Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome

Wang, David G.; Fan, Jian‐Bing; Siao, Chia-Jen; Berno, Anthony; Young, Peter R.; Sapolsky, Ron; Ghandour, Ghassan; Perkins, Nancy; Winchester, Ellen; Spencer, Jessica B.; Kruglyak, Leonid; Stein, Lincoln; Hsie, Linda; Topaloglou, Thodoros; Hubbell, Earl; Robinson, Elizabeth A.; Mittmann, Michael; Morris, Macdonald; Shen, Naiping; Kilburn, Dan; Rioux, John D.; Nusbaum, Chad; Rozen, Steve; Hudson, Thomas J.; Lipshutz, Robert J.; Chee, Mark S.; Lander, Eric S.

doi:10.1126/science.280.5366.1077

Cited by 1,927 publications

(1,172 citation statements)

References 19 publications

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“…LD is a property of populations, and thus depends on the natural history of the disease gene containing a chromosome segment of the test population, and on the recombination distance between the disease gene and the test marker. LD mapping is generally performed using single nucleotide polymorphisms (SNPs), since these are more common than, and less mutable than, microsatellites [67]. In reverse genetics approaches, the genetic marker data are used to drive or refine the phenotypes, based on genetic marker data, that is, to define phenotypic groupings that are distinguished by higher rates of allele-sharing or distorsion of genetic equilibria.…”

Section: Genetic Strategy To Find Susceptibility Genes For Arhlmentioning

confidence: 99%

Ageing and hearing loss

Yan

2007

The Journal of Pathology

266

178

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Although many adults retain good hearing as they age, hearing loss associated with ageing is common among elderly persons. There are a number of pathophysiolological processes underlying age-related changes to functional components in the inner ear. Genetic factors determine the ageing process but are under the influence of intrinsic and environmental factors. It is difficult to distinguish changes of normal ageing from those of other contributing factors. The effects of age-related deafness can have significant physical, functional and mental health consequences. Although a deficit in hearing can be corrected to some degree by a hearing aid or other appropriate amplification devices, hearing-related rehabilitative needs are much more than simply amplifying external sound. Only by better understanding the process of ageing and its effect on the auditory function can we better accommodate elderly people in our day-to-day interactions. We review here the structure and function of the inner ear, pathophysiology associated with age-related hearing loss (ARHL), heritability, allelism and modifier genes of ARHL, and evaluate the genetic analyses for identification of genetic factors that are involved.

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Section: Genetic Strategy To Find Susceptibility Genes For Arhlmentioning

confidence: 99%

Ageing and hearing loss

Yan

2007

The Journal of Pathology

266

178

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“…The results obtained to date in chickens indicate higher ratios than in mammals: SNPs mined from EST sequence traces gave a ratio of 2.3 [74] or 4 [39] and a survey of 138 SNPs from non-coding DNA in chickens gave a ratio of 2.36 (Vignal and Weigend, unpublished data). One probable explanation for this bias is the high spontaneous rate of deamination of 5-methyl cytosine (5mC) to thymidine in the CpG dinucleotides, leading to the generation of higher levels of C ⇔ T SNPs, seen as G ⇔ A SNPs on the reverse strand [13,80].…”

Section: Definition Of Snps and The Generation Of Single Nucleotide Pmentioning

confidence: 99%

“…The densities thus obtained are extremely high and reliability is improved by using a tiled array scheme, multiplying the number of probes used for each base position questioned [29,80].…”

Section: Direct Hybridisation Techniques: From Aso To Chipsmentioning

confidence: 99%

A review on SNP and other types of molecular markers and their use in animal genetics

et al. 2002

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-During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types.SNP / microsatellite / molecular marker / genome / polymorphism

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“…[19][20][21] Moreover, SNPs in the coding regions or the regulatory regions of genes are more likely to cause functional differences than SNPs located elsewhere. 19 Therefore, this study was undertaken to examine those possible relationship between three novel SNPs found in CDK5 promoter region and the risk of lung cancer occurrence in Korean lung cancer patients.…”

Section: Introductionmentioning

confidence: 99%

Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population

et al. 2009

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Cyclin-dependent kinase 5 (CDK5), a proline-directed serine/threonine kinase, which was originally known for its regulatory role in neuronal activities, has recently been suggested to play a role in extraneuronal activities. For example, a recent study detected overexpression of the CDK5 gene in non-small-cell lung cancer. Therefore, in order to explore the association of the CDK5 gene with lung cancer risk in a Korean population, the genotypes of the CDK5 promoter region were determined in 407 lung cancer patients and 402 normal participants. The result showed that the À904 G4A genotype affected susceptibility to lung cancer risk (odd ratios (OR)¼1.53, 95% confidence interval (CI)¼1.02-2.32). Furthermore, subsequent haplotype analysis of three single-nucleotide polymorphism (SNP) regions suggested that the A-G-C haplotype was associated with a higher overall risk of lung cancer (OR¼1.59, 95% CI¼1.16-2.18). These results suggest that CDK5 promoter polymorphisms contribute to the genetic susceptibility to lung cancer in the Korean population.

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Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome

Cited by 1,927 publications

References 19 publications

Ageing and hearing loss

Ageing and hearing loss

A review on SNP and other types of molecular markers and their use in animal genetics

Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population

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