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

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What about 23andMe's SNP test gives it such bad efficacy as a diagnostic tool?

The recent news about the FDA stopping the google backed 23andMe service selling any more kits got me thinking. I understand the company may have been selling it as a medical tool prematurely, but ...
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86 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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444 views

How do you merge SNP data with a reference genome?

My Data I have a 23andMe file listing SNPs in the form: ...
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75 views

What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
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163 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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654 views

Effect of single nucleotide deletion or insertion on primer annealing

How is primer annealing, and, consequently, PCR amplification affected by single nucleotide deletion or insertion inside the primer ? Imagine a primer like this: GCGTCATAAAGGGGACGTG (primer) and ...
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153 views

Is there any source for raw data of SNP genotype frequency?

On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares ...
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2k views

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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129 views

Understanding these SNP annotations

I am looking at the PharmaPGKB database for SNPs and trying to understand what the following annotation means: rs1801131 at 1:11854475 in CLCN6, MTHFR (VIP) Ok, ...
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107 views

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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128 views

Publicly available genotype data?

I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this: ...
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120 views

Regarding the NCBI FTP site

I am trying to extract information about SNP data from the FTP server of NCBI. Could someone please explain to me how the directory is organised? There are many many files and folders and I can't ...
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49 views

What is the genetic distance where linkage can be ignored?

I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree ...
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126 views

Comparing SIFT and PolyPhen to other methods

I'm looking for a database of nsSNP (non synonymous single nucleotide polymorphisms) and their effects. As I understand, the common methods to predict this are SIFT and PolyPhen, and I want to compare ...
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190 views

Real-time PCR delay in Cq due to insertion SNP in primer

I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR. I am most interested in how much there is a delay in ...
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194 views

Why only heterogeneous SNVs for validation using genotyping arrays?

I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called ...
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51 views

Genetic variation in humans and model organisms (measured by SNPs)

I was wondering what is the range of SNP density across species and model organisms. I.e., what would be a reasonable estimate for the SNP density (i.e., x SNPs for each 1 Kb) in: humans humans ...
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3k views

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'...
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1k views

Definition and example of Gene Variant

Could someone clearly define what a gene variant is with an example. I am totally confusing myself with SNPs, alleles, variants and how the major and minor allele are defined. An example with gene ...
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78 views

Are genes associated with obesity selected for?

I've read that there are several SNPs associated with increased risk of clinical or morbid obesity. I was wondering if there is any evidence that these are under positive selection. Would you expect ...
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2k views

Why is Sanger sequencing inferior for detecting SNPs in cancer cells?

I am familiar with Sanger sequencing, but at the level of an undergraduate. A lecturer of mine tried to describe Sanger sequencing as losing the sequence information in noise when used to detect ...
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70 views

variation in expression accounted for a SNP — what's a usual percent?

I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the ...
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65 views

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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377 views

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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43 views

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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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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115 views

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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758 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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79 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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49 views

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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133 views

Single Nucleotide Polymorphisms and diseases

I am writing a report on how Single Nucleotide Polymorphisms occurring in each of these regions: Transcription factor (TF) binding sites Epigentic signals Splicing variants MicroRNA binding sites ...
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81 views

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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58 views

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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50 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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41 views

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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55 views

Alleles notation in SNPPedia criteria

I can understand the allele notation when is in the form rs8176719(T;T) or rs8176719(G) but recently i found this ones rs8176719(T;-) or rs8176719(-;T). So im confused, rs8176719(T;-) is the same as ...
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1k views

How to compare SNP from genotyping results for multiple people with a known phenotype?

I'm looking at different genotyping profiles available at opensnp.org and am trying to compare profiles for people with different phenotypes. For example, given 10 profiles of people who can roll ...
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322 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
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151 views

Interpreting SNP-in-gene associations from GWAS studies

For most SNPs identified in GWAS studies, is the underlying assumption that if it is indeed associated with a phenotype (and lets assume its associated because it affects protein function), that you ...
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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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47 views

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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607 views

SNP genotyping using PCR

I read this wikipedia article on SNP genotyping and wasn't able to understand this part : In examining the results, if a genomic sample is homozygous, then the PCR products that result will be ...
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3k views

What is the difference between SNP and STR?

I thought that these were just different format of the same data. But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right? ...
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41 views

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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213 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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95 views

SNPs mapping into protein

Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means?
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Difference in associated SNPs in GWAS

I noticed that when GWAS studies are being replicated, some SNPs near a gene known to cause a trait are enriched in frequency in those with the trait. However, among the different studies, the most ...
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20 views

Dominant model Disease SNP

Say that you have genotyped a SNP in a case control setting, and get the following result AA AB BB Cases 17 51 29 Controls 39 44 20 where A ...
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14 views

Finding SNPs and Haplotypes?

I have the following alignment file. How can I identify the SNP sites and how can I find the haplotypes. I know these are related but can't seem to apply it to the below data. Any help would be ...
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9 views

What's the regulation of natural antisense transcripts?

By running an in silico approach on TF binding site prediction, I've discovered binding motif similarity on a nucleotide sequence within the EGFR-AS1. I was quite surprised, given that the ...