijkmpq i j k m p i Genetic effects Age Year Season Breed
25 Results - Dataset 1 GWAS for Heterozygote advantage: SNP on BTA6 (position: 10,245,091) significant at the suggestive level Significance thresholds Bonferroni correction for multiple testing: -log 10 (0.05 / N) genome-wide threshold -log 10 (1 / N) suggestive threshold where N, the number of SNPs Genome-Wide Suggestive rs Chr 6 rs Chr
26 Results - Dataset 1 GWAS for Heterozygote advantage: SNP on BTA6 (position: 10,245,091) significant at the suggestive level Further Q.C. for the SNP Significance thresholds Bonferroni correction for multiple testing: -log 10 (0.05 / N) genome-wide threshold -log 10 (1 / N) suggestive threshold where N, the number of SNPs Genome-Wide Suggestive rs Chr 6 rs Chr
27 CMDS - Dataset 2 Classical Multidimensional Scaling (CMDS)» visualising the level of dissimilarities between individuals based on their genome-wide IBS pairwise distances matrix ( GenABEL, R/2.15.2)
28 CMDS - Dataset 2 Classical Multidimensional Scaling (CMDS)» visualising the level of dissimilarities between individuals based on their genome-wide IBS pairwise distances matrix ( GenABEL, R/2.15.2)» Calculate Principal Components (PCs)» Identify individuals clustering separately Individuals forming a distinct cluster (n = 40) originating from the same herd (possibly crossbreeding)
29 CMDS - Dataset 2 Approaches to control for possible genetic substructure 1. Adjust for stratification by principal components 2. Remove the 40 individuals clustering separately
30 Results - Dataset 2 CMDS analysis: the SNP identified was consistently present across all approaches used to control for substructure Genome- Wide Suggestive rs chr 6 (1. PCs) rs chr 6 (2. minor cluster removed) rs chr 25 (3. minor cluster removed)
31 Results - Dataset 3 Analysis for the reduced dataset after removing herds contributing no controls pattern on chromosome 6 still visible Genome-Wide Suggestive rs chr 6 rs chr
32 Results Genotypic frequencies and HWE test Hardy-Weinberg Equilibrium (HWE) test» genotypic frequencies are calculated for each of the genotypic classes» x 2 test: significant departure for the observed genotypic frequencies from the expectations under HWE» (a) full dataset, (b) separately for cases and controls and (c) pairwise between cases and controls rs CASES CONTROLS A/A A/G G/G TOTALS CONTROLS AA AG GG Total Observed Expected NA Significant departure from HWE expectations for the controls (x 2 =28.6, p<0.001) but not for the cases Significantly less heterozygotes in the controls (x 2 = 11.5, p<0.001)
33 ASReml Analysis 1. Predicted genotypic means in ASReml (Gilmour et al. 2002)» LM: Linear mixed model (genotypes for the SNP of interest as a fixed effect) Y ijkmpβ = μ + a i + D j + S k + R m + B p + X β + u i + e i SNP genotypes 2. Linear mixed model with interaction component with a significant SNP identified by standard GWAS 3. Generalized Linear (Mixed) Model for binomial analysis (case-control)» Threshold Models (TMs) link functions: PROBIT, LOGIT, LOGLOG
34 ASReml analysis - Estimated Genotypic Effects F = (P < 0.001) Predicted Value Standard Error GG AG AA F = (P < 0.001) PROBIT Predicted Value Standard Error GG AG AA F = (P < 0.001) F = (P < 0.001) LOGIT Predicted Value Standard Error GG AG AA LOGLOG Predicted Value Standard Error GG AG AA Interaction was not significant (P>0.1) The SNP identified explains 1.7% of the total phenotypic variance
