Molecular Photofitting: Predicting Ancestry and Phenotype Using DNA
Regular price
43.000 KD
inc. VAT
Couldn't load pickup availability
Table of contents
- Table of Contentsv
- Forewordxi
- Prefacexiii
- Acknowledgmentsxv
- Chapter 1: Forensic DNA Analysis: From Modest Beginnings to Molecular Photofitting, Genics, Genetics1
- Part I: Introduction: Brief History of DNA in Forensic Sciences1
- The Statistics of Forensic DNA Analysis6
- The Nature of Human Genetic Variation10
- Population Genetics and Population Genomics11
- The Promise of Molecular Photofitting as a Tool in Forensic Science16
- Part II: The Basic Principles19
- Lack of Human Diversity Relative to Other Species32
- Chapter 2: Ancestry and Admixture35
- What Are Ancestry and Admixture?35
- The Need for Molecular Tests for Ancestry37
- Ancestry Informative Markers43
- Biogeographical Ancestry Admixture as a Tool for Forensics and Physical Profiling54
- Chapter 3: Biogeographical Ancestry Admixture Estimation-Theoretical Considerations57
- Estimating by Anthropometric Trait Value57
- Admixture and Gene Flow Estimated from Single Loci59
- Admixture in Individual Samples68
- Using the Hanis Method on Population Models k>271
- Parameter Uncertainty75
- Bayesian Methods for Accommodating Parameter Uncertainty84
- Sampling Error88
- Assumptions about Marker Linkage and Intensity of Admixture in Parents90
- Pritchard’s Structure Program92
- In Defense of a Simple Admixture Model94
- Practical Considerations for Building an Ancestry Admixture Test95
- Selecting AIMs from the Genome-How Many Are Needed?103
- Comparing the Power of Specific Loci for Specific Resolutions110
- Genomic Coverage of AIMs114
- More Elaborate Methods of Selecting Markers for Information Content115
- Shannon Information116
- Fischerian Information Content118
- Informativeness for Assignment119
- Type of Polymorphisms123
- Interpretation of Ancestry Estimates125
- Objective Interpretation132
- Genetic Mapping and Admixture133
- Appendix (Ancestry Frequency Table)137
- Chapter 4: Biogeographical Ancestry Admixture Estimation-Practicality and Application145
- The Distribution of Human Genetic Variability and Choice of Population Model146
- Marker Selection163
- Sample Collection164
- Presenting Individual Biogeographical Ancestry (BGAA) Results179
- Conceptual Issues190
- Chapter 5: Characterizing Admixture Panels203
- Parental Sample Plots203
- Model Choices and Dimensionality205
- Size of Confidence Contours210
- Repeatability213
- Sensitivity220
- Analysis of Results for Genealogists222
- Analysis of Results for Nongenealogists230
- Blind Challenge of Concordance with Self-Assessed Race232
- Confidence Interval Warping235
- Sampled Pedigrees237
- Simulated Pedigrees240
- Comparing Different Algorithms with the Same AIM Panel241
- Analysis Using Subsets of Markers243
- Resolving Sample Mixtures245
- Sample Quantity250
- Nonhuman DNA251
- Performance with Altered Parental Allele Frequencies253
- Correlation with Anthropometric Phenotypes257
- Simulations260
- Creating Simulated Samples262
- Source of Error Measured with Simulations263
- Relationship between Error in Populations and within Individuals265
- Precision of the 71 AIM Panel from Simulations268
- Trends in Bias from the 71 AIM Panel270
- 95% Confidence Threshold for 71 AIM Panel273
- Precision of the 171 AIM Panel from Simulations275
- MLE Thresholds for Assumption of Bona Fide Affiliation277
- Comparison of 71 and 171 AIM Panels277
- Observed and Expected Bias277
- What Do the Simulations Teach Us about Interpreting BGA Admixture Results?279
- Bias Symmetry280
- Impact of MLE Algorithm Dimensionality282
- Simulations of Admixed Individuals284
- MLE Precision from the Triangle Plots285
- Confidence of Nonzero Affiliation286
- Standard Deviation from Confidence Intervals286
- Testing the Relation between Confidence Measures in Individuals and Populations288
- Space outside the Triangle Plot289
- Combined Sources Suggest an Average Error294
- Chapter 6: Apportionment of Autosomal Diversity With Continental Markers297
- The Need for Population Databases-Words Mean Less Than Data297
- Trends on an Ethnic Level: Autosomal Versus Sex Chromosome Pattern299
- What Do Continental Ancestry AIMs Say about Ethnicity?303
- The Significance of Fractional Affiliation Results on a Population Level305
- Reconstructing Human Histories from Autosomal Admixture Results310
- Shared Recent Ancestry Versus Admixture: What Does Fractional Continental Affiliation for an Ethnic311
- Returning Briefly to the Naming Problem-Relevance for Interpreting the Apportionment of Autosomal Di313
- A Sampling of Ethnicities Using the 171 AIM Panel316
- Interpretation of Ancestry Profiles for Ethnic Populations322
