Mathematical and statistical methods for genetic analysis:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
New York [u.a.]
Springer
2002
|
| Edition: | 2. ed. |
| Series: | Statistics for biology and health
|
| Subjects: | |
| Online Access: | Table of contents Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XVII, 361 S. graph. Darst. : 25 cm |
| ISBN: | 0387953892 |
Staff View
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Record in the Search Index
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| adam_text | Contents
Preface to the Second Edition vii
Preface to the First Edition ix
References xi
1 Basic Principles of Population Genetics 1
1.1 Introduction 1
1.2 Genetics Background 1
1.3 Hardy Weinberg Equilibrium 4
1.4 Linkage Equilibrium 8
1.5 Selection 9
1.6 Balance Between Mutation and Selection 11
1.7 Problems 12
1.8 References 19
2 Counting Methods and the EM Algorithm 21
2.1 Introduction 21
2.2 Gene Counting 21
2.3 Description of the EM Algorithm 23
2.4 Ascent Property of the EM Algorithm 24
2.5 Allele Frequency Estimation by the EM Algorithm 26
2.6 Classical Segregation Analysis by the EM Algorithm .... 27
2.7 Binding Domain Identification 31
2.8 Problems 32
2.9 References 37
3 Newton s Method and Scoring 39
3.1 Introduction 39
3.2 Newton s Method 39
3.3 Scoring 40
3.4 Application to the Design of Linkage Experiments 43
3.5 Quasi Newton Methods 45
3.6 The Dirichlet Distribution 47
3.7 Empirical Bayes Estimation of Allele Frequencies 48
3.8 Empirical Bayes Estimation of Haplotype Frequencies ... 51
3.9 Problems 52
3.10 References 56
xiv Contents
4 Hypothesis Testing and Categorical Data 59
4.1 Introduction 59
4.2 Hypotheses About Genotype Frequencies 59
4.3 Other Multinomial Problems in Genetics 62
4.4 The Zmax Test 63
4.5 The Wd Statistic 65
4.6 Exact Tests of Independence 67
4.7 Case Control Association Tests 69
4.8 The Transmission/Disequilibrium Test 70
4.9 Problems 73
4.10 References 76
5 Genetic Identity Coefficients 81
5.1 Introduction 81
5.2 Kinship and Inbreeding Coefficients 81
5.3 Condensed Identity Coefficients 84
5.4 Generalized Kinship Coefficients 86
5.5 From Kinship to Identity Coefficients 86
5.6 Calculation of Generalized Kinship Coefficients 88
5.7 Problems 91
5.8 References 94
6 Applications of Identity Coefficients 97
6.1 Introduction 97
6.2 Genotype Prediction 97
6.3 Covariances for a Quantitative Trait 99
6.4 Risk Ratios and Genetic Model Discrimination 102
6.5 An Affecteds Only Method of Linkage Analysis 106
6.6 Problems 109
6.7 References 113
7 Computation of Mendelian Likelihoods 115
7.1 Introduction 115
7.2 Mendelian Models 115
7.3 Genotype Elimination and Allele Consolidation 118
7.4 Array Transformations and Iterated Sums 120
7.5 Array Factoring 122
7.6 Examples of Pedigree Analysis 124
7.7 Problems 133
7.8 References 136
8 The Polygenic Model 139
8.1 Introduction 139
8.2 Maximum Likelihood Estimation by Scoring 140
8.3 Application to Gc Measured Genotype Data 144
Contents xv
8.4 Multivariate Traits 145
8.5 Left and Right Hand Finger Ridge Counts 147
8.6 QTL Mapping 148
8.7 Factor Analysis 149
8.8 A QTL Example 150
8.9 The Hypergeometric Polygenic Model 152
8.10 Application to Risk Prediction 155
8.11 Problems 156
8.12 References 163
9 Descent Graph Methods 167
9.1 Introduction 167
9.2 Review of Discrete Time Markov Chains 168
9.3 The Hastings Metropolis Algorithm and Simulated Annealingl71
9.4 Descent States and Descent Graphs 173
9.5 Descent Trees and the Founder Tree Graph 175
9.6 The Descent Graph Markov Chain 179
9.7 Computing Location Scores 182
9.8 Finding a Legal Descent Graph 183
,9.9 Haplotyping 184
9.10 Application to Episodic Ataxia 185
9.11 The Lander Green Kruglyak Algorithm 185
9.12 Genotyping Errors 189
9.13 Marker Sharing Statistics 190
9.14 Problems 193
9.15 References 196
10 Molecular Phylogeny 199
10.1 Introduction 199
10.2 Evolutionary Trees 199
10.3 Maximum Parsimony 201
10.4 Review of Continuous Time Markov Chains 205
10.5 A Nucleotide Substitution Model 207
10.6 Maximum Likelihood Reconstruction 210
10.7 Origin of the Eukaryotes 211
10.8 Codon Models 214
10.9 Variation in the Rate of Evolution 215
10.10 Illustration of the Codon and Rate Models 217
10.11 Problems 218
10.12 References 223
11 Radiation Hybrid Mapping 225
11.1 Introduction 225
11.2 Models for Radiation Hybrids 226
11.3 Minimum Obligate Breaks Criterion 227
xvi Contents
11.4 Maximum Likelihood Methods 230
11.5 Application to Haploid Data 232
11.6 Polyploid Radiation Hybrids 233
11.7 Maximum Likelihood Under Polyploidy 234
11.8 Obligate Breaks Under Polyploidy 238
11.9 Bayesian Methods 239
11.10 Application to Diploid Data 242
11.11 Problems 244
11.12 References 247
