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Molecular Photofitting : Predicting Ancestry and Phenotype Using DNA.
Title:
Molecular Photofitting : Predicting Ancestry and Phenotype Using DNA.
Author:
Frudakis, Ph.D., Tony.
ISBN:
9780080551371
Personal Author:
Physical Description:
1 online resource (711 pages)
Contents:
Front Cover -- Molecular Photofitting -- Copyright Page -- Table of Contents -- Foreword -- Preface -- Acknowledgments -- Chapter 1: Forensic DNA Analysis: From Modest Beginnings to Molecular Photofitting, Genics, Genetics, Genomics, and the Pertinent Population Genetics Principles -- Part I: Introduction: Brief History of DNA in Forensic Sciences -- The Statistics of Forensic DNA Analysis -- The Nature of Human Genetic Variation -- Population Genetics and Population Genomics -- The Promise of Molecular Photofitting as a Tool in Forensic Science -- Part II: The Basic Principles -- Lack of Human Diversity Relative to Other Species -- Chapter 2: Ancestry and Admixture -- What Are Ancestry and Admixture? -- The Need for Molecular Tests for Ancestry -- Ancestry Informative Markers -- Biogeographical Ancestry Admixture as a Tool for Forensics and Physical Profiling -- Chapter 3: Biogeographical Ancestry Admixture Estimation-Theoretical Considerations -- Estimating by Anthropometric Trait Value -- Admixture and Gene Flow Estimated from Single Loci -- Admixture in Individual Samples -- Using the Hanis Method on Population Models k>2 -- Parameter Uncertainty -- Bayesian Methods for Accommodating Parameter Uncertainty -- Sampling Error -- Assumptions about Marker Linkage and Intensity of Admixture in Parents -- Pritchard's Structure Program -- In Defense of a Simple Admixture Model -- Practical Considerations for Building an Ancestry Admixture Test -- Selecting AIMs from the Genome-How Many Are Needed? -- Comparing the Power of Specific Loci for Specific Resolutions -- Genomic Coverage of AIMs -- More Elaborate Methods of Selecting Markers for Information Content -- Shannon Information -- Fischerian Information Content -- Informativeness for Assignment -- Type of Polymorphisms -- Interpretation of Ancestry Estimates -- Objective Interpretation.
Genetic Mapping and Admixture -- Appendix (Ancestry Frequency Table) -- Chapter 4: Biogeographical Ancestry Admixture Estimation-Practicality and Application -- The Distribution of Human Genetic Variability and Choice of Population Model -- Marker Selection -- Sample Collection -- Presenting Individual Biogeographical Ancestry (BGAA) Results -- Conceptual Issues -- Chapter 5: Characterizing Admixture Panels -- Parental Sample Plots -- Model Choices and Dimensionality -- Size of Confidence Contours -- Repeatability -- Sensitivity -- Analysis of Results for Genealogists -- Analysis of Results for Nongenealogists -- Blind Challenge of Concordance with Self-Assessed Race -- Confidence Interval Warping -- Sampled Pedigrees -- Simulated Pedigrees -- Comparing Different Algorithms with the Same AIM Panel -- Analysis Using Subsets of Markers -- Resolving Sample Mixtures -- Sample Quantity -- Nonhuman DNA -- Performance with Altered Parental Allele Frequencies -- Correlation with Anthropometric Phenotypes -- Simulations -- Creating Simulated Samples -- Source of Error Measured with Simulations -- Relationship between Error in Populations and within Individuals -- Precision of the 71 AIM Panel from Simulations -- Trends in Bias from the 71 AIM Panel -- 95% Confidence Threshold for 71 AIM Panel -- Precision of the 171 AIM Panel from Simulations -- MLE Thresholds for Assumption of Bona Fide Affiliation -- Comparison of 71 and 171 AIM Panels -- Observed and Expected Bias -- What Do the Simulations Teach Us about Interpreting BGA Admixture Results? -- Bias Symmetry -- Impact of MLE Algorithm Dimensionality -- Simulations of Admixed Individuals -- MLE Precision from the Triangle Plots -- Confidence of Nonzero Affiliation -- Standard Deviation from Confidence Intervals -- Testing the Relation between Confidence Measures in Individuals and Populations.
Space outside the Triangle Plot -- Combined Sources Suggest an Average Error -- Chapter 6: Apportionment of Autosomal Diversity With Continental Markers -- The Need for Population Databases-Words Mean Less Than Data -- Trends on an Ethnic Level: Autosomal Versus Sex Chromosome Pattern -- What Do Continental Ancestry AIMs Say about Ethnicity? -- The Significance of Fractional Affiliation Results on a Population Level -- Reconstructing Human Histories from Autosomal Admixture Results -- Shared Recent Ancestry Versus Admixture: What Does Fractional Continental Affiliation for an Ethnic Group Mean? -- Returning Briefly to the Naming Problem-Relevance for Interpreting the Apportionment of Autosomal Diversity -- A Sampling of Ethnicities Using the 171 AIM Panel -- Interpretation of Ancestry Profiles for Ethnic Populations -- East Asian Admixture in the Middle East and South Asia -- Resolution within Continents Based on the Four-Population Model -- Interpretation of Continental BGA Results in Light of What We Have Learned from Application to Ethnic Populations -- Appropriateness of a Four-Population Model -- Do Allele Frequency Estimation Errors Account for the Secondary Affiliations in Ethnic Subpopulations? -- Indications of Cryptic Population Structure -- Chapter 7: Apportionment of Autosomal Diversity with Subcontinental Markers -- Subpopulation AIMs and Ethnic Stratification -- Within the European BGA Group-A Brief History of Europeans -- How Do We Subdivide Europeans for Forensics Use? -- Development of a Within-European AIM Panel -- The Euro 1.0 AIM Panel for a Four-Population Subcontinental Model -- Establishing the Optimal Parental Representatives -- Blind Challenge with Ethnically Admixed European-American Samples -- Population Isolates and Transplants -- Correlations with Anthropometric Traits -- Test Error.
