Experimental Design and Reproducibility in Preclinical Animal Studies

In: Laboratory Animal Science and Medicine Ser. v.1

Abstract

Intro -- Contents -- Part I The Animal and Its Environment -- An Introduction to Reproducibility in the Context of Animal Research -- 1 An Introduction to Reproducibility in the Context of Animal Research -- 1.1 Reproducibility -- 2 Part I: The Animal and Its Environment -- 3 Part II: Statistics: Basics and Explanation of Different Designs and Tests -- 4 Part III: Systematic Reviews and Publishing -- References -- Rodent Genetics -- 1 Introduction to Mendelian Genetics and Genomics -- 1.1 Genes, Alleles and Their Interactions -- 1.1.1 Dominance, Recessivity and Co-dominance -- 1.1.2 Epistasis and Pleiotropy -- 1.1.3 Penetrance and Expressivity -- 1.2 Genomes and Genetic Variation -- 1.2.1 Genes, Gene Families and Pseudogenes -- 1.2.2 Repetitive DNA Sequences -- 1.2.3 Copy Number Variations, Indels, Transposable Elements and SNPs -- 1.2.4 Functional Annotation of the Mouse Genome -- 2 Standardized Strains of Laboratory Rodents -- 2.1 Inbred Strains and Substrains -- 2.2 F1 Hybrids -- 2.3 Co-isogenic, Congenic and Consomic Strains -- 2.4 Recombinant Inbred Strains and Recombinant Congenic Strains -- 2.5 The Mouse Collaborative Cross -- 2.6 Outbred Stocks -- 3 Genetically Altered (GA) Rodents -- 3.1 Spontaneous and Chemically Induced Mutants -- 3.2 Classical Transgenesis by Pronuclear Microinjection (Random Insertion) -- 3.3 Targeted Mutagenesis Using ES Cells -- 3.4 Gene Editing Using Nucleases -- 3.4.1 Zinc-Finger Nucleases and TALEN -- 3.4.2 CRISPR-Cas System -- 4 Genetic Quality Control for Mice and Rats -- 4.1 Current Tools for Genetic Quality Control -- 4.1.1 Microsatellite (SSLP) Markers -- 4.1.2 Single Nucleotide Polymorphisms (SNPs) -- 4.2 Genetic Quality Control of Inbred Strains and Outbred Stocks -- 4.2.1 Genetic Monitoring to Confirm Strain Identity -- 4.2.2 Discrimination of Substrains -- 4.2.3 Genetic Monitoring for Outbred Colonies.