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Questions tagged [gwas]

Questions pertaining to genome-wide association studies.

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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?

I recently started analyzing a GWAS summary dataset. It has a column for the reference allele in which it mentions the base in the reference genome. There is another column for the alternate allele (...
hgz's user avatar
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2 votes
1 answer
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Why are there only 3 types of data (0,1,2 ) in some GWAS tables?

I am wondering about the format of raw genotyping data in a GWAS article published on 21 December 2023, the supplementary data contains a table named "Diversity_genotyping_raw" (inside ...
anonymous67's user avatar
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Can co-mutations be potential expression quantitative trait loci (eQTLs)?

I'm wondering if it is possible to test this and how? Usually we do this for single SNPs, I wanted to know if it was plausible for pairs of SNPs. Which method would you suggest? I want to test whether ...
Caterina's user avatar
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1 answer
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How to access Target Data for PRS analysis on GWAS Dataset

I am working on conducting a PRS analyses on a GWAS Dataset that deals with the alzheimer's disease. The data is split into cases(Participants with the disease) and controls(participants without the ...
lamdeb's user avatar
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1 vote
1 answer
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Why would GREML in GCTA treat SNP effects as random effects?

I've read many papers, but none of them gave clear answer to my question. For example, https://www.nature.com/articles/s41576-019-0137-z#Sec5 The univariate GREML approach can model multiple random ...
John Smith's user avatar
1 vote
1 answer
84 views

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: ...
abc's user avatar
  • 241
2 votes
1 answer
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Correlation between polygenic scores and reproductive success

I was looking through this article in the journal Behavior Genetics. The researchers has investigated 400 000 people in the UK Biobank and calculated polygenic scores for 33 traits. Then they ...
Agerhell's user avatar
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3 votes
1 answer
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How can SNP arrays be used to detect deletions within a gene?

I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
ceno980's user avatar
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Phenotype-to-genotype mapping

My understanding is that GWAS or QTL attemp to extract potential SNP candidates responsible of a particular trait. However, is there any framework that attempts to do the opposite? This is, link the ...
Neggor's user avatar
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2 answers
75 views

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?

I am learning about genome-wide association studies (GWAS) and I know that they are used to see whether certain SNPs are associated with a disease of interest. From everything that I have watched and ...
ceno980's user avatar
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Genome-wide association study (GWAS) search engine?

I am not a biologist and came across the term genome-wide association study or 'GWAS' for the first time today. Now I would like to see if there is a GWAS on the particular condition I am interested ...
stevec's user avatar
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1 vote
1 answer
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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 ...
Andreas Adinatha's user avatar
2 votes
1 answer
47 views

Quantifying the Genetic Basis of Complex Diseases

In general, there are 2 types of diseases for which we understand "causality" very well: Infectious disease, where there is some etiological agent that causes the disease and Monogenic genetic ...
gilead22's user avatar
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1 answer
225 views

What does the MAF/MinorAlleleCount mean?

I'm not sure why reporting the second most frequent allele is helpful? what is the Major allele?
eyesun's user avatar
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N value in a GWAS?

Just like the title says. I am reading about a GWAS but I don't know much about them. I understood most of it but I couldn't figure out what the "n" value was.
help's user avatar
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2 votes
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269 views

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,...
DN1's user avatar
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1 answer
117 views

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 ...
Federico Parravicini's user avatar
1 vote
1 answer
68 views

How to set the phenotype in GWAS analysis?

In the GWAS analysis, my animal sample phenotype is whether an individual dies or survives. And I have every sample death time. How do I set the phenotype in GWAS analysis?
flystar's user avatar
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1 vote
1 answer
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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 ...
Trace's user avatar
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1 vote
0 answers
23 views

How many samples to run an association study on B-Cell receptors

We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/) to ...
user491880's user avatar
4 votes
1 answer
5k views

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

I'm trying to get my head round the correct GWAS terminology. I keep seeing the terms like "tag", "lead" and "index" SNP to be used almost interchangeably and I would like to get a clarification from ...
Ophiothrix's user avatar
6 votes
1 answer
588 views

Recommendations for textbooks on statistical and quantitative genetics, and genetic epidemiology

I'm looking for a textbook on statistical genetics, quantitative genetics, association mapping, and genetic epidemiology. My interests include, but are not limited to, complex trait analysis, and the ...
Ólavur's user avatar
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1 vote
0 answers
345 views

What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?

