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A fairly easy-to-understand example is that of the ABO blood group system. In this case, there is a single gene involved - ABO, which codes for an enzyme that modifies sugar groups on the surface of red blood cells. This ABO gene has three variants or alleles — i, IA, and IB. i (coding for Type O blood) is recessive, which means that its phenotype can ...


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It is because the two genes overlap: CLCN6 is on the plus strand and MTHFR is on the minus strand. The SNP is annotated to both because it falls in a region of the genome claimed by both genes.


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This is called the "Thrifty Gene Hypothesis" which was first used to explain why diabetes is so common. Basically it suggests that these alleles would have provided some kind of advantage, over the other possible alleles at that loci, until the environment changed. Then the environment changed and the allele became harmful. Environments are always changing ...


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. Figure 1. Schematic presentation of the tetra-primer ARMS-PCR method. The single nucleotide polymorphism used here as an example is a G→A substitution, but the method can be used to type other types of single base substitutions. Two allele-specific amplicons are generated using two pairs of primers, one pair (indicated by pink and red arrows, respectively) ...


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The long and short of it is that genetic variation is actually not very predictive in comparison to "environmental" effects such as lifestyle. Only a quarter of the variation in lifespan between twins is attributable to inherited factors (including genetics and epigenetics) [1] - the rest is environmental, from lifestyle to air quality. Most genetic ...


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SNP Let's start with the definition that has nothing to do with the rest of the question :). A Single-Nucleotide-Polymorphism (SNP) is a kind of genetic variation that you find in population. This genetic variation is defined as a variation caused by only one single nucleotide (as its name indicates it). For example if you have in the populations the two ...


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If you look into a certain population, you will find mutations (for example SNPs) in some ratio with the wild-type allele. When a mutation reaches fixation, it will be the only allele, reaching 100% penetrance in this population. See here for more information. In the context given I would interpret it in the way that a total of 464 SNPs were found, 430 of ...


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We used this kind of primers to generate out of frame mutations or to add additional bases. In my experience your PCR will work (probably a a lower efficiency) and you will get a product with an additional base. We used primers with bigger differences in PCR based site directed mutagenesis of plasmids, there up to 10 bases didn't match but the primers where ...


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eQTLs (expression quantitative trait loci) are variants that affect the expression of one or more genes. There have been several 'genome-wide' studies of SNPs that directly affect expression. The actual effect sizes are hard to pin down in most of them, but in the supplementary data for this paper is a list of the SNPs with the largest effects and ...


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In the Sanger approach, DNA would be isolated from the biopsy and would contain both normal alleles and mutant alleles of genes associated with the development of the tumour. If, for example, PCR amplification was then used to derive a sample of a target template region, this material would end up being sequenced as a mixed population: the derived sequence ...


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SNPs in all these regions will modify the DNA sequence. Effects will depend on where exactly the SNP is. I'll summarize the conditions in which effects can be maximum Transcription Factors (TFs) binding sites: SNP in the nucleotide positions that bind to the recognition amino acids in the TF Epigentic signals: C->X [x: A,G,T] SNPs can disrupt DNA ...


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The solution is in the name! SNP: single nucleotide polymorphism The name tells us that it is a change that affect one single nucleotide and that there can be multiple of these (polymorphism could be rewritten as multiple forms) From the SNP Wikipedia page: [A SNP] is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the ...


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I think you must have misremembered what you heard. The cut-off distance for genetic linkage is 50 centimorgans which corresponds to 50% recombination. In the human genome 1 centimorgan is approximately 106 base pairs, so the 'unlinked distance' is 5 * 107 base pairs.


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that's the stated purpose of the thousand genomes project. the thousand genomes project has.. 1000 genomes. its all downloadable. http://www.1000genomes.org/


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Too long for a comment, but sort of: Mainly you do this because these populations have segregated long time ago and developed differently, so it is more likely to identify these polymorphisms. It is also helpful to use populations for this which mixed not too much with other populations (thats why north-americans are usually not used here, as America was ...


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Getting SNP data from FTP Site of NCBI SNP: It's actually simple to download the data from the NCBI, if you follow the method given by FAQ( as given by @WYSIWYG). Step 1: Goto organism FTP: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/ Step 2 Open your required organism folder: From here you can download any file you wanted. If you trying to study ...


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The '-' means that that allele has a single base deletion.


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First, you need to know which genome sequence does the SNP file refer to. They must have mentioned the reference sequence that they used. As others mentioned the case of CT is heterozygosity. If you just want to mark the changes then discard the residue that is already present in the reference genome and use the other allele. However, you want to keep a ...


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How about the allele frequency database? http://alfred.med.yale.edu/alfred/index.asp One of the main problems with SNP databases is that there are a lot of them so you can get lost quickly. This sight gives some overview on the available resources: http://www.humgen.nl/SNP_databases.html Hope this helps.


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I will strongly suggest you: PredictSNP: It's the best tool for nsSNP detection as it compares and throw out result from all the tools available. http://loschmidt.chemi.muni.cz/predictsnp/ Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168/


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As @WYSIWYG pointed out, having the indel difference in the 3' end can be informative, but I'm having a harder time finding evidence in the middle of the primer. Putting the mutation/indel at the 3' end will change the ΔCT. To do it well, you need wide coverage on your mutation site. I think that it is possible that there could be a difference with a ...


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The purpose of validating is to find genuine SNPs and not those caused by sequencing or amplification errors. It is extremely unlikely you will have a false homozygous SNP as a result of error. Just think about it. The same error, at the same base, occuring 80%+ of the time? Its not going to happen unless you have low coverage, and these SNPs should be ...


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I agree with @gchadwick that more infor would help. However, based on my understanding of what you are trying to do (SNP genotyping on several genes), I suggest. 1) Enrich your DNA with DNA from the organism you want 2) Enrich your DNA with DNA in the desired regions (if any). Solution: Target enrichment. You are probably aware that companies such as ...


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SNP Density Human = ~1.18 SNPs per kbases Based on CgsSNP, the average numbers of SNPs per 10 kb was 8.33, 8.44, and 8.09 in the human genome, in intergenic regions, and in genic regions, respectively. Source: Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. by Zhao Z, Fu ...


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Each rsid identifies a unique SNP in the genome. Thus there should not be any entry in the files that have the same rsid but different chromosomes and/or positions. If you do find this, it is likely that you have data from different versions of the assembled genomes. To find genetic variants associated, i.e. correlated, with your trait, you need to focus ...


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You might be able to get some raw data on SNP frequency by batch querying the dbSNP database. I have not used it myself, though.


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In order: Unfortunately, there's no easy way to batch query with only location. You could look up SNPs within genes here. (You could find the gene a SNP is located in by searching an annotated human genome file for the position.) You can figure out whether it's in 3'UTR by comparing to a list of human 3' UTRs. The UCSC genome browser page here will help: ...


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Well SNPs are single nucleotide polymorphisms. Some SNPs are in the coding regions of genes and they can result in changes in the resulting protein. For example, the SNP rs1801131 is a human variation where some individuals have a G instead of an A at position 1515 of the gene MTHFR. When the gene is transcribed and then translated into protein, this ...


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In short, yes. If a gwas study links a SNP to a particular phenotype then yes, it is an effect of a single copy. Bear in mind, however, that a SNP is not a knockout or even a knockdown. It can be, but it is not always the case. SNPs can produce a change in the protein sequence or in the regulation of the production of that protein. Both types of variation ...



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