Statistical genetics: gene mapping through linkage and association
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
New York, NY [u.a.]
Taylor & Francis
2008
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XXVIII, 574 S. Ill., graph. Darst. |
| ISBN: | 9780415410403 |
Internformat
MARC
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| 084 | |a BIO 180f |2 stub | ||
| 084 | |a BIO 107f |2 stub | ||
| 245 | 1 | 0 | |a Statistical genetics |b gene mapping through linkage and association |c ed. by Benjamin M. Neale ... [et al.] |
| 264 | 1 | |a New York, NY [u.a.] |b Taylor & Francis |c 2008 | |
| 300 | |a XXVIII, 574 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Includes bibliographical references and index | ||
| 650 | 7 | |a Genen |2 gtt | |
| 650 | 7 | |a Genetica |2 gtt | |
| 650 | 7 | |a Statistische methoden |2 gtt | |
| 650 | 4 | |a Chromosome Mapping |x methods |v Congresses | |
| 650 | 4 | |a Gene mapping |x Statistical methods |v Congresses | |
| 650 | 4 | |a Linkage (Genetics) |v Congresses | |
| 650 | 4 | |a Linkage (Genetics) |x Statistical methods |v Congresses | |
| 650 | 4 | |a Models, Statistical |v Congresses | |
| 650 | 0 | 7 | |a Methode |0 (DE-588)4038971-6 |2 gnd |9 rswk-swf |
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| 700 | 1 | |a Neale, Benjamin M. |e Sonstige |4 oth | |
| 856 | 4 | 2 | |m Digitalisierung TU Muenchen |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272278&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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Datensatz im Suchindex
| _version_ | 1804137311416352768 |
|---|---|
| adam_text | Contents
About the editors
xi
List of contributors
xiii
Preface
xvii
Acknowledgements
xix
Foreword by Nicholas
G. Martin,
Dorret
I. Boomsma, Michael C. Neale,
and
Hermine
H.
Maes
xxi
Abbreviations
xxv
Statistical symbols
xxvii
THE BASICS
Chapter
1
Introduction
1
Nicholas G. Martin
Chapter
2
Basics of
DNA
and genotyping
5
Jesen
A. Fagerness and Dale R. Nyholt
2.1 DNA
Structure
5
2.2 DNA
Recombination and Genetic Distance
8
2.3
Genotyping
11
2.4
Genotyping Technologies
13
2.5
Conclusion
15
Chapter
3
Introduction to biometrical genetics
17
Johnny S.H. Kwan, Shaun
Purceii
and
Рак С.
Sham
3.1
Historical Background
17
3.2
Mendelian Inheritance
18
3.3
Random Mating
19
3.4
Polygenic Inheritance
21
3.5
Kinship and Genetic Sharing
23
3.6
Fisher s Model for a Single Locus
26
3.7
Fisher s Model for Multiple Loci and
Environmental Effects
36
3.8
Conclusion
41
Chapter
4
Introduction to statistics
43
Frühling
V. Rijsdijk
4.1
Introduction
43
4.2
Descriptive Statistics
44
4.3
Inferential Statistics
48
4.4
Linear Regression 50
4.5
Likelihood 53
4.6
Mixture Distributions 5^
4.7
Conclusion
.
58
Chapter
5
Statistical power 61
Conor V. Dolan and
Stéphanie M.
