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Table of Contents
Intro
Introduction and Overview: Single Nucleotide Polymorphisms, Human Variation, and a Coming Revolution in Biology and Medicine
Introduction
Overview of the Book
Part I: An Overview of Human Genome Sequencing and How to Access Information About SNVs
Part II: A Broad Survey of SNPs, Their Classification into Synonymous and Non-synonymous, and the Undesirable Consequences of Using the Term "Silent" for Synonymous Changes
Part III: The Role of SNPs in Human Diseases
Part IV: An Examination of the Mechanisms by Which Synonymous Mutations Affect Protein Levels or Protein Folding, Which Affect Human Physiology and Response to Therapy
Part V: The Role of SNPs in Personalized Medicine and the Platform Technology of Codon Optimization
Summary
References
Contents
Part I: An Overview of Human Genome Sequencing and How to Access Information About SNVs
Chapter 1: SNPs Classification and Terminology: dbSNP Reference SNP (rs) Gene and Consequence Annotation
1.1 Introduction
1.2 What Is dbSNP Used for?
1.3 dbSNP Molecular Consequences (AKA Function Class)
1.4 Computed Molecular vs. Observed Functional Consequences
1.5 Computing Molecular Consequences in dbSNP
1.6 Splicing Variants
1.7 Other Non-CDS Variants
1.8 Searching dbSNP by Variant Consequences
References
Part II: A Broad Survey of SNPs, Their Classification into Synonymous and Non-synonymous and the Undesirable Consequences of Using the Term "Silent" for Synonymous Changes
Chapter 2: Evolutionary Forces That Generate SNPs: The Evolutionary Impacts of Synonymous Mutations
2.1 Introduction
2.2 Evidence for the Evolutionary Impacts of Synonymous Mutations
2.2.1 Indirect Evidence
2.2.2 Direct Evidence
2.3 Changing Evolutionary Perspectives on Synonymous Mutations
2.3.1 Phase I: Mostly Neutral
2.3.2 Phase II: Weak Translational Selection
2.3.3 Phase III: Pervasive (Sometimes Strong) Selection, Diverse Mechanisms
2.4 Summary and Future Directions
2.4.1 Building a Cohesive Evolutionary Framework
2.4.2 Predicting the Evolutionary Fate of Synonymous Mutations
2.4.3 Developing New Methods to Identify Signatures of Selection
2.4.4 Determining the Evolutionary History of Mechanisms Driving Selection at Synonymous Sites
References
Chapter 3: Recording Silence - Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease
3.1 Synonymous But Not Silent
3.2 An Ironic Oversight in Structural Biology
3.3 Lost Opportunities in the Machine Learning Revolution
3.4 Silently Shaping the Edifice of Life
References
Part III: The Role of SNPs in Human Disease
Introduction and Overview: Single Nucleotide Polymorphisms, Human Variation, and a Coming Revolution in Biology and Medicine
Introduction
Overview of the Book
Part I: An Overview of Human Genome Sequencing and How to Access Information About SNVs
Part II: A Broad Survey of SNPs, Their Classification into Synonymous and Non-synonymous, and the Undesirable Consequences of Using the Term "Silent" for Synonymous Changes
Part III: The Role of SNPs in Human Diseases
Part IV: An Examination of the Mechanisms by Which Synonymous Mutations Affect Protein Levels or Protein Folding, Which Affect Human Physiology and Response to Therapy
Part V: The Role of SNPs in Personalized Medicine and the Platform Technology of Codon Optimization
Summary
References
Contents
Part I: An Overview of Human Genome Sequencing and How to Access Information About SNVs
Chapter 1: SNPs Classification and Terminology: dbSNP Reference SNP (rs) Gene and Consequence Annotation
1.1 Introduction
1.2 What Is dbSNP Used for?
1.3 dbSNP Molecular Consequences (AKA Function Class)
1.4 Computed Molecular vs. Observed Functional Consequences
1.5 Computing Molecular Consequences in dbSNP
1.6 Splicing Variants
1.7 Other Non-CDS Variants
1.8 Searching dbSNP by Variant Consequences
References
Part II: A Broad Survey of SNPs, Their Classification into Synonymous and Non-synonymous and the Undesirable Consequences of Using the Term "Silent" for Synonymous Changes
Chapter 2: Evolutionary Forces That Generate SNPs: The Evolutionary Impacts of Synonymous Mutations
2.1 Introduction
2.2 Evidence for the Evolutionary Impacts of Synonymous Mutations
2.2.1 Indirect Evidence
2.2.2 Direct Evidence
2.3 Changing Evolutionary Perspectives on Synonymous Mutations
2.3.1 Phase I: Mostly Neutral
2.3.2 Phase II: Weak Translational Selection
2.3.3 Phase III: Pervasive (Sometimes Strong) Selection, Diverse Mechanisms
2.4 Summary and Future Directions
2.4.1 Building a Cohesive Evolutionary Framework
2.4.2 Predicting the Evolutionary Fate of Synonymous Mutations
2.4.3 Developing New Methods to Identify Signatures of Selection
2.4.4 Determining the Evolutionary History of Mechanisms Driving Selection at Synonymous Sites
References
Chapter 3: Recording Silence - Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease
3.1 Synonymous But Not Silent
3.2 An Ironic Oversight in Structural Biology
3.3 Lost Opportunities in the Machine Learning Revolution
3.4 Silently Shaping the Edifice of Life
References
Part III: The Role of SNPs in Human Disease