- East Asian Admixture in the Middle East and South Asia337
- Resolution within Continents Based on the Four-Population Model351
- Interpretation of Continental BGA Results in Light of What We Have Learned from Application to Ethni352
- Appropriateness of a Four-Population Model355
- Do Allele Frequency Estimation Errors Account for the Secondary Affiliations in Ethnic Subpopulation357
- Indications of Cryptic Population Structure359
- Chapter 7: Apportionment of Autosomal Diversity with Subcontinental Markers361
- Subpopulation AIMs and Ethnic Stratification361
- Within the European BGA Group-A Brief History of Europeans363
- How Do We Subdivide Europeans for Forensics Use?366
- Development of a Within-European AIM Panel367
- The Euro 1.0 AIM Panel for a Four-Population Subcontinental Model369
- Establishing the Optimal Parental Representatives370
- Blind Challenge with Ethnically Admixed European-American Samples378
- Population Isolates and Transplants380
- Correlations with Anthropometric Traits384
- Test Error387
- Hierarchical Nature of Euro 1.0-Prior Information Required397
- Euro 1.0 Pedigrees as an Aid to Interpreting Results403
- Euro 1.0-Interpretation of Variation within Groups407
- An Historical Perspective410
- More Detailed Subpopulation Stratifications„k = 7412
- What Do the Groups NOR1, NOR2 . . . Mean?414
- Evaluating the Results from the k = 7 European Model416
- Comparison with Previous Studies Based on Gene Markers417
- Comparison with Results from Other Studies419
- Blind Challenge of the k = 7 Model Results with Ethnic Samples420
- Correlation with Anthropometric Traits423
- Pedigrees425
- Substantial Variation in Admixture within Ethnic Groups425
- Alternative Styles for Estimating Ethnic Admixture427
- Chapter 8: Indirect Methods for Phenotype Inference429
- Estimates of Genomic Ancestry Allows for Inference of Certain Phenotypes429
- Phenotype Variation as a Function of Human Population History and Individual Ancestry430
- Sources of Phenotypic Variation432
- Empirical Observation of Admixture-Based Correlation Enables Generalization438
- Empiricism as a Tool for the Indirect Method of Molecular Photofitting440
- Reverse Facial Recognition Using Genomic Ancestry Estimates450
- Estimating Phenotype from 2D Digital Photographs454
- Estimating Phenotype from 3D Digital Photographs456
- Examples of Database Queries-Global Characteristics from Digital Photographs458
- Examples of Database Queries-Ethnic Descriptors and Geopolitical Affiliations461
- Variation and Parameterization of Database Observations464
- Can Social Construct Such as Race Be Inferred from DNA?468
- Indirect Approach Using Finer Population Models472
- Indirect Inference of Skin Pigmentation477
- Sources of the Ancestry-Skin Pigmentation Correlation485
- Can We Infer M Knowing Genomic Ancestry?488
- Inferences of Composite Characteristics490
- Why Not Use the Direct Method Instead?490
- Indirect Inference of Iris Pigmentation491
- Chapter 9: Direct Method of Phenotype Inference497
- Pigmentation500
- History of Pigmentation Research503
- The Genetics of Human Pigmentation-A Complex Puzzle504
- Biochemical Methods of Quantifying Pigment507
- Iris Color513
- Iris Color Phenotyping: The Need for a Thoughtful Approach514
- Making Iris Color Measurements517
- Population Surveys of Iris Melanin Index (IMI) Values523
- Relation of IMI to Self-Described Iris Color524
- History of Genetic Research on Iris Color527
- Recent History of Association Mapping Results530
- OCA2-The Primary Iris Color Gene534
- An Empirical OCA2-Based Classifier for the Inference of Iris Color543
- The Empirical Method of Direct Phenotype Inference553
- Case Reports558
- Hair Color562
- Skin Pigmentation583
- Final Considerations for the Direct Inference of Skin Pigmentation596
- Chapter 10: The First Case Studies of Molecular Photofitting599
- Case Reports599
- Louisiana Serial Killer Multiagency Homicide Task Force Investigation599
- Operation Minstead603
- The Boulder, Colorado Chase Case607
- Other Cases607
- Chapter 11: The Politics and Ethics of Genetic Ancestry Testing609
- Resistance610
- Articles-Insight into Public Reaction613
- Molecular Eyewitness: DNA Gets a Human Face613
- DNA Tests Offer Clues to Suspect’s Race618
- Concerns of the Defense-Minded626
- Concerns of the Prosecution-Minded629
- Resistance in the Scientific Community632
- Racism and Genetic Ancestry Testing647
- Racism and the Common Racist Mantra648
- The Data Does Not and Probably Cannot Support the Racist Viewpoint652
- Subjective Nature of the Word Intelligence655
- According to Nature, Diversity Is a Good Thing656
- Bibliography661
- Index677
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
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