van den Berg
5.1
Probabilities of
(Incorrect
Decisions
62
5.2
Maximum-likelihood Estimation
64
5.3
Summary 75
5.4
Example 75
5.5
Least-squares Estimation 77
5.6
Sufficient Statistics
8°
5.7
Conclusions and Limitations
81
Chapter
6
Population genetics and its relevance
to gene mapping
87
Naomi R. Wray and Peter M. Visscher
6.1
Introduction
87
6.2
Hardy-Weinberg (Dis)equilibrmm
88
6.3
Genetic Drift and Inbreeding
94
6.4
Linkage Disequilibrium
100
6.5
Conclusion
110
LINKAGE ANALYSIS
__________
Chapter
7
Principles of linkage analysis
113
Dale R. Nyholt
7.1
Gene Mapping
113
7.2
Model-based Linkage Analysis
114
7.3
Model-free Linkage Analysis of
Affection Traits
120
7.4
Empirically Deriving Genome-wide
Linkage Significance
128
7.5
Conclusion
130
Chapter
8
Algorithms for IBD estimation
135
Gonçalo R. Abecasis
8.1
Introduction
135
8.2
The Computational Problem: Dealing
with Unknown Phase
135
8.3
Analysis of Pedigree Data
137
8.4
Practical Examples
143
Chapter
9
Regression methods for linkage analysis
153
Stacey S. Cherny
9.1
Introduction
153
Contents
vii
9.2 Haseman-Elston 153
9.3
Extensions
to Haseman-Elston
154
9.4
Full-pedigree Regression-based Linkage
155
9.5
Simulation Studies
162
9.6
Examples using MERLIN-regress
173
9.7
Conclusion
175
Chapter
10
Variance components linkage
analysis for quantitative traits
181
Danielle
Posthuma
and
Hermine H.
Maes
10.1
Introduction
181
10.2
The VC Linkage Model
182
10.3
Conducting Variance Components Linkage
Analysis with MERLIN
187
10.4
VC Linkage Analysis in General Structural
Equation Packages
190
10.5
Conclusion
203
Chapter I I Extensions to univariate linkage anal/sis
207
Sarah
E. Mediana
11.1
Parent-of-Origin Effects
207
11.2
Genotype-by-Environment Interaction
216
11.3
Х
-chromosome Linkage
224
11.4
Implementation of Extensions to
Univariate Linkage Analysis
231
Chapter 1
2
QTL detection in multivariate
data from sibling pairs
239
Jouke Jan Hottenga and
Dorret
I. Boomsma
12.1
Introduction
239
12.2
A Brief History of Multivariate Analysis
in Human Genetics/Twin Studies
240
12.3
Trait Selection
242
12.4
Multivariate VC Linkage Analysis
244
12.5
Multivariate QTL Analyses: Practical
Issues
251
12.6
Conclusion
258
Chapter 1
3
Factors affecting type-l error
and power of linkage analysis
Manuel A.R.
Ferreira
13.1
Selective Sampling
13.2
Sample Size
13.3.
Deviations in Trait Distribution
13.4
Outliers
13.5
Pedigree Errors
13.6
Genotyping Errors
265
266
271
278
283
285
287
viii Contents
13.7 Marker Informativeness,
Density
and Genetic Map
290
13.8
Quality Control Guidelines
300
ASSOCIATION ANALYSIS
Chapter 1
4
Introduction to association
311
Danielle M. Dick
14.1
Introduction
311
14.2
Methods Used in Association
311
14.3
Concepts Central to Association
314
14.4
The International HapMap Project
315
14.5
Power to Detect Association
317
14.6
Uses of Association
317
14.7
Conclusion
319
Chapter 1
5
Single-locus association models
323
Sophie van
der Sluis
and Danielle
Posthuma
15.1
Introduction
323
15.2
Association Analysis with Random
Population Samples
325
15.3
Case-control Studies
329
15.4
Family-based Association Studies
333
15.5
Conclusion
351
Chapter 1
6
Analyzing genome-wide association
study data: a tutorial using PLINK
355
Patrick F. Sullivan and Shaun
Purceii
16.1
Introduction
355
16.2
GWAS
355
16.3
GWAS
SNP Genotyping
and
Data Handling
360
16.4
Preparing GWAS Data for Analysis
366
16.5
Outline of GWAS Data Analysis
370
16.6
Quality Control
370
16.7
Copy Number Variation
376
16.8
Descriptive Analyses of the ALS/Control
GWAS Data
377
16.9
Association Analyses of GWAS Data
383
16.10
Additional Features in PLINK
390
16.11
Future Developments
391
16.12
Conclusion
391
Chapter
17
Haplotype estimation
395
Andrew P. Morris
17.1
Introduction
395
17.2
Population-Based Haplotype
Reconstruction 39fi
Contents ix
17.3
Family-Based Haplotype
Reconstruction
17.4
Using Estimated Haplotypes for
Disease-Gene Mapping
17.5
Conclusion
407
411
418
Chapter
18
Regional multilocus association models
423
Jo Knight,
Рак С.
