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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: 2007-06-05
SNP CONSORTIUM THE
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  • Abstract
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  • Claims
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AI Technical Summary

Benefits of technology

[0005]Surprisingly, the genetic variations that lead to gene involvement in human disease are relatively small. Approximately 1% of the DNA bases which comprise the human genome contain polymorphisms that vary at least 1% of the time in the human population. The genomes of all organisms, including humans, undergo spontaneous mutation in the course of their continuing evolution. The majority of such mutations create polymorphisms, thus the mutated sequence and the initial sequence co-exist in the species population. 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. Some polymorphisms that lie within genes or their promoters do have a phenotypic effect and it is this small proportion of the genome's variation that accounts for the genetic component of all difference between individuals, e.g., physical appearance, disease susceptibility, disease resistance, and responsiveness to drug treatments.

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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  • Identification and mapping of single nucleotide polymorphisms in the human genome

Examples

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example 1

Cloning and Identification of SNP Nucleic Acids

[0035]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 we...

example 2

Generation of SNP Maps

[0040]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 ...

example 3

SNP Profiling to Identify an Individual

[0042]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 (SeeQuence; 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% NaDodSO4 at room temperature, washed once in 2× SSPE, 0.5% NaDodSO4 at 55° C. and then briefly rinsed twice in 2× PBS (1× PBS is 137 mM NaCl / 2,7 mM K...

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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

CROSS REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority to the following provisional applications: U.S. patent application Ser. No. 60 / 243,096, Oct. 24, 2000; U.S. patent application Ser. No. 60 / 252,147, Nov. 20, 2000; U.S. patent application Ser. No. 60 / 250,092, Nov. 30, 2000; U.S. patent application Ser. No. 60 / 261,766, Jan. 16, 2001; and U.S. patent application Ser. No. 60 / 289,846, May 9, 2001.BACKGROUND OF THE INVENTION[0002]The Sequence Listing portion of this application is contained on a compact disk (CD), which is incorporated by reference herein in its entirety. The compact disk labled “Sequence Listing Part” contains file “108827-135.zip,” 193,477 KB in length, created on Sep. 17, 2003, which is the compressed file “108827-135.st25,” 820,249,461 KB in length.FIELD OF THE INVENTION[0003]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 involv...

Claims

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Application Information

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Patent Type & Authority Patents(United States)
IPC IPC(8): C12Q1/68
CPCC12Q1/6883C12Q2600/156
Inventor WANG, DAVID G.
Owner SNP CONSORTIUM THE
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