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

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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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74 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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65 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 ...
3
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1answer
48 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 ...
3
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1answer
36 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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36 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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27 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) ...
2
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1answer
538 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 ...
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3answers
138 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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73 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: ...
3
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1answer
31 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 ...
5
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1answer
57 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 ...
4
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1answer
340 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 ...
3
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1answer
113 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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1answer
137 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 ...
5
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1answer
142 views

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 ...
2
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1answer
62 views

Could someone clearly define what a gene variant is with an example

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. A clear example with ...
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1answer
673 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? ...
3
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2answers
139 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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1answer
398 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 ...
2
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1answer
71 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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1answer
120 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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1answer
227 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: ...
4
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3answers
104 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 ...
2
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1answer
839 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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1answer
67 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?
3
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1answer
76 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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1answer
95 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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1answer
62 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 ...