35 ASReml analysis - Estimated Genotypic Effects F = (P < 0.001) Predicted Value Standard Error GG AG AA F = (P < 0.001) PROBIT Predicted Value Standard Error GG AG AA F = (P < 0.001) F = (P < 0.001) LOGIT Predicted Value Standard Error GG AG AA LOGLOG Predicted Value Standard Error GG AG AA Interaction was not significant (P>0.1) The SNP identified explains 1.7% of the total phenotypic variance Heterozygotes are more likely to have a diseased phenotype, displaying a heterozygote disadvantage pattern
36 Discussion SNP resides within the peroxiredoxin-6-like pseudogene» pseudogene contains two exons and the SNP lies down-stream of exon 1 Pseudogene Functional homologue Pseudogenes» non-functional but sometimes maintain some functionality (e.g. gene expression regulation)» derive from parental gene through (a) reverse transcription or (b) gene duplication Parental gene (PRDX6) (peroxiredoxin-6: enzyme involved in lipid internalising and degradation in alveolar macrophages)
37 Discussion SNP adjacent to candidate genes and CNV regions» Ensemble genome browser, region: 6:8,300,000-10,300,000 bp» contains three previously identified Copy Number Variation (CNV) regions associated with gastrointestinal nematodes resistance in cattle (Hou et al. 2012)
38 Conclusions It is feasible to use markers across the genome to select individuals more resistant to bovine Tuberculosis A SNP identified suggesting association between locus heterozygosity and increased susceptibility to btb in cattle» significantly fewer than expected heterozygotes in the controls: i.e. heterozygotes more likely to be diseased» possibly a fitness disadvantage for the heterozygotes» as documented for Rhesus blood group system & chromosomal rearrangements Comparison with results from standard genome scans» no interaction was observed with significant marker from GWAS Further studies are needed to confirm these findings» effects of the sample size on the power of the GWAS
39 Practical Implementation Breeding for resistance to btb Implementing results» Calculating Breeding Values for btb resistance in dairy cattle Stage 1: Using the skin test and abattoir confirmed results and linking the animals by pedigree Stage 2: Expand to Genomic Selection with SNPs» SNP chip genotypes on widely used sires are already available Stage 3: Incorporating results from our studies» after validation
40 Thank you! Bishop S.C. Woolliams J.A. Glass E.J. Pong-Wong R. Matika O. Pooley C.M. Bermingham M.L. Allen A.R. Skuce R.A. McBride S.H. Wright D.M. McDowell S.W.J. We acknowledge financial support from the Roslin Institute and the University of Edinburgh through the Principal's Career Development PhD, the Greek State Scholarship Foundation and the Biotechnology and Biological Sciences Research Council.
Genomic Selection in. Applied Training Workshop, Sterling. Hans Daetwyler, The Roslin Institute and R(D)SVS
Genomic Selection in Dairy Cattle AQUAGENOME Applied Training Workshop, Sterling Hans Daetwyler, The Roslin Institute and R(D)SVS Dairy introduction Overview Traditional breeding Genomic selection Advantages
Basics of Marker Assisted Selection
asics of Marker ssisted Selection Chapter 15 asics of Marker ssisted Selection Julius van der Werf, Department of nimal Science rian Kinghorn, Twynam Chair of nimal reeding Technologies University of New
GENOMIC SELECTION: THE FUTURE OF MARKER ASSISTED SELECTION AND ANIMAL BREEDING
GENOMIC SELECTION: THE FUTURE OF MARKER ASSISTED SELECTION AND ANIMAL BREEDING Theo Meuwissen Institute for Animal Science and Aquaculture, Box 5025, 1432 Ås, Norway, theo.meuwissen@ihf.nlh.no Summary
Tutorial on gplink. http://pngu.mgh.harvard.edu/~purcell/plink/gplink.shtml. PLINK tutorial, December 2006; Shaun Purcell, shaun@pngu.mgh.harvard.
