How to find the association between SNP and multiple traits or diseases

Question

[wtvxy]

A disease may relate to multiple traits or diseases which means multiple traits may cause a disease. Now I have a data of 10 related traits of 10 column, 1 represent a sample have this trait, 0 represent doesn't have. Each row represents a sample.

A 6 samples examlpe:

0 0 0 0 0 0 0 0 0 0

1 0 0 1 0 0 0 0 0 0

1 1 1 1 0 0 0 1 1 1

0 1 1 1 0 1 0 0 0 0

1 1 1 1 1 1 1 1 1 1

Each sample has many SNPS:

3 2 1 2 1 1 1 1 1 1 1

2 2 2 2 3 2 1 1 1 1 1

3 3 1 1 3 2 3 1 1 1 1

3 1 1 2 2 1 2 2 2 2 2

2 2 2 3 2 1 2 1 3 1 2

2 1 1 2 1 1 1 1 3 3 1

The question is: How can I find the relation between SNPs and traits?

In this question,the disease/trait label more than one dimension.

Which algorithm should I use?

Answer 1

[vakul.mohanty]

You could build a linear regression model between the trait and the genotype. Yo can add covariates to the model to account for confounding factors. You can use tools like plink or MatrixEQTL to carry out the analysis

Answer 2

[chrishengbee]

Hi,guy! Guess u are doing modeling competition ha? It's the last night. Good luck for u!