Questions tagged [gwas]

Questions pertaining to genome-wide association studies.

0
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0answers
23 views

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.
2
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0answers
41 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,...
0
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1answer
41 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 ...
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0answers
34 views

How should I interpret a weighted genetic risk score?

I created a weighted GRS by summing the product of the dosages times their regression coefficients from the GWAS in which I found them. So GRS=sum(dosage1*coefficient1 + dosage2*coefficient2 +...). ...
1
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1answer
42 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?
1
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1answer
19 views

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 ...
1
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0answers
19 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 ...
3
votes
1answer
1k 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 ...
6
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1answer
215 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 ...
1
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0answers
309 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 ...
0
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2answers
56 views

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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0answers
46 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 ...
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2answers
83 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?
1
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1answer
206 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 ...
3
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1answer
452 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. ...
4
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1answer
170 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 ...
6
votes
2answers
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 ...
0
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2answers
714 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 ...
0
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1answer
141 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 ...
0
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0answers
81 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 ...
1
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1answer
32 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 ...
1
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1answer
53 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) ...
3
votes
1answer
691 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 ...
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1answer
187 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 ...
11
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2answers
5k 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) ...
14
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1answer
268 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 ...
2
votes
1answer
80 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 ...
6
votes
2answers
362 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 ...