Question: What can be done with a small set of case/control SNP arrays?
1
gravatar for Adamc
4.2 years ago by
Adamc540
United States
Adamc540 wrote:

I'm just getting into working with SNP arrays after a while of working with gene expression data. We've got a small dataset (12 samples) of SNP arrays (Illumina Human Omni 5) which represent disease case and control. We don't have family data. Obviously 12 samples is much too small for a GWAS. I ran PennCNV already, but there has to be more I can look at with this- any suggestions? The data I have available is derived from Illumina "Final Report" files- Allele1-Top, Allele2-Top, and the B-allele frequency and Log R ratio.

 

Thanks!

snp microarray illumina • 1.5k views
ADD COMMENTlink modified 3.8 years ago by reza.jabal300 • written 4.2 years ago by Adamc540

Also, as a secondary question- we don't currently have replicates. Do you usually run replicates (technical in this case) for SNP arrays?

ADD REPLYlink written 4.2 years ago by Adamc540
0
gravatar for Adamc
3.8 years ago by
Adamc540
United States
Adamc540 wrote:

I know I posted this a little while ago, but it's something I'm still wondering about- has anyone worked with SNP array datasets where 1) you weren't sure what mutation you were looking for and 2) you had less than 15 samples?

ADD COMMENTlink written 3.8 years ago by Adamc540
0
gravatar for reza.jabal
3.8 years ago by
reza.jabal300
United Kingdom
reza.jabal300 wrote:

I assume this is what DTC genetics companies like 23&me do on a daily basis. I am not sure if it is relevant, but have a look at this:

https://livewello.com/genetics

ADD COMMENTlink written 3.8 years ago by reza.jabal300
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