Tutorial on gplink http://pngu.mgh.harvard.edu/~purcell/plink/gplink.shtml Basic gplink analyses Data management Summary statistics Association analysis Population stratification IBD-based analysis gplink
Presentation by: Ahmad Alsahaf. Research collaborator at the Hydroinformatics lab - Politecnico di Milano MSc in Automation and Control Engineering
Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen 9-October 2015 Presentation by: Ahmad Alsahaf Research collaborator at the Hydroinformatics lab - Politecnico di
GAW 15 Problem 3: Simulated Rheumatoid Arthritis Data Full Model and Simulation Parameters
GAW 15 Problem 3: Simulated Rheumatoid Arthritis Data Full Model and Simulation Parameters Michael B Miller , Michael Li , Gregg Lind , Soon-Young
Marker-Assisted Backcrossing. Marker-Assisted Selection. 1. Select donor alleles at markers flanking target gene. Losing the target allele
Marker-Assisted Backcrossing Marker-Assisted Selection CS74 009 Jim Holland Target gene = Recurrent parent allele = Donor parent allele. Select donor allele at markers linked to target gene.. Select recurrent
A Primer of Genome Science THIRD
A Primer of Genome Science THIRD EDITION GREG GIBSON-SPENCER V. MUSE North Carolina State University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts USA Contents Preface xi 1 Genome Projects:
Basic Principles of Forensic Molecular Biology and Genetics. Population Genetics
Basic Principles of Forensic Molecular Biology and Genetics Population Genetics Significance of a Match What is the significance of: a fiber match? a hair match? a glass match? a DNA match? Meaning of
Population Genetics and Multifactorial Inheritance 2002
Population Genetics and Multifactorial Inheritance 2002 Consanguinity Genetic drift Founder effect Selection Mutation rate Polymorphism Balanced polymorphism Hardy-Weinberg Equilibrium Hardy-Weinberg Equilibrium
Studi genomici negli animali
Studi genomici negli animali John Williams Parco Tecnologico Padano John.Williams@tecnoparco.org Agricultural needs 50-100- 70 Need for increased meat produc:on! World consump;on of meat products! 1961
Milk protein genetic variation in Butana cattle
Milk protein genetic variation in Butana cattle Ammar Said Ahmed Züchtungsbiologie und molekulare Genetik, Humboldt Universität zu Berlin, Invalidenstraβe 42, 10115 Berlin, Deutschland 1 Outline Background
Investigating the genetic basis for intelligence
Investigating the genetic basis for intelligence Steve Hsu University of Oregon and BGI www.cog-genomics.org Outline: a multidisciplinary subject 1. What is intelligence? Psychometrics 2. g and GWAS: a
DNA MARKERS FOR ASEASONALITY AND MILK PRODUCTION IN SHEEP. R. G. Mateescu and M.L. Thonney
DNA MARKERS FOR ASEASONALITY AND MILK PRODUCTION IN SHEEP Introduction R. G. Mateescu and M.L. Thonney Department of Animal Science Cornell University Ithaca, New York Knowledge about genetic markers linked
Simplifying Data Interpretation with Nexus Copy Number
Simplifying Data Interpretation with Nexus Copy Number A WHITE PAPER FROM BIODISCOVERY, INC. Rapid technological advancements, such as high-density acgh and SNP arrays as well as next-generation sequencing
SICKLE CELL ANEMIA & THE HEMOGLOBIN GENE TEACHER S GUIDE
AP Biology Date SICKLE CELL ANEMIA & THE HEMOGLOBIN GENE TEACHER S GUIDE LEARNING OBJECTIVES Students will gain an appreciation of the physical effects of sickle cell anemia, its prevalence in the population,
Report. A Note on Exact Tests of Hardy-Weinberg Equilibrium. Janis E. Wigginton, 1 David J. Cutler, 2 and Gonçalo R. Abecasis 1
Am. J. Hum. Genet. 76:887 883, 2005 Report A Note on Exact Tests of Hardy-Weinberg Equilibrium Janis E. Wigginton, 1 David J. Cutler, 2 and Gonçalo R. Abecasis 1 1 Center for Statistical Genetics, Department
Combining Data from Different Genotyping Platforms. Gonçalo Abecasis Center for Statistical Genetics University of Michigan
Combining Data from Different Genotyping Platforms Gonçalo Abecasis Center for Statistical Genetics University of Michigan The Challenge Detecting small effects requires very large sample sizes Combined
Logistic Regression (1/24/13)
STA63/CBB540: Statistical methods in computational biology Logistic Regression (/24/3) Lecturer: Barbara Engelhardt Scribe: Dinesh Manandhar Introduction Logistic regression is model for regression used
Single Nucleotide Polymorphisms (SNPs)
Single Nucleotide Polymorphisms (SNPs) Additional Markers 13 core STR loci Obtain further information from additional markers: Y STRs Separating male samples Mitochondrial DNA Working with extremely degraded
Chapter 9 Patterns of Inheritance
Bio 100 Patterns of Inheritance 1 Chapter 9 Patterns of Inheritance Modern genetics began with Gregor Mendel s quantitative experiments with pea plants History of Heredity Blending theory of heredity -
Step by Step Guide to Importing Genetic Data into JMP Genomics
Step by Step Guide to Importing Genetic Data into JMP Genomics Page 1 Introduction Data for genetic analyses can exist in a variety of formats. Before this data can be analyzed it must imported into one
PRINCIPLES OF POPULATION GENETICS
PRINCIPLES OF POPULATION GENETICS FOURTH EDITION Daniel L. Hartl Harvard University Andrew G. Clark Cornell University UniversitSts- und Landesbibliothek Darmstadt Bibliothek Biologie Sinauer Associates,
Chromosomes, Mapping, and the Meiosis Inheritance Connection
Chromosomes, Mapping, and the Meiosis Inheritance Connection Carl Correns 1900 Chapter 13 First suggests central role for chromosomes Rediscovery of Mendel s work Walter Sutton 1902 Chromosomal theory
Autoimmunity and immunemediated. FOCiS. Lecture outline
1 Autoimmunity and immunemediated inflammatory diseases Abul K. Abbas, MD UCSF FOCiS 2 Lecture outline Pathogenesis of autoimmunity: why selftolerance fails Genetics of autoimmune diseases Therapeutic
Forensic DNA Testing Terminology
Forensic DNA Testing Terminology ABI 310 Genetic Analyzer a capillary electrophoresis instrument used by forensic DNA laboratories to separate short tandem repeat (STR) loci on the basis of their size.
