Inhalt
(preliminary)
1. Special Considerations
S. Gabriel, J.C. Stephens, and M. Weiner
IN VITRO FLUORESCENCE
SECTION 1: STUDY DESIGN
Introduction
2. Population to Address/Collect
J.C. Stephens and M. Bamshad
3. Power Calculations
D. Purcell and S. Evans
4. Linkage v. Association Studies
A. Smith
5. Db–SNP/NCBI/Targeted SNP–Discovery
S. Sherry and M. Feolo
6. Using HapMap
A. Smith
SECTION 2: GENERATING DATA
Introduction
PART 1: PREPARING DNA
7. Isolation of Plant DNA for Genotyping Analysis
N. Springer
8. Preparing Mammal DNA from Buccal Cells or Blood
I.B. King
9. Preparing DNA from Mammalian Sources
A. Sahota, A.I. Brooks, and J.A. Tischfield
10. Mammalian DNA from Tissue
E. Cuppen
11. PCR–based Whole Genome Amplification
C. Brueck, C. Brown, S. Michalik, D. Vassar–Nieto, E. Mueller, and G. Davis
12. Rolling Circle Amplification Using f29 DNA Polymerase
N. Burtt
PART 2: SNP VARIATION ANALYSIS
13. Intermediate–throughput Laboratory–scale Genotyping Solutions
S.J. Macdonald
14. Lab–scale Genotyping Protocols
S.J. Macdonald and E. Cuppen
15. Fluorescence Polarization Detection: Template Directed Dye–Incorporation Assay
C. Ha and P.–Y. Kwok
16. Large–scale Tag Affy Arrays
G. Karlin–Neumann
17. Large–scale Genotyping (current platforms)
M. Weiner and S. Gabriel
PART 3: COMPLEX VARIATION ANALYSIS
18. Microsatellite Analysis
J. Gulcher
19. Comparative Genomic Hybridization (CGH) to Detect Variation in the Copy Number of Large DNA Segments
I.N. Holcomb and B.J. Trask
20. Representational Oligonucleotide Microarray Analysis for Detection of Genetic Variation
R. Lucito
21. Whole Genome Sampling Analysis to Detect Copy Number Changes
S. Jacobs
SECTION 3: DATA ANALYSIS
Introduction
22. Quality Control: Incomplete Data and Genotyping Errors
D. Cutler
23. tag SNP Selection
C. Carlson
24. Selection and Evaluation of tag SNPs Using Tagger and HapMap
P.I. Wen de Bakker
25. Haploview: Visualization and Analysis of SNP Genotype Data
J.C. Barrett
26. Considerations for Copy Number Analysis
S. Jacobs
27. Statistics: Assessing Significance of Results
M. Daly
28. Inference of Selection from Candidate Gene Analysis
M. Bamshad and J.C. Stephens
29. Inference of Selection from Whole Genome Analysis
C. Bustamante
SECTION 4: VARIATION STUDIES IN MODEL ORGANISMS
Introduction
30. Arabidopsis
J. Borevitz and Y. Li
31. Corn
W.B. Barbazuk, A.–P. Hsia, H.D. Chen, Y. Fu, K. Ohtsu, and P.S. Schnable
32. Rice
H. Leung, K. McNally, and D. Mackill
33. The Mouse
C.M. Wade and M.J. Daly
34. The Rat
E. Cuppen, N. Hübner, H.J. Jacob, and A.E. Kwitek
35. Feline
L. Lyons
36. Canine
K. Lindblad–Toh and E.A. Ostrander
37. Porcine
A. Archibald
38. The Chimpanzee
T.S. Mikkelsen, M.C. Zody, and K. Lindblad–Toh
SECTION 5: INTERPRETATIONS OF / INSIGHTS INTO HUMAN VARIATION
Introduction
39. Genealogical Markers: mtDNA and the Y–chromosome
M. Stoneking and M. Kayser
40. Forensic DNA Testing
J.M. Butler
41. Human Variation and Applications
M. Shriver
42. Human Genome–What Lies Ahead
S. Gabriel, C. Stephens, and M. Weiner
APPENDIX, Cautions, INDEX
Vorteile
Writing a laboratory manual on genetic variation in the golden era of
genetics, an era in which the rate of scientific discovery is beyond compare
to that in any other point in history, is perhaps a bit like trying to give
investment advice in today’s quickly changing world markets. Considered
in this light, the laboratory manual Genetic Variation is an impressive
accomplishment. 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.
