Explain the significance of snps in medical therapies.
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GENETIC VARIATION IN THE HUMAN GENOME
In the process of generating a draft sequence of the human genome, it has become clear that the extent of genetic variation is much larger than previously estimated (Lander et al, 2001; Venter et al, 2001). The most common sequence variation in the human genome is the stable substitution of a single base, the single-nucleotide polymorphism (SNP). By definition, a SNP has a minor allele frequency of greater than 1% in at least one population (Risch, 2000). Most SNPs are ‘silent’ and do not alter the function or expression of a gene. It makes sense to conceptually reserve the term ‘mutation’ for rare variants with a particularly high penetrance, usually associated with a detrimental phenotype, such as a classical monogenic disorder (e.g., sickle cell disease or haemophilia). For the purposes of this review, the focus will be on SNPs with low penetrance or no phenotypic effect.
The total number of SNPs in the human genome is estimated to be more than 10 million (Botstein and Risch, 2003) and the number of SNPs with a minor allele frequency over 10% is estimated to be perhaps as many as five million (Kruglyak and Nickerson, 2001). Single-nucleotide polymorphisms are distributed throughout the human genome, at an estimated overall frequency of at least on in every 1000 base pair (bp) (Carlson et al, 2003), but with marked regional differences. Single-nucleotide polymorphisms arise because of point mutations that are selectively maintained in populations. Single-nucleotide polymorphism frequencies are determined by: (1) the amount of time since the mutation occurred; (2) evolutionary pressure on biologically significant variants and those linked to the functional variant; (3) random genetic drift and (4) bottleneck events.
Single-nucleotide polymorphisms in the same chromosomal region are not inherited randomly, but as combinations of alleles, which form haplotype blocks. It appears that the genome is organised into distinct blocks of linkage disequilibrium (LD), intercepted by regions in which LD breaks down rapidly (Bonnen et al, 2002; Sabeti et al, 2002). Thus, the complexity of analysing SNPs in a gene or locus can be reduced by the analysis
In the process of generating a draft sequence of the human genome, it has become clear that the extent of genetic variation is much larger than previously estimated (Lander et al, 2001; Venter et al, 2001). The most common sequence variation in the human genome is the stable substitution of a single base, the single-nucleotide polymorphism (SNP). By definition, a SNP has a minor allele frequency of greater than 1% in at least one population (Risch, 2000). Most SNPs are ‘silent’ and do not alter the function or expression of a gene. It makes sense to conceptually reserve the term ‘mutation’ for rare variants with a particularly high penetrance, usually associated with a detrimental phenotype, such as a classical monogenic disorder (e.g., sickle cell disease or haemophilia). For the purposes of this review, the focus will be on SNPs with low penetrance or no phenotypic effect.
The total number of SNPs in the human genome is estimated to be more than 10 million (Botstein and Risch, 2003) and the number of SNPs with a minor allele frequency over 10% is estimated to be perhaps as many as five million (Kruglyak and Nickerson, 2001). Single-nucleotide polymorphisms are distributed throughout the human genome, at an estimated overall frequency of at least on in every 1000 base pair (bp) (Carlson et al, 2003), but with marked regional differences. Single-nucleotide polymorphisms arise because of point mutations that are selectively maintained in populations. Single-nucleotide polymorphism frequencies are determined by: (1) the amount of time since the mutation occurred; (2) evolutionary pressure on biologically significant variants and those linked to the functional variant; (3) random genetic drift and (4) bottleneck events.
Single-nucleotide polymorphisms in the same chromosomal region are not inherited randomly, but as combinations of alleles, which form haplotype blocks. It appears that the genome is organised into distinct blocks of linkage disequilibrium (LD), intercepted by regions in which LD breaks down rapidly (Bonnen et al, 2002; Sabeti et al, 2002). Thus, the complexity of analysing SNPs in a gene or locus can be reduced by the analysis
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Some of these genetic differences, however, have proven to be very important in the study of human health. Researchers have found SNPs that may help predict an individual's response to certain drugs, susceptibility to environmental factors such as toxins, and risk of developing particular disease
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