Questions tagged [snp]
Single nucleotide polymorphisms, or SNPs, are differences between two sequences of DNA at one individual nucleotide location.
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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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How many generations does it take for the average descendant not to be genetically related to the ancestor?
Parent 1 and 2 have children. Assume infinite, randomly-mating population size. How many generations until the median descendant by lineage of parent 1 has 0 base pairs inherited from parent 1?
I ...
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Population structure and SNP's in Linkage Disequilibrium
I am reading about population structure and how you could as an example use plink to analyze a set of SNPs for individuals in a vcf file to identify a given population structure.
I know that LD can be ...
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Is deleting two or three consecutive nucleotides and inserting exactly two or three back more common than two or three consecutive SNP?
I am looking at cancer mutations. I found that some of the mutations are e.g.
c.1251_1252delGGinsTT
c.151_152delGGinsTC
c.351_352delCAinsTT
I wonder if these are indeed two consecutive single ...
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How to list coding/noncoding genomic regions linked to significant SNPs?
For QTL analysis in mice GEMMA was used to get P values ("p_lrt" column) for SNPs. GEMMA output (...assoc.txt) file excerpt:
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How do genetic variants of a gene moderate an association, leading to counterintuitive result?
I have run moderation analysis to study the interaction between SNP (dominant model) of a gene (A) with DNA methylation on cognition measures. For this, I have calculated the mean DNA methylation ...
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Why people carrying the same SNP doesn't have the same Promethease report
I'm a frequent user of Promethease to run health analysis based on MyHeritage SNP data dump.
I ran two people through Promethease and both have the same SNP:
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How can a minor allele frequency be >50% (reported in GNOMAD)?
I'm receiving a data set to start an analysis. My collaborators ran GATK to find variants from sequencing data, and GNOMAD calculated the minor allele frequencies - and then I'm receiving this MAF ...
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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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How often are diseases caused by more than a single mutation of a gene?
Many genetic diseases are caused by mutations in a gene and often, it is a single nucleotide polymorphism (SNP) that has dramatic consequences (e.g. the E6V hemoglobin mutation in sickle cell disease)....
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Statistician confused about exact SNP data type
I'm from a statistical (not biological) background, and I'm very confused about what exactly is the "data" associated with a SNP. Below, I'll explain things as best I can--please correct me ...
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Blood and plucked-feather sample storage
This next field season I will be collecting both blood and feather samples and I wondered how best to store the samples. The blood samples will be used for microsatellite and/or SNP analysis. The ...
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if an SNP were edited using CRISPR What are the chances that, absent artificial selection, wild type alleles would reemerge?
I am researching a fatty acid amide hydrolase (FAAH) SNP RS324420 and FAAH out microdeletion that together lead to reduced pain sensitivity and reduced anxiety (Moreira et al 2008).
The causative ...
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What degree of influence do SNPs have on activity of ligands at receptors?
I know that generally, evolution tends to evolve towards having some wiggle room in respect to effect of polymorphisms on binding of endogenous ligands, but with synthetic ligands, especially modern ...
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What's the role of SNP (Single Nucleotide Polymorphism) in a disease when there is no gene associated to that SNP
I am quite new to the field of GWAS (genome-wide association studies), and I'm combining GWAS results and single cell analysis on type-1 diabetes (T1D), to see the role of cell specificity on the ...
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How to find the origin of each Single Nucleotide Variants (SNV) in child when having variant call data for both parents?
I am working with a trio (Mom, Dad, Child). I have variant call data for all three. Now I want to know each SNV in the child comes from which parent?
Is there any tool that could help me to achieve ...
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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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How do I interpret SNP nomenclature?
I am combing through my 23 & me raw data and I am a little confused on SNP terminology. I am using NCBI's genome browser and SNP database. As an example we can all follow here is a link to a ...
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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 ...
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Chromosome position mismatch for SNPs in dna tests
TL;DR: why is the position reported by DNA testing companies for an SNP on a particular chromosome different than the one in dbSNP/SNPedia databases?
I'm analyzing the raw DNA exports for the same ...
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Hardy–Weinberg equilibrium for SNPs
I have a SNP stats file structure, which contains all information about genotypes and imputed SNP/INDEL imputation qualities, allele frequencies and minor allele assignment.
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Why do individuals vary in the number of SNPs for a given gene ( e.g. FOXO3A )?
Individual #1, sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output:
1) rs1935949(C;T)
2) rs2802292(G;T)
3) rs13217795(C;T)
4) rs13220810(C;T)
5) rs2764264(...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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