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6

Lets state what a Mutation is first. Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/GrCH38 from 2013, which are the most current genome assembly). Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have ...


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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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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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I would link your data with the ENCODE dataset. This dataset provides locations of TFBS. It is also accessible via the UCSC genome browser. For the actual question TFBS are located pretty much everywhere, including exons (as described here), introns and of course intergenic regions (e.g. enhancers, silencers, control locus regions - here a reference).


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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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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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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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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 ...


3

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 ...


3

Here's a quick summary of a few mis-hits in your otherwise good analysis: Not many bioinformatics applications use Hadoop, Apache Spark or Apache Flink. In fact, I have never heard of the Apache Spark and Flink tools, and I've seen only 2 people use Hadoop to process alignment files. Reads are not "converted" real, physical DNA. They are representations ...


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RAM's answer is very good, I'll just add on the computational side, short reads are error prone. That's important to account for when aligning or assembling. The reads themselves can just be inaccurate, which we detect by having multiple reads overlapping by a lot; we assume that stray discrepancies seen in only a single read at a position are errors. ...


3

In GWAS we are interested in understanding which SNP has a causal influence on a specific phenotype. At the moment large scale studies are carried out by genotyping arrays. For each SNP we put on the array, we measure the alleles present in the patient. The cost of genotyping obviously depends on how many SNPs we would like to measure. So the problem when ...


2

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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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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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 ...


2

First off let's define some concepts. DNAse hypersensitive regions are DNA regions which are in an open chromatin conformation (i.e. euchromatin). This means that those regions are more active at the genomic level (i.e. higher gene expression, gene regulation and higher TF binding) and are less prone to form nucleosomes. Histone mark sites are DNA regions ...


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You can search by traits (mostly diseases) for genome wide association, in these databases: Gwasdb2 Human genome variation Database: it also links to a Copy number Variation (CNV) database.


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The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that have different breeding systems, e.g. in Silene [1]. Past bottlenecks are also expected to decrease polymorphisms [2]. So, the answer to your question would ...


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Reiterating the above comments. Have a look at Tajima's D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model. The general form of the estimation for a diploid population is $E[S]=4N\mu\sum_{i=0}^{n-1} \frac{1}{i}$. Here the mutation rate of is per-genome not per-site, so $\mu=L * 10^{-9}$ where $L$ ...


2

We will be needing some additional information to answer your question more completely: What sequencing platform are you using? Illumina HiSeq/MySeq; Ion proton What type of sequencing (as noted by @CMosychuk): Exome or Whole Genome? What type of variant caller (as noted by @CMosychuk): Unified Genotyper; Haplotype Caller; TVC The QUAL metric is heavily ...


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Fixation is a process when one of the polymorphic alleles becomes fixed in the population gene pool due to genetic drift or natural selection and ceases to be polymorphic anymore. Therefore fixed substitution and SNP are two absolutely different concepts. So, the term “fixed single nucleotide polymorphism” seems to be oxymoron as it bears a contradiction. To ...


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


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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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