Sham, Shaun
Purceii
and Benjamin M. Neale
18.1
Introduction and Basic Methods
423
18.2
Phased Versus Unphased
426
18.3
Utility of Multimarker Tests
430
18.4
WHAP Analysis
434
18.5
Conclusion
446
Chapter
19
Linkage disequilibrium and tagging
451
Benjamin M. Neale
19.1
Linkage Disequilibrium Statistics
451
19.2
Block-like Nature of the Genome
454
19.3
Tagging
457
19.4
Population Differences
459
19.5
Multiallelic Markers
460
19.6
Conclusion
461
Chapter
20
Practical guide to linkage disequilibrium
analysis and tagging using Haploview
467
David J. Bender and Julian B. Mailer
20.1
Introduction
467
20.2
Data Checks
468
20.3
Linkage Disequilibrium Analysis
471
20.4
Tagging Analysis
473
20.5
Viewing PLINK Results in Haploview
476
20.6
Additional Considerations
and Programs
483
20.7
Conclusion
484
Chapter
2
1 Factors affecting power and type-l
error in association
David M. Evans
21.1
Introduction
21.2
Factors Affecting Power to Detect
Association
21.3
Population Stratification
21.4
Genotyping Error
21.5
Genome-wide Association
21.6
Calculating Power to Detect
Association
21.7
Conclusion
487
487
488
499
510
515
518
526
χ
Contents
Chapter
22
Resampling approaches to
statistical inference
535
Michael C. Neale and Sarah
E. Mediana
22.1
Introduction
535
22.2
Bootstrap Estimation
537
22.3
Permutation Tests
544
Appendix
1
File formats
551
Al.l Overview
551
Al.
2
MERLIN/MERLIN-Regresss/Pedstats/
Minx/QTDT/GRR
551
A1.3 WRAP
560
Al.
4
Haploview
561
A1.5 PLINK
563
Al.
6
Running programs in DOS versus
Unix/Linux
565
Online resources
569
Index
571
|
| adam_txt |
Contents
About the editors
xi
List of contributors
xiii
Preface
xvii
Acknowledgements
xix
Foreword by Nicholas
G. Martin,
Dorret
I. Boomsma, Michael C. Neale,
and
Hermine
H.
Maes
xxi
Abbreviations
xxv
Statistical symbols
xxvii
THE BASICS
Chapter
1
Introduction
1
Nicholas G. Martin
Chapter
2
Basics of
DNA
and genotyping
5
Jesen
A. Fagerness and Dale R. Nyholt
2.1 DNA
Structure
5
2.2 DNA
Recombination and Genetic Distance
8
2.3
Genotyping
11
2.4
Genotyping Technologies
13
2.5
Conclusion
15
Chapter
3
Introduction to biometrical genetics
17
Johnny S.H. Kwan, Shaun
Purceii
and
Рак С.
Sham
3.1
Historical Background
17
3.2
Mendelian Inheritance
18
3.3
Random Mating
19
3.4
Polygenic Inheritance
21
3.5
Kinship and Genetic Sharing
23
3.6
Fisher's Model for a Single Locus
26
3.7
Fisher's Model for Multiple Loci and
Environmental Effects
36
3.8
Conclusion
41
Chapter
4
Introduction to statistics
43
Frühling
V. Rijsdijk
4.1
Introduction
43
4.2
Descriptive Statistics
44
4.3
Inferential Statistics
48
4.4
Linear Regression 50
4.5
Likelihood 53
4.6
Mixture Distributions 5^
4.7
Conclusion
.