Genetics Lecture Notes 7.03 2005. Lectures 1 2
Genetics Lecture Notes 7.03 2005 Lectures 1 2 Lecture 1 We will begin this course with the question: What is a gene? This question will take us four lectures to answer because there are actually several
SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis
SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis Goal: This tutorial introduces several websites and tools useful for determining linkage disequilibrium
Genetic improvement: a major component of increased dairy farm profitability
Genetic improvement: a major component of increased dairy farm profitability Filippo Miglior 1,2, Jacques Chesnais 3 & Brian Van Doormaal 2 1 2 Canadian Dairy Network 3 Semex Alliance Agri-Food Canada
Heritability: Twin Studies. Twin studies are often used to assess genetic effects on variation in a trait
TWINS AND GENETICS TWINS Heritability: Twin Studies Twin studies are often used to assess genetic effects on variation in a trait Comparing MZ/DZ twins can give evidence for genetic and/or environmental
Genomic selection in dairy cattle: Integration of DNA testing into breeding programs
Genomic selection in dairy cattle: Integration of DNA testing into breeding programs Jonathan M. Schefers* and Kent A. Weigel* *Department of Dairy Science, University of Wisconsin, Madison 53706; and
The impact of genomic selection on North American dairy cattle breeding organizations
The impact of genomic selection on North American dairy cattle breeding organizations Jacques Chesnais, George Wiggans and Filippo Miglior The Semex Alliance, USDA and Canadian Dairy Network 2000 09 Genomic
HLA data analysis in anthropology: basic theory and practice
HLA data analysis in anthropology: basic theory and practice Alicia Sanchez-Mazas and José Manuel Nunes Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Anthropology and Ecology,
GEMMA User Manual. Xiang Zhou. May 18, 2016
GEMMA User Manual Xiang Zhou May 18, 2016 Contents 1 Introduction 4 1.1 What is GEMMA...................................... 4 1.2 How to Cite GEMMA................................... 4 1.3 Models............................................
