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Questions tagged [snp]

Single nucleotide polymorphisms, or SNPs, are differences between two sequences of DNA at one individual nucleotide location.

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GEN file format, SNPs and alleles

I have a few questions I can't seem to get a straight answer to, regarding the .gen file format and also biology in general. The .gen file format specifies SNPs for individuals. Since each SNP has ...
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Are microsatellites viable markers for GWAS?

I'm just reading some papers on genome-wide association studies and find that most of them use SNPs as a marker. I understand that they're the most polymorphic and thus the best for accurate ...
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GWAS: marker map based on old genome assembly - can I use the new assembly to look for SNP positions?

I have an old set of pig SNP data and the positions were mapped using v10.2 of the assembly. I submitted a GWAS paper for review, and the reviewer wants to know if any of the significant SNPs that ...
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SNP coding for association analysis

I'm working on a project about detecting SNP association with a disease. As I understand, SNP is a single variation of the nucleotide that occurs for more than 1% of the population. However, I couldn'...
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Treatment validation on mouse models

I am struggling to set up a project proposal for validation of a known treatment for metastatic colorectal cancer in mouse models. I want to see how SNPs in patients contribute to their drug ...
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How is single nucleotide polymorphism denoted?

Currently I'm studying an article on TERT promoter mutations in human melanoma and find myself unfamiliar with included denotations,I would appreciate it if someone could explain to me what C228T in ...
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212 views

SNP vs common SNP

Wikipedia citing Nature defines SNP to be a one where each (thus the lowest frequency) allele exceeds some percentage threshold in the population. But I see a lot of papers and books calling such an ...
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DNA Analysis (AncestryDNA)

A recent1 AncestryDNA commercial highlights a customer who discovered that she was 26% Native American. Credit: ancestry.com/dna You can see the full commercial here. My question is, how can this ...
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Multi-protein drug treatments

Apologies if this an obvious question - I am very new to this. I am, as of now, under the impression that multiple SNP variations interact to create multiple mutated proteins, which ultimately results ...
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54 views

Is my RNA-seq experimental design correct to use it for SNP calling?

I am a newbie here and would highly appreciate your advice about one particular experimental design. We have data from RNAseq experiment which was originally designed to assess differential ...
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262 views

Definition of Cis-eqtl

I have simple question, do cis-eQTLs use the SNPs that are within 1 Mb from the gene's TSS on the same chromosome ?
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same SNP rs# referenced to be found in two different genes

Two GWAS papers have referenced the same SNP (rs7442295), but one states it's found in the gene GLUT9 and the other states it's found in SCL2A9. The ncbi dbSNP says it's in SCL2A9, and I thought that ...
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What are the exact reason causing missing calls in a VCF file from exome sequencing?

My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is ...
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Which is a good methodology to find out a domestication process?

I just started with my course in genomics and I'm working with domesticated animals (cows, chickens, pigs, etc) and I would like to know which methodology is better to trace the process of ...
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Single copy housekeeping genes

I am working on a tool for SNP calling in polyploid plants. To test my method, I need a list of housekeeping genes common in almost all plants. For my case, these genes must be single copy (ie each HK ...
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Relation between bases while changing into a SNP

Is there any relation or influence among the bases (A, C, G, T) while they are converted into a snp? Such as, is A converted ...
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219 views

what is the meaning of the genotype values in each snp

I understand that snp is a single base variation. For example, if person 1 has the sequence in DNA , AAGCCTA the second has AAGCTTA, then the allels are C,T. My question is what is the meaning of 0,...
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Personal Genomic Data Samples

a quick question. I am looking for complete personal genomic data of human individuals. The only requirement for the genomic data is that it contains the complete set of SNPs of a human individual. So ...
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Analysis over single chromosome data

I have no expertise in biology, I'm a data scientist, and I would like to know if it makes sense, from the biological point of view, to analyze data (SNP data) coming from a single chromosome, and not ...
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What is the difference between RFLP and DNA fingerprinting?

Is RFLP (restriction fragment length polymorphism) analysis the same as DNA fingerprinting? I looked for information online and I don't understand the difference.
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Whole Genome Sequencing vs Whole Exome Sequencing

I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:- I am looking at SNP's and ...
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What is the upper limit of number of SNP based mutation in any protein?

