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Table 4 Step 2 using r2 LD threshold: 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

RE

0.7

1562

1.39 (0.98)

0.73

2.00 (1.28)

0.80

0.73 (0.70)

0.85

RE

0.5

1240

1.21 (0.90)

0.73

1.67 (1.17)

0.81

0.59 (0.63)

0.85

RE

0.3

892

0.45 (0.53)

0.73

0.66 (0.68)

0.81

0.26 (0.39)

0.85

RE

0.1

435

0.32 (0.44)

0.72

0.40 (0.49)

0.80

0.18 (0.34)

0.85

MERLINLD

0.7

562

1.35 (0.97)

0.73

1.83 (1.22)

0.80

0.62 (0.61)

0.85

MERLINLD

0.5

575

1.12 (0.96)

0.73

1.53 (1.19)

0.80

0.53 (0.59)

0.85

MERLINLD

0.3

542

0.55 (0.61)

0.74

0.77 (0.77)

0.80

0.32 (0.43)

0.85

MERLINLD

0.1

423

0.51 (0.58)

0.74

0.69 (0.70)

0.81

0.29 (0.41)

0.85

SNPLINK

0.7

2596

3.94 (1.85)

0.73

5.10 (2.11)

0.80

2.06 (1.23)

0.85

SNPLINK

0.5

2351

3.63 (1.81)

0.73

4.88 (2.09)

0.80

1.97 (1.20)

0.85

SNPLINK

0.3

2057

3.04 (1.73)

0.73

4.10 (1.95)

0.80

1.56 (1.07)

0.85

SNPLINK

0.1

1519

2.69 (1.64)

0.73

3.57 (1.87)

0.80

1.28 (0.98)

0.85

  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