Question: Genome wide association studies (GWAS) Meta-analysis

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somayeh bakhshalizadeh •

**50**wrote:**Hi,**

I want to do meta-analysis (according to my research goals) by summaries of 60 articles. Due to absence of database for GWAS of livestock, can this meta-analysis be done by the statistical summaries available in the articles? Is the PLINK software capable of summaries analyzing of 60 articles? What software do you recommend for GWAS meta-analysis in estimating models with fixed and random effects?

Hello,

Thank you so much for your reply,

I have access to the parameters of the ID SNP, BTA, GeneName, Position, MAF, Estimate, SE, P-value for GWAS meta-analysis, but I do not have OR in some articles. Is there a way to calculate it? Can something be replaced?

50Please use

`ADD COMMENT/ADD REPLY`

when responding to existing posts to keep threads logically organized. This comment belongs under @Kevin's answer.96kIf you have the allele tallies, you can easily calculate odds ratios: A: SNP dataset and Z Score

The PLINK meta-analysis tool requires PLINK-formatted output, so, headers would be along the lines of:

I doubt that you have that for every study, in which case your best option may be METAL.

Alternatively, wait around for the PLINK developer to log in to follow up.

70kHello Mr Blighe

I do not have a case and control in my study. I work with quantitative traits. Is there a way to calculate OR for quantitative traits?

50So, if not case / control, what is your outcome variable, i.e., your phenotype?

70kYes, phenotype traits.

50Cool. What are you ultimately aiming to do? - use genotypes to predict the levels of continuous traits / phenotypes?

Can you confirm what is the

`BTA`

column in your data? - this is likely the. If you obtain the exponent of this, then you can have the odds ratio. For example (in R):beta coefficientIf they are the beta coefficients, then there are likely both positive and negative values in the list.

Can you confirm?

70kI want to work on the GWAS meta-analysis in QTL mapping for phenotype traits. Using systematic overviews such as meta-analysis, by aggregating existing information, increase the accuracy of the results of genomic predictions and QTL mapping.

To work with METAL, headers mentioned in METAL doucumentation :

MARKERLABEL SNP

ALLELELABELS RefAllele NonRefAllele

PVALUELABEL P-value

EFFECTLABEL Effect or OR

I do not work with the database and collect information manually. Because I did not find any database associated with GWAS livestock for research that has been done so far.

And I only have this information:

SNP

ALLELELABELS RefAllele NonRefAllele

BTA

Position

MAF

SE

P-value

I just do not have OR or Beta. I think the odds ratio in estimating models with fixed and random effects is necessary. Of course, METAL estimates only fixed effects.

If I approve the BTA column in the R software, does it respond? Does METAL not give errors despite these values (positive and negative)?

50Can you point me to one of these studies?

I am not saying that the BTA values are the ORs. I am saying that they

the beta coefficients (based on the name) - it is your job to find out to what this column means. Obtaining the exponent of a beta coefficient produces the OR.may be70kHello,

Thank you so much for your reply,

For example: (SNP name: rs41646593,

BTA:1, Position (bp): 2515412, Gene name:MIS18A)Here BTA = 1, as you said: Can you confirm what is the BTA column in your data? - this is likely the

beta coefficient. If you obtain the exponent of this, then you can have the odds ratio. For example (in R):exp (BTA)So I got in R this value to BTA: exp (1)= 2.718282

Is this the same beta coefficient or OR ?

50What are some of the other BTA values? What is the range of these?

70kIn my first study, I have these BTAs:

exp(1): 2.718282, exp(3):20.08554, exp(5): 148.4132, exp(8):2980.958, exp(9):8103.084, exp(11):59874.14, exp(14):1202604, exp(18):65659969, exp(19): 178482301, exp (21):1318815734, exp(23):9744803446

Ranged from 2.72 to 9744803446.

50Can you direct me to this first study so that I can take a look? The description of the results should be in the manuscript, somewhere.

70kIn Case-control study, effect size is mentioned in the terms of OR(odds-ratio) and in quantitative traits, effect size is mentioned in the terms of BETA. So if you have beta column then it is your effect size. If you use plink for GWAS then these are the terms for effect size.

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