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Identification and mapping of single nucleotide polymorphisms in the human genome

a single nucleotide polymorphism and human genome technology, applied in the field of human disease roles, can solve the problems of major dna base differences that are functionally inconsequential, and achieve the effect of relatively small genetic variation that leads to gene involvement in human diseas

Inactive Publication Date: 2008-07-01
SNP CONSORTIUM
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

"The invention provides a way to identify and map a large number of SNPs (small nucleotide polymorphisms) throughout the human genome. This can help researchers classify people based on their genetic variation and also help identify genes that are relevant to preventing, causing, or treating human disease conditions. The invention includes a set of SNP probes that can be used for this purpose, and methods for using the map of SNPs to conduct linkage studies and other genetic analyses."

Problems solved by technology

However, the majority of DNA base differences are functionally inconsequential in that they neither affect the amino acid sequence of encoded proteins nor the expression levels of the encoded proteins.

Method used

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Examples

Experimental program
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Effect test

example 1

Cloning and Identification of SNP Nucleic Acids

Genomic DNA was isolated from a plurality of unrelated human individuals and approximately equal amounts from each individual was pooled. The combined genomic DNA was then cut to completion with one of the following restriction enzymes: HindIII, EcoRI, EcoRV, and BamHI. Other restriction enzymes are also useful. The digested genomic DNA was then run on a preparative agarose gel along with size markers. The agarose gel containing the electrophoresed DNA was cut into size fractions such that a size range of about 200 base pairs was present in each slice (e.g., 500-700 base pairs, 1000-1200 base pairs, 2200-2400 base pairs). The DNA was extracted from the gel. Eluted size fractionated DNA fragments were ligated into a phosphatased vector which had been cut using the same restriction enzyme as was used for the digestion of the genomic DNA. Plasmid libraries were prepared by transforming E.coli with the ligated vectors according to well know...

example 2

Generation of SNP Maps

Each SNP was developed into an STS and mapped using the TNG panel by using the method of Stewart et al. (1997) Genome Research, vol. 7, pp. 422-433. Briefly, oligonucleotides for PCR amplification of the fragments containing the SNPs were chosen using PRIMER 3.0, a software package written at the Whitehead Genome Center. The oligonucleotide primers were chosen according to parameters that generate PCR products of 100-400 base pairs in length and that allow the use of a single set of PCR conditions for all STSs. PCR products are assayed by ethidium bromide staining following agarose gel electrophoresis. An STS containing an identified SNP is judged successful when the primers produce a distinct PCR product of the expected size from total human DNA, but fails to produce a distinct PCR product of this size from hamster genomic DNA. In addition, each successful STS is PCR amplified on a set of approximately 90 rodent-human somatic cell hybrids to assure that the ST...

example 3

SNP Profiling, to Identify an Individual

Oligonucleotides that recognize one allele of a SNP nucleic acid are immobilized on a filter. Preferably, the oligonucleotides comprise oligonucleotides complementary to at least 10 different SNP nucleic acids and are present on the filter in a pre-arranged array. Each filter with bound oligonucleotides is placed in 4 ml hybridization solution containing 5× SSPE, 0.5% NaDodSO4 and 400 ng of streptavidin-horseradish peroxidase conjugate (See Quence; Eastman Kodak). PCR-amplified DNA made with biotinylated primers (20 microliters) from a sample of blood from an individual is denatured by addition of an equal volume of 400 mM NaOH / 10 mM EDTA and added immediately to the hybridization solution, which is then incubated at 55° C. for 30 minutes. The filters are briefly rinsed twice in 2× SSPE, 0.1% NaDodS04 at room temperature, washed once in 2× SSPE, 0.5% NaDodS04 at 55° C. and then briefly rinsed twice in 2× PBS (1×PBS is 137 mM NaCI / 2,7 mM KCl / 8 ...

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Abstract

The invention relates to the role of genes in human diseases. More particularly, the invention relates to compositions and methods for identifying genes that are involved in human disease conditions. The invention provides identification and mapping of a very large number of SNPs throughout the entire human genome. This contribution allows scientists to isolate and identify genes that are relevant to the prevention, causation, or treatment of human disease conditions.

Description

BACKGROUND OF THE INVENTION1. Field of the InventionThe invention relates to the role of genes in human diseases. More particularly, the invention relates to compositions and methods for identifying genes that are involved in human disease conditions.2. Summary of the Related ArtDuring the past two decades, remarkable developments in molecular biology 10 and genetics have produced a revolutionary growth in understanding of the implication of genes in human disease. Genes have been shown to be directly causative of certain disease states. For example, it has long been known that sickle cell anemia is caused by a single mutation in the human beta globin gene. In many other cases, genes play a role together with environmental factors and / or other genes to either cause disease or increase susceptibility to disease. Prominent examples of such conditions include the role of DNA sequence variation in ApoE in Alzheimer's disease, CKR5 in susceptibility to infection by HIV; Factor V in risk ...

Claims

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Application Information

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Patent Type & Authority Patents(United States)
IPC IPC(8): C07H21/02
CPCC12Q1/6883C12Q2600/156
Inventor WANG, DAVID G.
Owner SNP CONSORTIUM
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