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Table 2 Haplotypes and their frequencies for simulations and validation. When simulating under a non-null genetic model, the high-risk allele lies exclusively on the second haplotype. For validation purposes, haplotype frequencies are compared between software in samples of 1000 affected sib-pair families, averaged over 25 runs, under a non-null genetic model.

From: SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values

Marker haplotype

Population frequency

Estimated frequency of haplotype in LD with trait locus

  

SLINK/SUP

SIMLA

1-1-1-1-1-1

0.5

0.463

0.461

1-1-1-1-1-2

0.25

0.305

0.308

1-1-1-1-2-2

0.125

0.115

0.116

1-1-1-2-2-2

0.0625

0.0592

0.0578

1-1-2-2-2-2

0.0312

0.0293

0.0292

1-2-2-2-2-2

0.0156

0.0143

0.0143

2-1-1-1-1-1

0.0078

0.00764

0.00716

2-2-1-1-1-1

0.0040

0.00352

0.00376

2-2-2-1-1-1

0.0020

0.00188

0.00208

2-2-2-2-1-1

0.0010

0.00048

0.00060

2-2-2-2-2-1

0.0005

0.00016

0.00008

2-2-2-2-2-2

0.0004

0.00001

0.00004