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Table 3 Step 2 using D' LD threshold and MT: Summary descriptive statistics of average maximum NPL LOD scores and average IC for families with 2, 3 or 4 affected sibling and ungenotyped* parents.

From: Handling linkage disequilibrium in qualitative trait linkage analysis using dense SNPs: a two-step strategy

   

2 affected sibs

3 affected sibs

4 affected sibs

Method

LD threshold

Ave # SNPs

MLS (SD)

IC

MLS (SD)

IC

MLS (SD)

IC

Unadjusted

 

3713

9.62 (2.75)

0.72

14.01 (3.43)

0.80

5.02 (1.95)

0.85

MT

8snp1cM

480

1.20 (0.96)

0.72

1.34 (1.01)

0.80

0.36 (0.47)

0.85

MT

4snp1cM

259

0.65 (0.67)

0.71

0.60 (0.63)

0.80

0.22 (0.36)

0.85

MT

2snp1cM

135

0.66 (0.68)

0.67

0.76 (0.74)

0.79

0.26 (0.38)

0.84

MT

1snp1cM

68

0.76 (0.73)

0.61

1.05 (0.88)

0.76

0.34 (0.47)

0.83

RE

0.7

409

0.44 (0.53)

0.73

0.54 (0.61)

0.80

0.2 (0.33)

0.85

RE

0.5

309

0.37 (0.50)

0.72

0.45 (0.55)

0.80

0.18 (0.34)

0.85

RE

0.3

200

0.43 (0.54)

0.7

0.58 (0.60)

0.80

0.23 (0.39)

0.85

RE

0.1

62

0.73 (0.73)

0.61

1.18 (0.96)

0.76

0.44 (0.57)

0.83

SNPLINK

0.7

531

0.65 (0.78)

0.73

0.66 (0.79)

0.80

0.3 (0.46)

0.85

SNPLINK

0.5

401

0.75 (0.81)

0.72

0.73 (0.83)

0.80

0.31 (0.46)

0.85

SNPLINK

0.3

287

0.85 (0.88)

0.71

0.81 (0.84)

0.80

0.33 (0.47)

0.85

SNPLINK

0.1

120

0.65 (0.74)

0.64

0.70 (0.81)

0.77

0.31 (0.46)

0.83

  1. *With complete data where both parents are genotyped, the unadjusted average MLS for 2, 3 or 4 affected sibs are 0.58, 0.5 and 0.47.