Gene Mapping Techniques
Gene Mapping Techniques OBJECTIVES By the end of this session the student should be able to: Define genetic linkage and recombinant frequency State how genetic distance may be estimated State how restriction
A Multi-locus Genetic Risk Score for Abdominal Aortic Aneurysm
A Multi-locus Genetic Risk Score for Abdominal Aortic Aneurysm Zi Ye, 1 MD, Erin Austin, 1,2 PhD, Daniel J Schaid, 2 PhD, Iftikhar J. Kullo, 1 MD Affiliations: 1 Division of Cardiovascular Diseases and
ASSIsT: An Automatic SNP ScorIng Tool for in and out-breeding species Reference Manual
ASSIsT: An Automatic SNP ScorIng Tool for in and out-breeding species Reference Manual Di Guardo M, Micheletti D, Bianco L, Koehorst-van Putten HJJ, Longhi S, Costa F, Aranzana MJ, Velasco R, Arús P, Troggio
Evolution (18%) 11 Items Sample Test Prep Questions
Evolution (18%) 11 Items Sample Test Prep Questions Grade 7 (Evolution) 3.a Students know both genetic variation and environmental factors are causes of evolution and diversity of organisms. (pg. 109 Science
Consistent Assay Performance Across Universal Arrays and Scanners
Technical Note: Illumina Systems and Software Consistent Assay Performance Across Universal Arrays and Scanners There are multiple Universal Array and scanner options for running Illumina DASL and GoldenGate
Introductory genetics for veterinary students
Introductory genetics for veterinary students Michel Georges Introduction 1 References Genetics Analysis of Genes and Genomes 7 th edition. Hartl & Jones Molecular Biology of the Cell 5 th edition. Alberts
Next Generation Sequencing: Technology, Mapping, and Analysis
Next Generation Sequencing: Technology, Mapping, and Analysis Gary Benson Computer Science, Biology, Bioinformatics Boston University gbenson@bu.edu http://tandem.bu.edu/ The Human Genome Project took
Genomes and SNPs in Malaria and Sickle Cell Anemia
Genomes and SNPs in Malaria and Sickle Cell Anemia Introduction to Genome Browsing with Ensembl Ensembl The vast amount of information in biological databases today demands a way of organising and accessing
Factors for success in big data science
Factors for success in big data science Damjan Vukcevic Data Science Murdoch Childrens Research Institute 16 October 2014 Big Data Reading Group (Department of Mathematics & Statistics, University of Melbourne)
Globally, about 9.7% of cancers in men are prostate cancers, and the risk of developing the
Chapter 5 Analysis of Prostate Cancer Association Study Data 5.1 Risk factors for Prostate Cancer Globally, about 9.7% of cancers in men are prostate cancers, and the risk of developing the disease has
Genetics of Rheumatoid Arthritis Markey Lecture Series
Genetics of Rheumatoid Arthritis Markey Lecture Series Al Kim akim@dom.wustl.edu 2012.09.06 Overview of Rheumatoid Arthritis Rheumatoid Arthritis (RA) Autoimmune disease primarily targeting the synovium
Human Genome Organization: An Update. Genome Organization: An Update
Human Genome Organization: An Update Genome Organization: An Update Highlights of Human Genome Project Timetable Proposed in 1990 as 3 billion dollar joint venture between DOE and NIH with 15 year completion
Package forensic. February 19, 2015
Type Package Title Statistical Methods in Forensic Genetics Version 0.2 Date 2007-06-10 Package forensic February 19, 2015 Author Miriam Marusiakova (Centre of Biomedical Informatics, Institute of Computer
An example of bioinformatics application on plant breeding projects in Rijk Zwaan
An example of bioinformatics application on plant breeding projects in Rijk Zwaan Xiangyu Rao 17-08-2012 Introduction of RZ Rijk Zwaan is active worldwide as a vegetable breeding company that focuses on
Genotyping and quality control of UK Biobank, a large- scale, extensively phenotyped prospective resource
Genotyping and quality control of UK Biobank, a large- scale, extensively phenotyped prospective resource Information for researchers Interim Data Release, 2015 1 Introduction... 3 1.1 UK Biobank... 3
Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research. March 17, 2011 Rendez-Vous Séquençage
Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research March 17, 2011 Rendez-Vous Séquençage Presentation Overview Core Technology Review Sequence Enrichment Application
NGS and complex genetics
NGS and complex genetics Robert Kraaij Genetic Laboratory Department of Internal Medicine r.kraaij@erasmusmc.nl Gene Hunting Rotterdam Study and GWAS Next Generation Sequencing Gene Hunting Mendelian gene
2. True or False? The sequence of nucleotides in the human genome is 90.9% identical from one person to the next. False (it s 99.
1. True or False? A typical chromosome can contain several hundred to several thousand genes, arranged in linear order along the DNA molecule present in the chromosome. True 2. True or False? The sequence
MOLECULAR MARKERS AND THEIR APPLICATIONS IN CEREALS BREEDING
MOLECULAR MARKERS AND THEIR APPLICATIONS IN CEREALS BREEDING Viktor Korzun Lochow-Petkus GmbH, Grimsehlstr.24, 37574 Einbeck, Germany korzun@lochow-petkus.de Summary The development of molecular techniques
Hardy-Weinberg Equilibrium Problems
Hardy-Weinberg Equilibrium Problems 1. The frequency of two alleles in a gene pool is 0.19 (A) and 0.81(a). Assume that the population is in Hardy-Weinberg equilibrium. (a) Calculate the percentage of
Heredity. Sarah crosses a homozygous white flower and a homozygous purple flower. The cross results in all purple flowers.
