Questions tagged [snp]

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

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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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What are the SNPs responsible for PCSK9 expression?

My understanding is that PCSK9 is an enzyme that affects how cholesterol is cleared from the liver, and thus how how high or low the LDL cholesterol number is in a person. I'm curious to know what are ...
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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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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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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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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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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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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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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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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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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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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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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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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 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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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?
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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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