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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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25 views

Simulating phenotype using gcta64 and 1000 Genomes

I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation? I'm trying to use ...
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26 views

Which side of the DNA helix is used for describing SNPs?

In genetic research I often come across references to single-nucleotide polymorphisms (SNPs). An example is rs3184504(C;T). As far as I understand it: In this ...
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Is it possible to buy a DNA sample with a specific mutation?

I would like to test a genotyping method (ARMS) on a specific human snp (heterozygous or homozygous ). Unfortunally, we do not have any dna samples with the mutation. Is it possible to buy somewhere a ...
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What are the consequences of less DARC expression as a result of a Duffy weak allele?

According to codegen.eu I'm a carrier of a Duffy weak allele. For SNP rs34599082 I have alleles C and T. T is a rare allele that found is less thatn ~1% of the population. Codegen.eu directs me to ...
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Studying the epigenetic variability, can I use SNPs?

So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed ...
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How do researchers define the region a lead SNP encompasses?

As I understand it, a lead SNP captures the variance for all unmeasured SNPs in a region due to it's low p-value and high linkage disequilibrium. However, in different papers the region size differs (...
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41 views

How would two SNPs interact to affect CYP3A5 gene activity?

If someone has a non-functional rs41303343(T;T) SNP, yet that individual also possess the partially functional rs776746(A;G) SNP, is their CYP3A5 genotype functional or nonfunctional? In other words, ...
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Are SNPs always in linkage disequilibrium with other SNPs

Is it possible to have a SNP that is not found is be non-randomly associating with any other SNP?
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53 views

What are the different types of SNPs?

When I search for this online I get answers such as substitutions, deletions, insertions etc. But I mean in the sense that I have been reading different terms infront of the word SNP such as: lead SNP,...
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84 views

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 ...
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1answer
51 views

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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28 views

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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1answer
34 views

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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1answer
298 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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47 views

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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1answer
58 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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1answer
279 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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1answer
31 views

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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3answers
184 views

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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354 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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73 views

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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544 views

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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102 views

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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1answer
103 views

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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38 views

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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548 views

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 read online that they have found around 10 million single nucleotide polymorphisms (SNPs) across individuals in the human genome [1]. However, this number includes all SNPs found in all people who ...
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1answer
168 views

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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1answer
105 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?
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57 views

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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2answers
248 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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1answer
113 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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2answers
96 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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1answer
115 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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1answer
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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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1answer
148 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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1answer
461 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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1answer
3k 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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1answer
162 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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3answers
371 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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523 views

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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2answers
79 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 ...