Is there any publicly available GWAS dataset?

How to compare two groups with only two measurements?

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1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

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What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

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Can NFL theorem be valid in infinite search space in ML?

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Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

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How to address this issue in the analysis of Real-Time PCR results?

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How to arrange coordinates and extract climate dataset out of MPI-ESM-MR netcdf files?

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Is there any Machine Learning/AI algorithm that lets you predict with incomplete features without missing value imputation process?

For instance, the model is trained with A,B,C,D,E features to predict F target. Then, I want to make prediction on a new data, but with only A,C,D,E is known without doing missing value imputation...

28 February 2021 1,556 6 View

Saikrishna Srimadh

May be this will be of some help to you !

http://www.ncbi.nlm.nih.gov/gap

Check this out!

http://www.genome.gov/26525384/

Gustavo Gilson Lacerda Costa

Hi Saikrishna, thank you for your answers. I did already know dbGap. The problem is that to download any raw GWAS data from there we have to have our institution registered, the institution signing official should register a PI and then I can request data. Too much bureaucracy and I think I would be almost impossible if I'm working on this by my own, without a granted project. Is there nay other alternative?

Thnaks Luis, but this data is not from a GWAS studies. It contains the variations found on the genomes from individuals from 1000 genomes project and Hapmap, but no phenotype (except for the etno-group) is assigned to each sample.

I would like to work with labeled genotype data, with control and cases (for some disease, condition on trait). I understand the ethical concerns about genetic privacy, but I'm certain that the benefits from turning these kinds of dataset public are enormous for people designing algorithms for predivtive modellinfg.

Of course, participants in those studies should be well informed and agree to share their data.

Francisco Diez-Fuertes

Did you try with GEO (Gene Expression Omnibus)?

http://www.ncbi.nlm.nih.gov/geo/

You can select data sets by organism, platform, article...

Francisco, thanks for your help. I have checked GEO, but as far as I know, GEO hosts data from gene expression, not genotype data from large control/case studies. Even when some study in GEO used RNA-Seq, it's not feasible to infer the genotype from regions not transcribed, or transcribed at low level. Even for regions that are highly expressed, we can not rule out the possibility of alelle specific expression and we can fail to call hetorozigotic loci. Moreover, most RNA-seq studies don't sample thousands of individuals (typically some dozens at most).

Kevin R Thornton

Little-to-nothing is public. You can apply for access to the WTCCC data, though. That's all that I'm aware of.

Walkiria Resende

Hi, Gustavo I'm with this same problem. Did you get any open dataset?

Thanks

Tushar Jain

Hi Gustavo and Walkiria, facing the same issue. Were you able to get any open dataset?

Kevin Blighe

You can download HapMap3 data in PLINK format from here:

ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-05_phaseIII/

Additionally, for 1000 Genomes Phase III data, you can produce it by following my tutorial, here:

https://www.biostars.org/p/271694/

Kevin

Raj Kishore

Hi,

For PRS analysis, I want to download some population specific studies dataset from GWAS. Ref Link: http://www.internationalgenome.org/category/population/ . I am interested to download South Asian datsets. Can anyone help me to share the download link or is there any privacy policies?.

I am trying hard to find out any downloading source but till now no positive results.