58
Chapter
5
Statistical power 61
Conor V. Dolan and
Stéphanie M.
van den Berg
5.1
Probabilities of
(Incorrect
Decisions
62
5.2
Maximum-likelihood Estimation
64
5.3
Summary 75
5.4
Example 75
5.5
Least-squares Estimation 77
5.6
Sufficient Statistics
8°
5.7
Conclusions and Limitations
81
Chapter
6
Population genetics and its relevance
to gene mapping
87
Naomi R. Wray and Peter M. Visscher
6.1
Introduction
87
6.2
Hardy-Weinberg (Dis)equilibrmm
88
6.3
Genetic Drift and Inbreeding
94
6.4
Linkage Disequilibrium
100
6.5
Conclusion
110
LINKAGE ANALYSIS
_
Chapter
7
Principles of linkage analysis
113
Dale R. Nyholt
7.1
Gene Mapping
113
7.2
Model-based Linkage Analysis
114
7.3
Model-free Linkage Analysis of
Affection Traits
120
7.4
Empirically Deriving Genome-wide
Linkage Significance
128
7.5
Conclusion
130
Chapter
8
Algorithms for IBD estimation
135
Gonçalo R. Abecasis
8.1
Introduction
135
8.2
The Computational Problem: Dealing
with Unknown Phase
135
8.3
Analysis of Pedigree Data
137
8.4
Practical Examples
143
Chapter
9
Regression methods for linkage analysis
153
Stacey S. Cherny
9.1
Introduction
153
Contents
vii
9.2 Haseman-Elston 153
9.3
Extensions
to Haseman-Elston
154
9.4
Full-pedigree Regression-based Linkage
155
9.5
Simulation Studies
162
9.6
Examples using MERLIN-regress
173
9.7
Conclusion
175
Chapter
10
Variance components linkage
analysis for quantitative traits
181
Danielle
Posthuma
and
Hermine H.
Maes
10.1
Introduction
181
10.2
The VC Linkage Model
182
10.3
Conducting Variance Components Linkage
Analysis with MERLIN
187
10.4
VC Linkage Analysis in General Structural
Equation Packages
190
10.5
Conclusion
203
Chapter I I Extensions to univariate linkage anal/sis
207
Sarah
E. Mediana
11.1
Parent-of-Origin Effects
207
11.2
Genotype-by-Environment Interaction
216
11.3
Х
-chromosome Linkage
224
11.4
Implementation of Extensions to
Univariate Linkage Analysis
231
Chapter 1
2
QTL detection in multivariate
data from sibling pairs
239
Jouke Jan Hottenga and
Dorret
I. Boomsma
12.1
Introduction
239
12.2
A Brief History of Multivariate Analysis
in Human Genetics/Twin Studies
240
12.3
Trait Selection
242
12.4
Multivariate VC Linkage Analysis
244
12.5
Multivariate QTL Analyses: Practical
Issues
251
12.6
Conclusion
258
Chapter 1
3
Factors affecting type-l error
and power of linkage analysis
Manuel A.R.
Ferreira
13.1
Selective Sampling
13.2
Sample Size
13.3.
