An SNP map of the human genome generated by reduced representation shotgun sequencing

Altshuler, David; Pollara, Victor J.; Cowles, Chris R.; Etten, William J. Van; Baldwin, Jennifer; Linton, Lauren; Lander, Eric S.

doi:10.1038/35035083

Cited by 644 publications

(493 citation statements)

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“…These two approaches have the inconvenient of depending highly on the choice of the individuals at the origin of the cDNA or BAC libraries. More recently, a new approach, termed reduced representation shotgun (RRS) [3] was used for the production of a very high number of SNPs in humans. In this approach, DNA from different individuals are mixed together and plasmid libraries composed of a reduced representation of these genomes are produced by using a subset of restriction fragments purified by agarose gel electrophoresis (Fig.…”

Section: Principal Strategiesmentioning

confidence: 99%

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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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Section: Principal Strategiesmentioning

confidence: 99%

“…3 Variable number of tandem repeats. 4 Although the RAPD, AFLP, RFLP, PCR-RFLP and SSCP techniques will detect base substitutions in the vast majority of cases, the two other types of DNA variation can also be analysed.…”

Section: The Use Of Fingerprinting Techniquesmentioning

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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“…[6]; b: Forward (M32791), Reverse (unpublished intron sequence); c: Forward (unpublished intron sequence), Reverse (M32791); d: Forward (AY299400), Reverse (AF089892); e: Forward (AY324228), Reverse (AF089892); f : Forward (AF089892), Reverse (AY324229); g: Forward (AY324229), Reverse (AF089892); h: Forward (AY341265), Reverse (AF033495); i: Forward (AY326194), Reverse (AY331391); j: Forward (X60191), Reverse (AY555066). 2 Annealing temperature for PCR amplification. 3 Column temperature for DHPLC detection.…”

Section: Primer Design and Pcr Amplificationmentioning

confidence: 99%

“…1 Refer to Genbank accession number. 2 Indicates minor allele frequencies. 3 Means some results were proven by previous studies; AB075215 and AY299454 are Genbank accession numbers; "SSC 1(+) 86752736∼86752792" refer to the inserted 57 bp sequences were nt 86752736∼86752792 of chromosome 1(+) published by the Chicken Genome Project (http://genome.wustl.edu/projects/chicken/).…”

Section: Pcr-rflp Dna Markersmentioning

confidence: 99%

“…In humans, several high resolution SNP maps have been created for several chromosomes or even the whole genome, providing useful resources for studies on haplotypes associated with human diseases [2,23,28]. Furthermore, an SNP map of porcine chromosome 2 has been reported [18], however such studies have not been performed in the chicken yet.…”

Section: Introductionmentioning

confidence: 99%

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Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Nie¹,

Lei²,

Ouyang³

et al. 2005

Genet. Sel. Evol.

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-The genes that are part of the somatotropic axis play a crucial role in the regulation of growth and development of chickens. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, 75 pairs of primers were designed and four chicken breeds, significantly differing in growth and reproduction characteristics, were used to identify single nucleotide polymorphisms (SNP) using the denaturing high performance liquid chromatography (DHPLC) technology. A total of 283 SNP were discovered in 31 897 base pairs (bp) from 12 genes of the growth hormone (GH), growth hormone receptor (GHR), ghrelin, growth hormone secretagogue receptor (GHSR), insulin-like growth factor I and II (IGF-I and -II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin, leptin receptor (LEPR), pituitary-specific transcription factor-1 (PIT-1), somatostatin (SS), thyroid-stimulating hormone beta subunit (TSH-β). The observed average distances in bp between the SNP in the 5'UTR, coding regions (non-and synonymous), introns and 3'UTR were 172, 151 (473 and 222), 89 and 141 respectively. Fifteen non-synonymous SNP altered the translated precursors or mature proteins of GH, GHR, ghrelin, IGFBP-2, PIT-1 and SS. Fifteen indels of no less than 2 bps and 2 poly (A) polymorphisms were also observed in 9 genes. Fifty-nine PCR-RFLP markers were found in 11 genes. The SNP discovered in this study provided suitable markers for association studies of candidate genes for growth related traits in chickens.chickens / genes / SNP / DHPLC * Corresponding author: xqzhang@scau.edu.cn 340 Q. Nie et al.

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Atherogenesis and Coronary Heart Disease

Tracy

2003

International Textbook of Diabetes Mellitus

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There are two major pathways by which atherosclerosis progresses: excess lipids in blood, which end up in atherosclerotic plaque, and inflammatory forces. Much recent research has demonstrated the association of chronic low‐level inflammation (microinflammation) with both diabetes and cardiovascular disease. It appears that microinflammation is not only a result of these diseases but also exhibits “positive feedback,” causing the disease process to accelerate. This downward spiral has a slope that is modified by genetic architecture and environmental variables, and may prove difficult to interrupt or modify effectively, since the pathways involved represent not only pathophysiology but also normal homeostatic physiology. We currently have some medications that do seem to work to modify this process, such as aspirin and statins. The role of the environment is clearly important, but the role of genetic architecture is only now emerging. There is a need for more effective public health efforts in education and behavior modification, as well as economic and political approaches to arrest the burgeoning global epidemic of obesity. We already know that if the lipid burden is decreased, atherosclerosis will decrease. If we can understand the microinflammatory pathways in enough detail, and learn how to modify these activities, we may be able to decrease atherosclerosis through this mechanism as well, and also affect the development of the other chronic diseases of old age. By attacking both major arms we may finally be able to limit chronic progressive atherosclerosis, and possibly the other chronic diseases of old age as well.

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An SNP map of the human genome generated by reduced representation shotgun sequencing

Cited by 644 publications

References 21 publications

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

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

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Atherogenesis and Coronary Heart Disease

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