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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 ...
terdon's user avatar
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4 votes
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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 ...
Remi.b's user avatar
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4 votes

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 ...
BagiM's user avatar
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3 votes

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 ...
Nicolai's user avatar
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3 votes
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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 ...
alec_djinn's user avatar
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3 votes

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 ...
Bryan Krause's user avatar
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3 votes

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....
bpedit's user avatar
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3 votes
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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!!" ...
Maximilian Press's user avatar
2 votes

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; ...
Rish's user avatar
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2 votes

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 ...
Artem's user avatar
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2 votes

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: ...
alec_djinn's user avatar
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2 votes
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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 ...
user7875084's user avatar
2 votes

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.
WYSIWYG's user avatar
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2 votes

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 ...
Nicolai's user avatar
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2 votes
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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 ...
WYSIWYG's user avatar
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2 votes

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, ...
laporp's user avatar
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2 votes
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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 ...
David's user avatar
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2 votes
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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 ...
mgkrebbs's user avatar
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2 votes
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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 ...
rotaredom's user avatar
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2 votes

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 ...
jakebeal's user avatar
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2 votes

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 ...
Maximilian Press's user avatar
2 votes
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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 ...
Maximilian Press's user avatar
2 votes

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 ...
Darlingtonia's user avatar
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1 vote
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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 ...
shigeta's user avatar
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1 vote

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 ...
Remi.b's user avatar
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1 vote
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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 ...
finswimmer's user avatar
1 vote

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 ...
Fabio Marroni's user avatar
1 vote

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
swbarnes2's user avatar
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1 vote
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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 ...
mgkrebbs's user avatar
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