Contents

1. Ethical Issues in Human Genetic Research: The Global Experience

K. Arnold and J. van der Walt

SECTION 1: STUDY DESIGN

Introduction

2. Population Choice as a Consideration for Genetic Analysis Study Design

J.C. Stephens and M. Bamshad

3. Power Calculations

D.M. Evans and S. Purcell

4. Genetic Anaylsis: Moving between Linkage and Association

A.V. Smith

5. NCBI dbSNP Database: Content and Searching

M.L. Feolo and S.T. Sherry

6. Using the HapMap Web Site

A.V. Smith

SECTION 2: LABORATORY PROTOCOLS

Introduction

PART 1: PREPARATION OF DNA AND RNA

7. Isolation of Plant DNA for Genotyping Analysis

N.M. Springer

8. Preparing RNA from Plant Tissues

A.-P. Hsia, H.D. Chen, K. Ohtsu, and P.S. Schnable

9. Preparing DNA from Mammalian Sources

A. Sahota, A.I. Brooks, and J.A. Tischfield

PART 2: SNP VARIATION ANALYSIS

10. Intermediate-Throughput Laboratory-Scale Genotyping Solutions

S.J. Macdonald

11. Intermediate-Throughput Laboratory-Scale Genotyping Protocols

E. Cuppen, S.J. Macdonald, C. Ha, P.-Y. Kwok, W.B. Barbazuk, A.-P. Hsia, H.D. Chen, Y. Fu, K. Ohtsu, and P.S. Schnable

12. Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping

G. Karlin-Neumann, M. Sedova, R. Sapolsky, J. Forman, Y. Wang, M. Moorhead, and M.Faham

13. Whole-Genome Genotyping

S.B. Gabriel and M.P. Weiner

PART 3: COPY NUMBER AND COMPLEX VARIATION ANALYSIS

14. Comparative Genomic Hybridization to Detect Variation in the Copy Number of Large DNA Segments

I.N. Holcomb and B.J. Trask

15. Representational Oligonucleotide Microarray Analysis Detection of Genetic Variation

R. Lucito

16. Whole-Genome Sampling Analysis to Detect Copy Number Changes in FFPE Samples

S. Jacobs

17. Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination

G.Karlin-Neumann, M. Sedova, R. Sapolsky, S. Lin, Y. Wang, M. Moorhead, and M. Faham

18. Microsatellite Markers for Linkage and Association Studies

J. Gulcher

SECTION 3: DATA ANALYSIS

Introduction

19. Considerations for SNP Selection

C. Carlson

20. Selection and Evaluation of tag-SNPs Using Tagger and HapMap

P. de Bakker

21. Haploview: Visualization and Analysis of SNP Genotype Data

J.C. Barrett

22. Considerations for Copy Number Analysis of FFPE Samples

S. Jacobs

23. Assessing Significance in Genetic Association Studies

M.J. Daly

24. Assessing Human Variation Data for Signatures of Natural Selection

M. Bamshad and J.C. Stephens

SECTION 4: VARIATION STUDIES IN MODEL ORGANISMS

Introduction

25. Arabidopsis

Y. Li and J.O. Borevitz

26. Maize

W.B. Barbazuk, A.-P. Hsia, H.D. Chen, Y. Fu, K. Ohtsu, and P.S. Schnable

27. Rice

H. Leung, K.L. McNally, and D. Mackill

28. The Mouse

C.M. Wade and M.J. Daly

29. The Rat

E. Cuppen, N. Hübner, H.J. Jacob, and A.E. Kwitek

30. The Cat

M.J. Lipinski, N. Billings, L.A. Lyons

31. The Dog

K. Lindblad-Toh and E.A. Ostrander

32. The Chimpanzee

T.S. Mikkelsen, M.C. Zody, and K. Lindblad-Toh

SECTION 5: INSIGHTS INTO HUMAN VARIATION

Introduction

33. Genealogical Markers: mtDNA and the Y Chromosome

M. Stoneking and M. Kayser

34. Forensic DNA Testing

J.M. Butler

35. The Human Genome: What Lies Ahead

M.P. Weiner and J.C. Stephens

APPENDIX: Cautions

INDEX

  “Not only did this editorial team assemble an impressive group of accomplished scientists as authors, but they produced a book of broad scope, covering a wide range of topics. In fact, it is the amazing breadth of this book that will ensure its relevance for some time to come.

This manual is relevant on many different levels and will no doubt provide any interested reader with a wealth of useful information. I for one have added this book to my collection of references on carrying out genetic studies on the underlying causes of disease and drug response in human and mouse populations.”
      —Nature Genetics

  “This is an edited volume that seeks to provide specialists with a guide to the study of genetic variation in the age of genomics. It will be most appealing to anyone studying human genetic variation since this is the primary area of coverage, although other model systems are touched upon. A strength of the book is its conciseness, which is achieved by limiting the contents to basic introductions of the issues and citing more comprehensive references.”
      —The Quarterly Review of Biology