What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
player777's user avatar
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2 answers
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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 ...
hb59's user avatar
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1 vote
0 answers
49 views

Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
user33904's user avatar
1 vote
2 answers
116 views

Difference between imputing and typing in GWAS studies?

In genome-wide association studies (GWAS), what is the difference between imputing and typing? Are they the same?
Svalf's user avatar
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1 vote
2 answers
360 views

Why are Mendelian mutations considered rare?

I was reading the Wikipedia articles about genome-wide association studies (GWAS) and whole exome sequencing. As I understand, GWAS is used to identify most common SNPs that are proved to be ...
F.N's user avatar
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3 votes
2 answers
497 views

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. ...
Nuclear Hoagie's user avatar
5 votes
1 answer
455 views

Linkage Disequilibrium in GWAS

I see a lot of studies on GWAS not filter out for linkage disequilibrium or even make the slightest mention of it. Why is this the case? I would imagine that you want to keep SNPs that are only in ...
Sid's user avatar
  • 151
7 votes
2 answers
4k views

GWAS: why is replication in another cohort so crucial?

Almost all the landmark GWAS (Genome-Wide Association Studies) reviews agree that, for a GWAS finding to be valid, it needs to be replicated in an independent cohort. What exactly is the rationale ...
WesternBlöd's user avatar
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2 answers
920 views

How to do whole genome sequence alignment in R or Ruby/C++, any good language? [closed]

I need to perform tuberculosis mutation analysis. First step I need to do is to align sequences in fasta format against one reference file. i tried CLC genomics workstation --- it hangs on 60 000 ...
VassiaAlk's user avatar
  • 241
0 votes
1 answer
157 views

How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis

I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be ...
VassiaAlk's user avatar
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0 votes
0 answers
91 views

Phenotype choice for one of a MZ twin pair in a genetic association study

I was having a discussion with a colleague and this question came up... It is commonplace in molecular genetics studies to only genotype one of a pair of monozygotic twins (and then implicitly impute ...
Joni's user avatar
  • 136
1 vote
1 answer
38 views

A question on exclusion of study participants for an Exome genotyping array

I'm reading a paper that used whole exome sequencing on an African American and European populations to discover novel low frequency and rare variants associated with lipid levels & the risk of ...
geneteics_diva's user avatar
1 vote
1 answer
62 views

Investigating rare variants in ethnically different populations (European ancestry & African ancestry)

If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) ...
geneteics_diva's user avatar
3 votes
1 answer
891 views

GWAS: matched-pairs and logistic regression

Logistic regression is a common analysis tool used for GWAS when your response variable of interested is qualitative. It comes as one of the standard tools in most GWAS packages (e.g. PLINK). Most ...
bdeonovic's user avatar
  • 133
1 vote
1 answer
214 views

Interpreting SNP-in-gene associations from GWAS studies

For most SNPs identified in GWAS studies, is the underlying assumption that if it is indeed associated with a phenotype (and lets assume its associated because it affects protein function), that you ...
Noopde's user avatar
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11 votes
2 answers
6k views

What is the difference between naive and adjusted p-values in a GWAS study?

What is the difference between a naive p-value and an adjusted p-value in the results of a GWAS study? See from this paper: After Bonferroni adjustment, a single gene, DCTN4 (encoding dynactin 4) ...
719016's user avatar
  • 1,790
14 votes
1 answer
300 views

Paralogous genes in genome-wide association studies?

Has anybody tested if paralogous genes are over-represented among the genes identified by genome-wide association studies (GWAS)? For example, if a GWAS study finds 200 genes associated to the ...
yahoo301503's user avatar
2 votes
1 answer
84 views

variation in expression accounted for a SNP -- what's a usual percent?

I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the ...
719016's user avatar
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6 votes
2 answers
398 views

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

I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more ...
719016's user avatar
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