Heredity 1. Sarah is doing an experiment on pea plants. She is studying the color of the pea plants. Sarah has noticed that many pea plants have purple flowers and many have white flowers. Sarah crosses
GOBII. Genomic & Open-source Breeding Informatics Initiative
GOBII Genomic & Open-source Breeding Informatics Initiative My Background BS Animal Science, University of Tennessee MS Animal Breeding, University of Georgia Random regression models for longitudinal
Chapter 8: Recombinant DNA 2002 by W. H. Freeman and Company Chapter 8: Recombinant DNA 2002 by W. H. Freeman and Company
Genetic engineering: humans Gene replacement therapy or gene therapy Many technical and ethical issues implications for gene pool for germ-line gene therapy what traits constitute disease rather than just
The Human Genome Project
The Human Genome Project Brief History of the Human Genome Project Physical Chromosome Maps Genetic (or Linkage) Maps DNA Markers Sequencing and Annotating Genomic DNA What Have We learned from the HGP?
DNA Copy Number and Loss of Heterozygosity Analysis Algorithms
DNA Copy Number and Loss of Heterozygosity Analysis Algorithms Detection of copy-number variants and chromosomal aberrations in GenomeStudio software. Introduction Illumina has developed several algorithms
The All-Breed Animal Model Bennet Cassell, Extension Dairy Scientist, Genetics and Management
publication 404-086 The All-Breed Animal Model Bennet Cassell, Extension Dairy Scientist, Genetics and Management Introduction The all-breed animal model is the genetic-evaluation system used to evaluate
Genetics Module B, Anchor 3
Genetics Module B, Anchor 3 Key Concepts: - An individual s characteristics are determines by factors that are passed from one parental generation to the next. - During gamete formation, the alleles for
Mendelian inheritance and the
Mendelian inheritance and the most common genetic diseases Cornelia Schubert, MD, University of Goettingen, Dept. Human Genetics EUPRIM-Net course Genetics, Immunology and Breeding Mangement German Primate
BioBoot Camp Genetics
BioBoot Camp Genetics BIO.B.1.2.1 Describe how the process of DNA replication results in the transmission and/or conservation of genetic information DNA Replication is the process of DNA being copied before
FHF prosjekt 900706:
FHF prosjekt 900706: Sporing av laks: SNP-tilnærming Matthew Kent, Harald Grove, Teresa Andersstuen, Mariann Arnyasi, Kristil Sundsaasen, Sigbjørn Lien CIGENE, Dept Animal and Aquaculture Sciences, Norwegian
Popstats Unplugged. 14 th International Symposium on Human Identification. John V. Planz, Ph.D. UNT Health Science Center at Fort Worth
Popstats Unplugged 14 th International Symposium on Human Identification John V. Planz, Ph.D. UNT Health Science Center at Fort Worth Forensic Statistics From the ground up Why so much attention to statistics?
Terms: The following terms are presented in this lesson (shown in bold italics and on PowerPoint Slides 2 and 3):
Unit B: Understanding Animal Reproduction Lesson 4: Understanding Genetics Student Learning Objectives: Instruction in this lesson should result in students achieving the following objectives: 1. Explain
Lecture 6: Single nucleotide polymorphisms (SNPs) and Restriction Fragment Length Polymorphisms (RFLPs)
Lecture 6: Single nucleotide polymorphisms (SNPs) and Restriction Fragment Length Polymorphisms (RFLPs) Single nucleotide polymorphisms or SNPs (pronounced "snips") are DNA sequence variations that occur
UKB_WCSGAX: UK Biobank 500K Samples Genotyping Data Generation by the Affymetrix Research Services Laboratory. April, 2015
UKB_WCSGAX: UK Biobank 500K Samples Genotyping Data Generation by the Affymetrix Research Services Laboratory April, 2015 1 Contents Overview... 3 Rare Variants... 3 Observation... 3 Approach... 3 ApoE
Polymorphism of retrotransposons in Bos taurus
Polymorphism of retrotransposons in Bos taurus Bernt Guldbrandtsen Goutam Sahana Mogens Sandø Lund Center for Quantitative Genetics and Genomics Aarhus University Denmark Transposons Type of jumping genes
From: Conner, J. and D. Hartl, A Primer of Ecological Genetics. In prep. for Sinauer
Conner and Hartl p. 4-1 From: Conner, J. and D. Hartl, A Primer of Ecological Genetics. In prep. for Sinauer Chapter 4: Quantitative genetics I: Genetic variation 4.1 Mendelian basis of continuous traits
Text file One header line meta information lines One line : variant/position
Software Calling: GATK SAMTOOLS mpileup Varscan SOAP VCF format Text file One header line meta information lines One line : variant/position ##fileformat=vcfv4.1! ##filedate=20090805! ##source=myimputationprogramv3.1!