Deviations in Trait Distribution
13.4
Outliers
13.5
Pedigree Errors
13.6
Genotyping Errors
265
266
271
278
283
285
287
viii Contents
13.7 Marker Informativeness,
Density
and Genetic Map
290
13.8
Quality Control Guidelines
300
ASSOCIATION ANALYSIS
Chapter 1
4
Introduction to association
311
Danielle M. Dick
14.1
Introduction
311
14.2
Methods Used in Association
311
14.3
Concepts Central to Association
314
14.4
The International HapMap Project
315
14.5
Power to Detect Association
317
14.6
Uses of Association
317
14.7
Conclusion
319
Chapter 1
5
Single-locus association models
323
Sophie van
der Sluis
and Danielle
Posthuma
15.1
Introduction
323
15.2
Association Analysis with Random
Population Samples
325
15.3
Case-control Studies
329
15.4
Family-based Association Studies
333
15.5
Conclusion
351
Chapter 1
6
Analyzing genome-wide association
study data: a tutorial using PLINK
355
Patrick F. Sullivan and Shaun
Purceii
16.1
Introduction
355
16.2
GWAS
355
16.3
GWAS
SNP Genotyping
and
Data Handling
360
16.4
Preparing GWAS Data for Analysis
366
16.5
Outline of GWAS Data Analysis
370
16.6
Quality Control
370
16.7
Copy Number Variation
376
16.8
Descriptive Analyses of the ALS/Control
GWAS Data
377
16.9
Association Analyses of GWAS Data
383
16.10
Additional Features in PLINK
390
16.11
Future Developments
391
16.12
Conclusion
391
Chapter
17
Haplotype estimation
395
Andrew P. Morris
17.1
Introduction
395
17.2
Population-Based Haplotype
Reconstruction 39fi
Contents ix
17.3
Family-Based Haplotype
Reconstruction
17.4
Using Estimated Haplotypes for
Disease-Gene Mapping
17.5
Conclusion
407
411
418
Chapter
18
Regional multilocus association models
423
Jo Knight,
Рак С.
Sham, Shaun
Purceii
and Benjamin M. Neale
18.1
Introduction and Basic Methods
423
18.2
Phased Versus Unphased
426
18.3
Utility of Multimarker Tests
430
18.4
WHAP Analysis
434
18.5
Conclusion
446
Chapter
19
Linkage disequilibrium and tagging
451
Benjamin M. Neale
19.1
Linkage Disequilibrium Statistics
451
19.2
Block-like Nature of the Genome
454
19.3
Tagging
457
19.4
Population Differences
459
19.5
Multiallelic Markers
460
19.6
Conclusion
461
Chapter
20
Practical guide to linkage disequilibrium
analysis and tagging using Haploview
467
David J. Bender and Julian B. Mailer
20.1
Introduction
467
20.2
Data Checks
468
20.3
Linkage Disequilibrium Analysis
471
20.4
Tagging Analysis
473
20.5
Viewing PLINK Results in Haploview
476
20.6
Additional Considerations
and Programs
483
20.7
Conclusion
484
Chapter
2
1 Factors affecting power and type-l
error in association
David M. Evans
21.1
Introduction
21.2
Factors Affecting Power to Detect
Association
21.3
Population Stratification
21.4
Genotyping Error
21.5
Genome-wide Association
21.6
Calculating Power to Detect
Association
21.7
Conclusion
487
487
488
499
510
515
518
526
χ
Contents
Chapter
22
Resampling approaches to
statistical inference
535
Michael C. Neale and Sarah
E. Mediana
22.1
Introduction
535
22.2
Bootstrap Estimation
537
22.3
Permutation Tests
544
Appendix
1
File formats
551
Al.l Overview
551
Al.
2
MERLIN/MERLIN-Regresss/Pedstats/
Minx/QTDT/GRR
551
A1.3 WRAP
560
Al.
4
Haploview
561
A1.5 PLINK
563
Al.
