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4 votes

Linkage Disequilibrium in GWAS

One possible reason to not filter for linkage disequilibrium is to produce peaks/hits with multiple SNPs, thereby clearly indicating a region of a causal genotype. For example, in the manhattan plot ...
user42909's user avatar
  • 535
4 votes

Correlation between polygenic scores and reproductive success

RLRS is defined as respondent i’s number of children, divided by the mean number of children of people born in the same year They fit a regression: RLRSi=α+β * PGSi+εi In this equation, RLRSi is ...
Bryan Krause's user avatar
  • 45.9k
3 votes

What does the MAF/MinorAlleleCount mean?

[W]hat is the Major allele [frequency]? If the Minor Allele Frequency is $p$, then, for a bi-allelic locus, the major allele frequency is obviously $1-p$. [W]hy reporting the second most frequent ...
Remi.b's user avatar
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3 votes
Accepted

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
3 votes
Accepted

How can SNP arrays be used to detect deletions within a gene?

In the materials and methods of the paper, you will observe the following statement regarding the CNV (deletion) analysis: CNV analysis was performed using CNV-WebStore (38). That citation points to ...
Maximilian Press's user avatar
3 votes
Accepted

GWAS terminology "Tag" vs "Lead" vs "Index" SNP

I found a review paper that addresses your questions, see Schaid, Chen, Larson (2018): From genome-wide associations to candidate causal variants by statistical fine-mapping Tag SNP. You correctly ...
Eff's user avatar
  • 680
3 votes

Why are Mendelian mutations considered rare?

I will focus more on the question of rarity, which the comments have not addressed. Recall that natural selection is operating on the human population. Because of this, bad mutations of large effect (...
Maximilian Press's user avatar
2 votes

Difference between imputing and typing in GWAS studies?

'Typing' is an SNV-typing. It is an explicit SNV detection using Affymetrix GeneChip arrays, Illumina BeadArray. 'Imputing' is an imputation. It is a statistical inferring from existing genotype data ...
Maxim Kuleshov's user avatar
2 votes
Accepted

Why are there only 3 types of data (0,1,2 ) in some GWAS tables?

Yes, that's an interesting question. The short answer is that most variants only have two alleles, and even though you can be heterozygous at a position in two different ways, both of these result in ...
BigMistake's user avatar
2 votes
Accepted

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
1 vote

In the context of GWAS we have an alternate allele and a reference allele. Why do we only have one possible alternate instead of three?

Estimates seem to be around 45-60 de novo mutations in an individual, e.g.: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9550265/ That means the other 2999950 mutations are inherited, they're shared ...
Bryan Krause's user avatar
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1 vote
Accepted

How many people need to have the same mutation of a gene in order for that gene to be seen as a feasible candidate for a disease?

Genomic analysis of copy number variants is routine for GWAS purposes. Here is one early example. In that case I believe they used array CGH rather than sequencing but the principle is the same, and ...
Maximilian Press's user avatar
1 vote

Quantifying the Genetic Basis of Complex Diseases

I'm not sure what you mean by "complex", but many diseases are known to arise due to exposure to toxins or to an absence of essential nutrients in the environment. Toxic metals: A good ...
tyersome's user avatar
  • 5,598
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
Accepted

How to set the phenotype in GWAS analysis?

Simply, First of all, you can group samples as survived animals and dead samples and you have a binary phenotype. In a different approach, you can use survival time (time to death) as an ordinal ...
SRhm's user avatar
  • 192
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
  • 5,230
1 vote
Accepted

same SNP rs# referenced to be found in two different genes

The NCBI dbSNP entry shows rs7442295 to be in the gene SLC2A9, not SCL2A9 stated in the original question. As the Wikipedia article for SLC2A9 says, synonymous names for SLC2A9 include: solute ...
mgkrebbs's user avatar
  • 9,054
1 vote

Difference between imputing and typing in GWAS studies?

No, they are different altogether. Typing in GWAS is genotyping individuals from a selected population to know say the genetic variation of SNP's (single nucleotide polymorphisms) among them via ...
Shab86's user avatar
  • 11
1 vote

What is the relative power of GWAS studies in different species?

question looks like it's been dormant for a while, but i think there's some discussion to be had here- I would argue that in many (most?) of the model organisms, power would be much greater than ...
Maximilian Press's user avatar

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