Appendix J. Genetic Implications of Recent Biotechnologies. Appendix Contents. Introduction
Genetic Improvement and Crossbreeding in Meat Goats Lessons in Animal Breeding for Goats Bred and Raised for Meat Will R. Getz Fort Valley State University Appendix J. Genetic Implications of Recent Biotechnologies
GenomeStudio Data Analysis Software
GenomeStudio Data Analysis Software Illumina has created a comprehensive suite of data analysis tools to support a wide range of genetic analysis assays. This single software package provides data visualization
From Disease Association to Risk Assessment: An Optimistic View from Genome-Wide Association Studies on Type 1 Diabetes
From Disease Association to Risk Assessment: An Optimistic View from Genome-Wide Association Studies on Type 1 Diabetes Zhi Wei 1., Kai Wang 2., Hui-Qi Qu 3, Haitao Zhang 2, Jonathan Bradfield 2, Cecilia
B I O I N F O R M A T I C S
B I O I N F O R M A T I C S Kristel Van Steen, PhD 2 Montefiore Institute - Systems and Modeling GIGA - Bioinformatics ULg kristel.vansteen@ulg.ac.be CHAPTER 4: GENOME-WIDE ASSOCIATION STUDIES 1 Setting
GWASrap User Manual v1.1
GWASrap User Manual v1.1 1 / 28 Table of contents Introduction... 3 System Requirements... 3 Welcome... 3 Features... 4 Create New Run... 5 GWAS Representation... 7 GWAS Annotation... 13 GWAS Prioritization...
Inheritance of Color And The Polled Trait Dr. R. R. Schalles, Dept. of Animal Sciences and Industry Kansas State University
Inheritance of Color And The Polled Trait Dr. R. R. Schalles, Dept. of Animal Sciences and Industry Kansas State University Introduction All functions of an animal are controlled by the enzymes (and other
Genetics 301 Sample Final Examination Spring 2003
Genetics 301 Sample Final Examination Spring 2003 50 Multiple Choice Questions-(Choose the best answer) 1. A cross between two true breeding lines one with dark blue flowers and one with bright white flowers
SNPbrowser Software v3.5
Product Bulletin SNP Genotyping SNPbrowser Software v3.5 A Free Software Tool for the Knowledge-Driven Selection of SNP Genotyping Assays Easily visualize SNPs integrated with a physical map, linkage disequilibrium
Information leaflet. Centrum voor Medische Genetica. Version 1/20150504 Design by Ben Caljon, UZ Brussel. Universitair Ziekenhuis Brussel
Information on genome-wide genetic testing Array Comparative Genomic Hybridization (array CGH) Single Nucleotide Polymorphism array (SNP array) Massive Parallel Sequencing (MPS) Version 120150504 Design
The Functional but not Nonfunctional LILRA3 Contributes to Sex Bias in Susceptibility and Severity of ACPA-Positive Rheumatoid Arthritis
The Functional but not Nonfunctional LILRA3 Contributes to Sex Bias in Susceptibility and Severity of ACPA-Positive Rheumatoid Arthritis Yan Du Peking University People s Hospital 100044 Beijing CHINA
Roberto Ciccone, Orsetta Zuffardi Università di Pavia
Roberto Ciccone, Orsetta Zuffardi Università di Pavia XIII Corso di Formazione Malformazioni Congenite dalla Diagnosi Prenatale alla Terapia Postnatale unipv.eu Carrara, 24 ottobre 2014 Legend:Bluebars
Association between Dopamine Gene and Alcoholism in Pategar Community of Dharwad, Karnataka
International Journal of Scientific and Research Publications, Volume 3, Issue 10, October 2013 1 Association between Dopamine Gene and Alcoholism in Pategar Community of Dharwad, Karnataka SOMASHEKHAR
Pedigree Based Analysis using FlexQTL TM software
Pedigree Based Analysis using FlexQTL TM software Marco Bink Eric van de Weg Roeland Voorrips Hans Jansen Outline Current Status: QTL mapping in pedigreed populations IBD probability of founder alleles
GenomeStudio Data Analysis Software
GenomeStudio Analysis Software Illumina has created a comprehensive suite of data analysis tools to support a wide range of genetic analysis assays. This single software package provides data visualization