12 Models of Recombination 251
12.1 Introduction 251
12.2 Mather s Formula and Its Generalization 252
12.3 Count Location Model 254
12.4 Stationary Renewal Models 255
12.5 Poisson Skip Model 258
12.6 Chiasma Interference 264
12.7 Application to Drosophila Data 266
12.8 Problems 268
12.9 References 272
13 Sequence Analysis 275
13.1 Introduction • • • 275
13.2 Pattern Matching 275
13.3 Alphabets, Strings, and Alignments 277
13.4 Minimum Distance Alignment 279
13.5 Parallel Processing and Memory Reduction 283
13.6 Maximum Similarity Alignment 284
13.7 Local Similarity Alignment 285
13.8 Multiple Sequence Comparisons 286
13.9 References 290
14 Poisson Approximation 293
14.1 Introduction 293
14.2 The Law of Rare Events 294
14.3 Poisson Approximation to the Wd Statistic 294
14.4 Construction of Somatic Cell Hybrid Panels 295
14.5 Biggest Marker Gap 298
14.6 Randomness of Restriction Sites 300
14.7 DNA Sequence Matching 302
14.8 Problems 305
14.9 References 309
15 Diffusion Processes 311
15.1 Introduction 311
Contents xvii
15.2 Review of Diffusion Processes 311
15.3 Wright Fisher Model 314
15.4 First Passage Time Problems 316
15.5 Process Moments 319
15.6 Equilibrium Distribution 320
15.7 Numerical Methods for Diffusion Processes 322
15.8 Numerical Methods for the Wright Fisher Process 326
15.9 Specific Example for a Recessive Disease 327
15.10 Problems 330
15.11 References 332
Appendix A: Molecular Genetics in Brief 335
A.I Genes and Chromosomes 335
A.2 From Gene to Protein 337
A.3 Manipulating DNA 339
A.4 Mapping Strategies 340
A.5 References 342
Appendix B: The Normal Distribution 345
B.I Univariate Normal Random Variables 345
B.2 Multivariate Normal Random Vectors 346
B.3 References 348
Index 349
|
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| discipline | Biologie Mathematik |
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| spelling | Lange, Kenneth 1946- Verfasser (DE-588)142260576 aut Mathematical and statistical methods for genetic analysis Kenneth Lange 2. ed. New York [u.a.] Springer 2002 XVII, 361 S. graph. Darst. : 25 cm txt rdacontent n rdamedia nc rdacarrier Statistics for biology and health Literaturangaben Génétique - Modèles mathématiques Génétique - Méthodes statistiques Mathematisches Modell Genetics -- Mathematical models Genetics -- Statistical methods Mathematische Methode (DE-588)4155620-3 gnd rswk-swf Statistik (DE-588)4056995-0 gnd rswk-swf Genetik (DE-588)4071711-2 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Genetik (DE-588)4071711-2 s Genanalyse (DE-588)4200230-8 s Mathematische Methode (DE-588)4155620-3 s Statistik (DE-588)4056995-0 s 1\p DE-604 DE-604 http://www.loc.gov/catdir/toc/fy022/2001054918.html Table of contents HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009853098&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Lange, Kenneth 1946- Mathematical and statistical methods for genetic analysis Génétique - Modèles mathématiques Génétique - Méthodes statistiques Mathematisches Modell Genetics -- Mathematical models Genetics -- Statistical methods Mathematische Methode (DE-588)4155620-3 gnd Statistik (DE-588)4056995-0 gnd Genetik (DE-588)4071711-2 gnd Genanalyse (DE-588)4200230-8 gnd |
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| title | Mathematical and statistical methods for genetic analysis |
| title_auth | Mathematical and statistical methods for genetic analysis |
| title_exact_search | Mathematical and statistical methods for genetic analysis |
| title_full | Mathematical and statistical methods for genetic analysis Kenneth Lange |
| title_fullStr | Mathematical and statistical methods for genetic analysis Kenneth Lange |
| title_full_unstemmed | Mathematical and statistical methods for genetic analysis Kenneth Lange |
| title_short | Mathematical and statistical methods for genetic analysis |
| title_sort | mathematical and statistical methods for genetic analysis |
| topic | Génétique - Modèles mathématiques Génétique - Méthodes statistiques Mathematisches Modell Genetics -- Mathematical models Genetics -- Statistical methods Mathematische Methode (DE-588)4155620-3 gnd Statistik (DE-588)4056995-0 gnd Genetik (DE-588)4071711-2 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Génétique - Modèles mathématiques Génétique - Méthodes statistiques Mathematisches Modell Genetics -- Mathematical models Genetics -- Statistical methods Mathematische Methode Statistik Genetik Genanalyse Aufsatzsammlung |
| url | http://www.loc.gov/catdir/toc/fy022/2001054918.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009853098&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT langekenneth mathematicalandstatisticalmethodsforgeneticanalysis |