Chapter 11: Genome-Wide Variation and Trait Analysis
When available, the links under the Suggested Readings section will take you to websites
that either provide free electronic full-text versions of these references, or links to online
abstracts. All of these abstracts are themselves free. Many of the abstract sites contain
links to online full-text versions of the references; some of these full-text versions are
free, while others require personal or institutional subscriptions. None of the sites that can
be accessed through the links below are affiliated with McGraw-Hill Publishers
Polymorphism Analysis
Suggested Readings:
 Jeffreys AJ, Wilson V, and SL Thein. 1985. Individual-specific "fingerprints" of
human DNA. Nature 316:76-79. [Entrez-PubMed link]
The paper that introduced the concept of DNA fingerprinting, also known as
DNA typing or DNA profiling.

Schulze, TG, K Zhang, YS Chen, et al. 2004. Defining Haplotype Blocks and Tag
Single-nucleotide Polymorphisms in the Human Genome. Hum Mol Genet.
13(3):335-342. [Entrez-PubMed link]
This paper describes the relationship between SNPs and haplotype blocks
(HapBlocks) in the human genome. The paper shows how the final haplotype map
is influenced by the initial parameters of SNP choice.

Syvanen, AC. 2001. Accessing genetic variation: genotyping single nucleotide
polymorphisms. Nat Rev Genet 2:930-42. [Entrez-PubMed link]
The paper discusses the importance of identifying SNPs in the human genome in
order to identify genes associated with disease.

Weber JL, and PE May. 1989. Abundant class of human DNA polymorphisms
which can be typed using the polymerase chain reaction. Am. J. Hum. Genet.
44:388-96. [Entrez-PubMed link]
An early paper describing how the use of PCR to detect CA repeats.

Wiltshire, T., MT Pletcher, S Batalov, et al. 2003. Genome-wide Singlenucleotide Polymorphism Analysis Defines Haplotype Patterns in Mice. Proc
Natl Acad Sci. 100(6):3380-3385. [full-text link]
This article discusses the importance of understanding SNPs in relation to
susceptibility of disease. The authors compare polymorphism patterns in mice to
that of humans.
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Sex Determination in Mice
Suggested Readings:
 Koopman P, J Gubbay, N Vivian, P. Goodfellow, and R. Lovell-Badge. 1991.
Male development of chromosomally female mice transgenic for Sry. Nature
351:117-21. [Entrez-PubMed link]
The authors examine the Sry gene in mice in order to determine which parts of the
gene are responsible for testis development. The mouse Sry gene is the homolog
of SRY in humans.

Chaboissier MC, A Kobayashi, VI Vidal, et al. 2004. Functional Analysis of Sox8
and Sox9 During Sex Determination in the Mouse. Development. 131(9):18911901 [Entrez-PubMed link]
The authors examine the cascade of gene expression that is responsible for testis
formation in mice. They examine the interaction of Sry with Sox8 and Sox9 genes
to assess when the switch from ovarian to testis formation pathways occur.
DNA Fingerprinting in Dolly
Suggested Readings:
 Ashworth D, M Bishop, K Campbell, et al. 1998. DNA Microsatellite Analysis of
Dolly. Nature 394(6691):329. [Entrez-PubMed link]
The authors utilize microsatellite analysis to prove that Dolly was the first cloned
mammal

Jeffreys AJ, Wilson V, and SL Thein. 1985. Individual-specific "fingerprints" of
human DNA. Nature 316:76-79. [Entrez-PubMed link]
The paper that introduced the concept of DNA fingerprinting, also known as
DNA typing or DNA profiling.

Signer EN, YE Dubrova, AJ Jeffreys, et al. 1998. DNA fingerprinting Dolly.
Nature 394:329-330. [Entrez-PubMed link]
Examines the application of the DNA fingerprinting technique to prove that Dolly
was the first cloned mammal.
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The SNP Consortium
Websites:

SNP Consortium
http://snp.cshl.org/
The website for the nonprofit organization that has identified over 1.5 million
SNP markers. From the homepage, you can click on individual chromosomes to
view known SNP markers.

SNP Fact sheet at DOE
http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml
Contains information on SNPs and the formation of the SNP Consortium.
The HapMap Project
Suggested Readings:

International HapMap Consortium. 2003. The International HapMap Project.
Nature. 426(6968):789-796. [Entrez-PubMed link]
Describes the formation and goals of the HapMap Project.

International HapMap Consortium. 2005. A Haplotype Map of the Human
Genome. Nature. 437(7063):1299-1320 [Entrez-PubMed link]
Provides an update on the HapMap project and the prospects for using the
information obtained by the project in genetic association studies for human
disease.
Websites:

HapMap Project
http://www.hapmap.org/
Homepage of the International HapMap Project. The “About the Project” link at
the top of the page provides information on the formation of the project and its
goals.
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