Validation and Replication
Validation and Replication Overview Definitions of validation and replication Difficulties and limitations Working examples from our group and others Why? False positive results still occur. even after
GENOMIC information is transforming animal and plant
GENOMIC SELECTION Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking Hans D. Daetwyler,*,1 Mario P. L. Calus, Ricardo Pong-Wong, Gustavo de los Campos,
Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays. Design and Ordering Guide
Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays Design and Ordering Guide For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in
Focusing on results not data comprehensive data analysis for targeted next generation sequencing
Focusing on results not data comprehensive data analysis for targeted next generation sequencing Daniel Swan, Jolyon Holdstock, Angela Matchan, Richard Stark, John Shovelton, Duarte Mohla and Simon Hughes
Step-by-Step Guide to Bi-Parental Linkage Mapping WHITE PAPER
Step-by-Step Guide to Bi-Parental Linkage Mapping WHITE PAPER JMP Genomics Step-by-Step Guide to Bi-Parental Linkage Mapping Introduction JMP Genomics offers several tools for the creation of linkage maps
Analysis of gene expression data. Ulf Leser and Philippe Thomas
Analysis of gene expression data Ulf Leser and Philippe Thomas This Lecture Protein synthesis Microarray Idea Technologies Applications Problems Quality control Normalization Analysis next week! Ulf Leser:
Farming of the black tiger prawn Challenges and Opportunities
Farming of the black tiger prawn Challenges and Opportunities Dean R Jerry Director ARC Research Hub for Advanced Prawn Breeding James Cook University Australia Presentation overview Global production
LECTURE 6 Gene Mutation (Chapter 16.1-16.2)
LECTURE 6 Gene Mutation (Chapter 16.1-16.2) 1 Mutation: A permanent change in the genetic material that can be passed from parent to offspring. Mutant (genotype): An organism whose DNA differs from the
SNP Data Integration and Analysis for Drug- Response Biomarker Discovery
B. Comp Dissertation SNP Data Integration and Analysis for Drug- Response Biomarker Discovery By Chen Jieqi Pauline Department of Computer Science School of Computing National University of Singapore 2008/2009
Forensic Statistics. From the ground up. 15 th International Symposium on Human Identification
Forensic Statistics 15 th International Symposium on Human Identification From the ground up UNTHSC John V. Planz, Ph.D. UNT Health Science Center at Fort Worth Why so much attention to statistics? Exclusions
Genetics for the Novice
Genetics for the Novice by Carol Barbee Wait! Don't leave yet. I know that for many breeders any article with the word genetics in the title causes an immediate negative reaction. Either they quickly turn
Abbreviation key: NS = natural service breeding system, AI = artificial insemination, BV = breeding value, RBV = relative breeding value
Archiva Zootechnica 11:2, 29-34, 2008 29 Comparison between breeding values for milk production and reproduction of bulls of Holstein breed in artificial insemination and bulls in natural service J. 1,
Heredity - Patterns of Inheritance
Heredity - Patterns of Inheritance Genes and Alleles A. Genes 1. A sequence of nucleotides that codes for a special functional product a. Transfer RNA b. Enzyme c. Structural protein d. Pigments 2. Genes
Biology 1406 - Notes for exam 5 - Population genetics Ch 13, 14, 15
Biology 1406 - Notes for exam 5 - Population genetics Ch 13, 14, 15 Species - group of individuals that are capable of interbreeding and producing fertile offspring; genetically similar 13.7, 14.2 Population
vision evolving guidelines
vision To foster a collective, industry supported strategy for the future of the Holstein Breed which will act as a tool for Canadian dairy producers to maximize profitability and genetic improvement.