I want to know if there is any upper limit of, how many point mutation a protein can have because of disease or nsSNPs? The general studies only focus mostly on a single or double site mutation of any ...
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Genetic entropy [closed]

One day my internet acquaintance told me, that genetic entropy can be evidence in favor of intelligent design and he also provides me this waiting time problem and this simulating evolution by gene ...
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Calculate signifficance of SNP in specific trinucleotides [closed]

So, I have calculated the frequency of all SNPs (single nucleotide mutations) in some samples and have also found the nucleotides on the 3' and 5' sides of the mutated nucleotide. So I have a list of ...
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Interpreting Allele frequency and allele count

In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never ...
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SNPs in the Human Genome

I have read online that they have found around 10 million SNPs in the human genome [1]. I was wondering how many SNPs there are in a single person on average, I could not find any well-found evidence ...
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Figuring out if populations from two regions share the same Neanderthal haplotypes

I am going to preface this post in that I am not sure if it belongs here, but considering it has been ignored everywhere else I have tried I thought it is worth a shot. I am a graduate student who is ...
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Parameters of Variant calling analysis [closed]

What is the good or stringent parameter for variant calling. At present using the DP > 10 and Q > 30 for Variant calling. Is it ok.? Thanks
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What is the best test for SNV clustering?

I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
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239 views

How to predict the effect of a non coding SNP variant on the expressed protein?

I am writing a paper for non coding SNPs on patients with metastatic breast cancer. Having used a specific gene panel (NGS) of approximately 60 genes, I'm currently running out of ideas on what to ...
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How can I find the most studied SNP of a gene?

How can I find the most studied SNP of a gene and diseases that the most studied SNP has been related to? I search in dbSNP database but I can't find it. What is the process?
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identifying which SNPs sit in TFBS (Yeast)

i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the ...
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110 views

Understanding different genetic terminology - Genotype vs SNP

I recently came across a study that refereed to variations in genes like this: IGF1 (CA)19/(CA)19, IGF1(CA)19/X, IGF1 X/X (From this study: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3274549/) I ...
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What is pQTL and why do we need eQTL?

eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia). There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly ...
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genes map to eQTL/pQTL

Of the 192 target genes, 79 map to a significant eQTL or pQTL in at least one dietary condition. is the line for a paper "Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a ...
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Why perform imputation?

Genetics datasets contain measurements for millions of single nucleotide polymorphisms (SNPs). Some (usually small) percentage of these values are of low confidence, and are labeled as missing values. ...
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2k views

Why do almost all SNPs have two alleles?

Reading the Wikipedia page for SNPs I find the sentence "Almost all common SNPs have only two alleles." This is consistent with terminology elsewhere, such as the therm "Minor allele frequency", which ...
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153 views

How does the MET gene work and what happens when the promoter region gets mutated?

I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET ...
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What fraction of sites are expected to be polymorphic?

Question Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals ...
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Cut-off values for LD, LOD and D-prime as algorithmic input

I created an algorithm to generate SNPs for random people of different descents - based on HapMap data. While this works good, there is something else I want to take into consideration. So if a SNP ...
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Database of medically validated SNPs

I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of ...
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What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different ...
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Affymetrix SNP data, how to filter out rows based on rsid [closed]

This is my first time on stackexchange. I am new to bioinformatics, and I have some new SNP data from an Affymetrix Axiom array. I have the genotypes exported into a giant tab-delimited table txt ...
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389 views

Trying to understand the big picture behind DNA sequencing, alignment and searching

I'm about to start a bioinformatics research project but I haven't any biological background. I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like ...
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294 views

SNPs in DNase hypersensitive and histone marks sites

I am investigating a role of SNPs in DNase hypersensitive sites and in the DNA regions of histone marks and have some questions about it. SNPs in DNase hypersensitive sites might mean that those SNPs ...
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186 views

Location of TFBS in genome

I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether ...
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3k views

What is the difference between a fixed substitution and a single nucleotide polymorphism (SNP)?

I recently read a report that stated "We found 430 fixed substitutions […], with an additional 34 single nucleotide polymorphisms (SNPs) fixed within individual patients." What is the difference ...
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Where can I upload non-human Genotype data?

I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype ...
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Investigating rare variants in ethnically different populations (European ancestry & African ancestry)

If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) ...
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Ancestral Allele explanation

I'm having some trouble understanding the concept of ancestral allele. What exactly does it mean? What does it have to do with Identity by descent/state? What does it have to do(if anything) with SNP'...