Hierarchical Nature of Euro 1.0-Prior Information Required -- Euro 1.0 Pedigrees as an Aid to Interpreting Results -- Euro 1.0-Interpretation of Variation within Groups -- An Historical Perspective -- More Detailed Subpopulation Stratifications-k = 7 -- What Do the Groups NOR1, NOR2 . . . Mean? -- Evaluating the Results from the k = 7 European Model -- Comparison with Previous Studies Based on Gene Markers -- Comparison with Results from Other Studies -- Blind Challenge of the k = 7 Model Results with Ethnic Samples -- Correlation with Anthropometric Traits -- Pedigrees -- Substantial Variation in Admixture within Ethnic Groups -- Alternative Styles for Estimating Ethnic Admixture -- Chapter 8: Indirect Methods for Phenotype Inference -- Estimates of Genomic Ancestry Allows for Inference of Certain Phenotypes -- Phenotype Variation as a Function of Human Population History and Individual Ancestry -- Sources of Phenotypic Variation -- Empirical Observation of Admixture-Based Correlation Enables Generalization -- Empiricism as a Tool for the Indirect Method of Molecular Photofitting -- Reverse Facial Recognition Using Genomic Ancestry Estimates -- Estimating Phenotype from 2D Digital Photographs -- Estimating Phenotype from 3D Digital Photographs -- Examples of Database Queries-Global Characteristics from Digital Photographs -- Examples of Database Queries-Ethnic Descriptors and Geopolitical Affiliations -- Variation and Parameterization of Database Observations -- Can Social Construct Such as Race Be Inferred from DNA? -- Indirect Approach Using Finer Population Models -- Indirect Inference of Skin Pigmentation -- Sources of the Ancestry-Skin Pigmentation Correlation -- Can We Infer M Knowing Genomic Ancestry? -- Inferences of Composite Characteristics -- Why Not Use the Direct Method Instead? -- Indirect Inference of Iris Pigmentation.
Chapter 9: Direct Method of Phenotype Inference -- Pigmentation -- History of Pigmentation Research -- The Genetics of Human Pigmentation-A Complex Puzzle -- Biochemical Methods of Quantifying Pigment -- Iris Color -- Iris Color Phenotyping: The Need for a Thoughtful Approach -- Making Iris Color Measurements -- Population Surveys of Iris Melanin Index (IMI) Values -- Relation of IMI to Self-Described Iris Color -- History of Genetic Research on Iris Color -- Recent History of Association Mapping Results -- OCA2-The Primary Iris Color Gene -- An Empirical OCA2-Based Classifier for the Inference of Iris Color -- The Empirical Method of Direct Phenotype Inference -- Case Reports -- Hair Color -- Skin Pigmentation -- Final Considerations for the Direct Inference of Skin Pigmentation -- Chapter 10: The First Case Studies of Molecular Photofitting -- Case Reports -- Louisiana Serial Killer Multiagency Homicide Task Force Investigation -- Operation Minstead -- The Boulder, Colorado Chase Case -- Other Cases -- Chapter 11: The Politics and Ethics of Genetic Ancestry Testing -- Resistance -- Articles-Insight into Public Reaction -- Molecular Eyewitness: DNA Gets a Human Face -- DNA Tests Offer Clues to Suspect's Race -- Concerns of the Defense-Minded -- Concerns of the Prosecution-Minded -- Resistance in the Scientific Community -- Racism and Genetic Ancestry Testing -- Racism and the Common Racist Mantra -- The Data Does Not and Probably Cannot Support the Racist Viewpoint -- Subjective Nature of the Word Intelligence -- According to Nature, Diversity Is a Good Thing -- Bibliography -- Index.
Abstract:
In the field of forensics, there is a critical need for genetic tests that can function in a predictive or inferential sense, before suspects have been identified, and/or for crimes for which DNA evidence exists but eye-witnesses do not. Molecular Photofitting fills this need by describing the process of generating a physical description of an individual from the analysis of his or her DNA. The molecular photofitting process has been used to assist with the identification of remains and to guide criminal investigations toward certain individuals within the sphere of prior suspects. Molecular Photofitting provides an accessible roadmap for both the forensic scientist hoping to make use of the new tests becoming available, and for the human genetic researcher working to discover the panels of markers that comprise these tests. By implementing population structure as a practical forensics and clinical genomics tool, Molecular Photofitting serves to redefine the way science and history look at ancestry and genetics, and shows how these tools can be used to maximize the efficacy of our criminal justice system. * Explains how physical descriptions of individuals can be generated using only their DNA * Contains case studies that show how this new forensic technology is used in practical application * Includes over 100 diagrams, tables, and photos to illustrate and outline complex concepts.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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