6
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Whole Genome Sequencing vs Whole Exome Sequencing
WES, almost certainly. First of all, the vast majority of phenotype-causing variants are found in exons. For most analyses that are looking into disease causing mutations, WGS is pointless. It only ...
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SNPs in the Human Genome
I was wondering how many SNPs there are in a single person on average
A SNP is a polymorphism in the population, it is not a thing a haplotype can carry. Each individual has a given variant for any ...
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4
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Statistician confused about exact SNP data type
SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism" only means there is a variability (between individuals) in a single ...
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Studying the epigenetic variability, can I use SNPs?
Starting from what appears to be your main question:
Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region?
I would ...
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Personal Genomic Data Samples
Here is the link to the 1000 Genomes project, all the data is available for download. They already have a comprehensive list of SNPs as well.
It is not the only project around but it is definitely the ...
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DNA Analysis (AncestryDNA)
These tests don't actually tell your ancestry, there is no way for a genetic test to do that because there is too much genetic variation among populations, as well as between.
Instead, the test is ...
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Genetic entropy
I'm new to this idea but did a bit of searching. The origin of this idea of "genetic entropy" appears to be a guy named John Sanford. He is also the author of the "waiting time problem" you reference....
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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
SNPs do not signify anything about the functionality of a particular piece of DNA. You can think of a SNP as just a sign that says "hey, something in my neighborhood might be interesting!!" ...
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Parameters of Variant calling analysis
We will be needing some additional information to answer your question more completely:
What sequencing platform are you using? Illumina HiSeq/MySeq; ...
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Single copy housekeeping genes
There is no single answer for a gene. The most correct thing to do is to use a set of genes across many locus and measure the correlation of copy number across them first, and only use the ones which ...
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Single copy housekeeping genes
The following is probably a good set, it's for Arabidopsis you need to check if it fits with your need.
CBP20 Gene
Gene Locus: At5g44200
Actin-2 Gene
Gene Locus: At3g18780
UBC Gene
Gene Locus: ...
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Single copy housekeeping genes
Just flying from the waist: filter approach:
If there is a data source that has the expression data for cells in multiple tissues for any organism i would use that to find the housekeeping genes by ...
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Which side of the DNA helix is used for describing SNPs?
It is described with respect to the reference sequence. See the VCF format description.
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GEN file format, SNPs and alleles
From what I could find the .gen file format for SNPs was developed for the IMPUTE2 program and is generally meant to be a flexible file format for SNP data. The ...
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Analysis over single chromosome data
You can analyse a single chromosome. All the bioinformatics tools I know, allow that. Consider only the reads that map to the desired chromosome (or any segment of the genome). However, most next-gen ...
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Which side of the DNA helix is used for describing SNPs?
DNA has a "sense" strand and an antisense strand. The sense strand for that gene is the one you care about when discussing SNPs in that gene, because its the one being transcribed (and, as a result, ...
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Which side of the DNA helix is used for describing SNPs?
@WYSIWYG is correct, but in view of the brevity of his answer (and a second answer contradicting him) I provide chapter and verse.
The definition of RefSNP reference number is given by NCBI as:
“A ...
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Chromosome position mismatch for SNPs in dna tests
Most or all consumer DNA companies doing autosomal SNP tests deliver their raw data (at least by default) based on human reference genome build 37 (GRCh37). This is effectively the standard for this ...
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How do I interpret SNP nomenclature?
Quick answer is yeah, the G is the "reference allele" as you put it. The greater than symbol is acting as an arrow, ie, G goes to C, that is, G is replaced with C.
Actually you get a pretty clear ...
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How often are diseases caused by more than a single mutation of a gene?
I think that this question cannot be quantitatively answered, because the baseline "non-disease" state is not well defined.
Let's take as a starting point the example that you gave, of ...
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How can a minor allele frequency be >50% (reported in GNOMAD)?
Minor allele critically depends on what the reference population or genome is. And it also depends exactly how those data are sliced, it would be easier to say if we saw them.
Especially in large ...
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How to list coding/noncoding genomic regions linked to significant SNPs?
I would suggest seeing what others have done when using GEMMA. For example, you can see this paper's methods:
We converted p-values to LOD scores and used a 1.5-LOD support interval to approximate a ...
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How many generations does it take for the average descendant not to be genetically related to the ancestor?
Graham Coop performed simulations related to this question, based on actual transmission data for each chromosome in humans. He found that after 10 or 11 generations there was >50% chance that any ...
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Are SNPs always in linkage disequilibrium with other SNPs
Linkage disequilibrim is a result of two SNPs both appearing after a cross (e.g. in offspring). As such even at great distances two SNPs could both appear in offspring 50% of the time. Linkage ...
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Are SNPs always in linkage disequilibrium with other SNPs
There can be a number of reasons for Linkage Disequilibriunm (LD). Here is a non-exhaustive (non-referenced also) list.
Random LD happens
Epistasis
A recent selective sweep
Hybridization
Population ...
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GEN file format, SNPs and alleles
The definition of allele depends on the context.
If you look at the DNA of a single person you have usually two copies of each autosomal chromosomes. Each copy is ...
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Are microsatellites viable markers for GWAS?
Microsatellites could be used for GWAS. Actually they were the basis for linkage studies and were also used in the first association studies. The main reason why they have been replaced by SNPs is ...
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GWAS: marker map based on old genome assembly - can I use the new assembly to look for SNP positions?
Why haven't you tried using LiftOver to convert the coordinates?
https://genome.ucsc.edu/cgi-bin/hgLiftOver
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SNP coding for association analysis
Each chromosome location which has been identified as being a SNP is a location at which more than one nucleotide occurs at appreciable frequencies in the general population. This means that there ...
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