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Table 2 Haplotype frequencies and disease incidence for variants in positive LD

From: Inference of disease associations with unmeasured genetic variants by combining results from genome-wide association studies with linkage disequilibrium patterns in a reference data set

Measured tagSNP

Target variant (e.g., HLA-DRB1*04)

 

Minor allele

Major allele

Relative frequency

Incidence

Derivation

Minor allele

sp

q-sp

q

I a

I a = I b R obs

Major allele

(1-s)p

1-q-(1-s)p

1-q

I b

I b = I o [R(1-s)p+(1-q)-(1-s)p]/[1-q]

Relative frequency

p

1-p

1

  

Incidence

RI o

I o

 

I total

I tota l = I b [1+q(R obs -1)] I total = I o [1+p(R-1)]

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BMC Proceedings

ISSN: 1753-6561

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