Although the technologies to generate data on large scales may change
rapidly, other issues covered in this book related to consent, experimental
design and the analysis and interpretation of high-dimensional data will
change far more slowly, if at all.
The book is broken up into five sections covering study design; laboratory
protocols for preparing RNA and DNA and then assessing SNP, copy
number and more complex variations in these samples; data analysis;
genetic variation studies carried out in model organisms; and insights
into human DNA variation. In a refreshing departure from more traditional
laboratory manuals, the book begins by addressing the many ethical
issues facing human genetic research. In an age where genotype, molecular
and clinical phenotype data are being generated on massive scales and
then dropped into public domain databases, it is important to remind
novices and experts alike of their obligations regarding consent, privacy,
and data-use issues for studies involving human subjects. Even beyond
the use of genetic variation information in a clinical or forensic science
setting, we are seeing direct-to-consumer services emerge (23andMe,
for example) with a significant recreational component (“Where am I
descended from?”) where samples are also incredibly broadly consented
for science research. If we want continued public support to collect these
types of data, we must act responsibly. This type of chapter does not
appear frequently enough in this type of reference.
Second only to the consideration of ethical issues are experimental
design issues, a subject covered in the first section. Because massive
amounts of genomic data can now be generated cheaply and efficiently
via outsourcing to core laboratories, almost any basic science group can
carry out studies of genetic variation. But generating data quickly and
cheaply will not make up for poorly designed studies. Forming the appropriate
hypotheses to be tested, identifying the best populations available
to address such hypotheses and performing power calculations to ensure
a study is appropriately powered are some of the topics discussed in this
section, reminding the expert and providing the novice with invaluable
insights into the important design components of any study.
The second section of this book does an excellent job providing a
comprehensive guide on generating data in a variety of genetic variation
experiments. Many state-of-the-art techniques are covered in three
parts in this section, with a first set of chapters detailing DNA and RNA
isolation techniques. A second set of chapters details intermediate-tolarge
scale genotyping assays available for SNP-based markers, and a
third set of chapters focuses on the detection of copy number variations
using comparative genomic hybridization methods and complex variation
analysis.
The third section will be most useful to the less experienced researcher,
given its focus on data analysis issues facing those attempting to interpret
hundreds of thousands or even millions of markers genotyped in thousands
of individuals and their association to biological trait data. From
the selection of SNPs covered in the first two chapters to the assessment
of significance covered by the fourth chapter in this section, failing to
address these important issues before designing a genetics study could
lead to unnecessary limitations in addressing hypotheses of interest, or
worse, to a misinterpretation of the results that would then motivate
time-consuming follow-up studies based on erroneous conclusions. The
chapter by Daly provides the beginning steps that must be understood to
successfully analyze data in any genetic association study.
The fourth section provides a broad sampling of applications in model
organisms that have relatively complete genomic information available.
Covering several major plant (Arabidopsis, maize and rice) and animal
(mouse, rat, cat, dog and chimpanzee) species, a wealth of information
is provided relating to the history of the species in scientific research, the
state of the genome for a given species, phenotypes studied and resources
available for scientific research that in many cases are specific to a given
species. The final section in this book focuses on insights into human
variations, including a chapter on genealogical markers that are now finding
use not only in the study of the origins of the Polynesians and other
cultures (chapter 33 by Stoneking and Kayser), but also in studies with a
strong recreational genetics component. In addition, there is an interesting
chapter by Butler on the application of genetics in forensic science,
highlighting many issues not discussed in the popular TV series CSI.
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.
Eric E. Schadt is in the Department of Genetics, Rosetta Inpharmatics,
LLC, Seattle, Washington 98109, USA.
Autoreninfo
Edited By Michael P. Weiner, RainDance Technologies, Inc., Guilford, Connecticut; J. Claiborne Sphenste, Motif BioSciences, New York; Staceyl Gabrie, The Broad Institute, Massachusetts Institute of Technology, Cambridge
|
|
CRISPR-Cas:
Budding Yeast
Learning and Memory
Conservation Science: Balancing the Needs of People and Nature
Introduction to Optical Microscopy
Organic Chemistry
CURRENT PROTOCOLS Wiley USA