6
Running programs in DOS versus
Unix/Linux
565
Online resources
569
Index
571 |
| any_adam_object | 1 |
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| discipline_str_mv | Biologie |
| format | Book |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content (DE-588)1071861417 Konferenzschrift gnd-content |
| genre_facet | Aufsatzsammlung Konferenzschrift |
| id | DE-604.BV023069111 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:32:17Z |
| indexdate | 2024-07-09T21:10:17Z |
| institution | BVB |
| isbn | 9780415410403 |
| language | English |
| lccn | 2007042274 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016272278 |
| oclc_num | 175174341 |
| open_access_boolean | |
| owner | DE-29T DE-12 DE-M49 DE-BY-TUM DE-11 DE-188 DE-1028 |
| owner_facet | DE-29T DE-12 DE-M49 DE-BY-TUM DE-11 DE-188 DE-1028 |
| physical | XXVIII, 574 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Taylor & Francis |
| record_format | marc |
| spelling | Statistical genetics gene mapping through linkage and association ed. by Benjamin M. Neale ... [et al.] New York, NY [u.a.] Taylor & Francis 2008 XXVIII, 574 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Genen gtt Genetica gtt Statistische methoden gtt Chromosome Mapping methods Congresses Gene mapping Statistical methods Congresses Linkage (Genetics) Congresses Linkage (Genetics) Statistical methods Congresses Models, Statistical Congresses Methode (DE-588)4038971-6 gnd rswk-swf Genetik (DE-588)4071711-2 gnd rswk-swf Statistik (DE-588)4056995-0 gnd rswk-swf Genkartierung (DE-588)4123274-4 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content (DE-588)1071861417 Konferenzschrift gnd-content Genetik (DE-588)4071711-2 s Statistik (DE-588)4056995-0 s Genkartierung (DE-588)4123274-4 s DE-604 Methode (DE-588)4038971-6 s DE-188 Neale, Benjamin M. Sonstige oth Digitalisierung TU Muenchen application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272278&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Statistical genetics gene mapping through linkage and association Genen gtt Genetica gtt Statistische methoden gtt Chromosome Mapping methods Congresses Gene mapping Statistical methods Congresses Linkage (Genetics) Congresses Linkage (Genetics) Statistical methods Congresses Models, Statistical Congresses Methode (DE-588)4038971-6 gnd Genetik (DE-588)4071711-2 gnd Statistik (DE-588)4056995-0 gnd Genkartierung (DE-588)4123274-4 gnd |
| subject_GND | (DE-588)4038971-6 (DE-588)4071711-2 (DE-588)4056995-0 (DE-588)4123274-4 (DE-588)4143413-4 (DE-588)1071861417 |
| title | Statistical genetics gene mapping through linkage and association |
| title_auth | Statistical genetics gene mapping through linkage and association |
| title_exact_search | Statistical genetics gene mapping through linkage and association |
| title_exact_search_txtP | Statistical genetics gene mapping through linkage and association |
| title_full | Statistical genetics gene mapping through linkage and association ed. by Benjamin M. Neale ... [et al.] |
| title_fullStr | Statistical genetics gene mapping through linkage and association ed. by Benjamin M. Neale ... [et al.] |
| title_full_unstemmed | Statistical genetics gene mapping through linkage and association ed. by Benjamin M. Neale ... [et al.] |
| title_short | Statistical genetics |
| title_sort | statistical genetics gene mapping through linkage and association |
| title_sub | gene mapping through linkage and association |
| topic | Genen gtt Genetica gtt Statistische methoden gtt Chromosome Mapping methods Congresses Gene mapping Statistical methods Congresses Linkage (Genetics) Congresses Linkage (Genetics) Statistical methods Congresses Models, Statistical Congresses Methode (DE-588)4038971-6 gnd Genetik (DE-588)4071711-2 gnd Statistik (DE-588)4056995-0 gnd Genkartierung (DE-588)4123274-4 gnd |
| topic_facet | Genen Genetica Statistische methoden Chromosome Mapping methods Congresses Gene mapping Statistical methods Congresses Linkage (Genetics) Congresses Linkage (Genetics) Statistical methods Congresses Models, Statistical Congresses Methode Genetik Statistik Genkartierung Aufsatzsammlung Konferenzschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272278&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT nealebenjaminm statisticalgeneticsgenemappingthroughlinkageandassociation |