Maximum linkage scores of nonparametric linkage analysis


Chr

95 % C.I. (cM)

Peak marker

Locus

NPL Z (threshold)

LOD

IC

Delta

Diagnostic model

Empirical P value (threshold)


3

18.5

rs4855407

3p14.1

3.56 (3.34)

2.34

0.91

0.50

ASM3

0.46 (0.63)

3

3.49

rs4855407

3p14.1

3.49 (3.32)

2.32

0.91

0.49

ASM2

0.48 (0.63)

3

18.5

rs4855407

3p14.1

3.56 (3.30)

2.34

0.91

0.43

ASM1

0.41 (0.63)

 The table displays maximum linkage scores for the suggestive linkage results of the nonparametric and parametric linkage analyses
 A 1000fold simulation analysis generated genomewide thresholds for suggestive linkage Z and parametric HLOD scores (shown in parentheses). The approximate 95 % confidence intervals for the highest linkage scores are defined as a LODdrop, or Zdrop, corresponding to a unit of 1.0. The mean information content (IC) estimate across all chromosomes was 0.92 (range 0.96–0.70), indicating that most of the genetic information was successfully captured using our high density mapping approach. The fraction of linked families, alpha, was less than 0.29 for regions showing suggestive linkage, indicating that there is evidence for a marked heterogeneity with respect to linked loci in these 46 pedigrees

Abbreviations: NPL Z the linkage statistics for the estimation of identitybydescent (IBD) allele sharing. LOD is the LOD calculated from NPL Z sores according to Kong and Cox (1997). IC the information content and is a measure of the probability that the IBD status at a certain locus can be determined for a given pairs of relatives. Alpha a measure of the locus heterogeneity that indicates the proportion of families with alleles linked to disease at a certain locus. HLOD estimate of the heterogeneity LOD score. Delta measure of allele sharing among affected individuals within pedigrees. Empirical P value estimated probability of having a score by chance that is at least as large as the observed one, after correction for multiple comparisons