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Affected-only parametric linkage analyses was undertaken with SwiftLink [ 6] using default parameters with a disease allele frequency of 0.0001 and variable phenocopy rates.
To confirm these previous findings, 2 genome-wide linkage analyses was done and identified chromosome 6p21 as a major leprosy susceptibility locus in the HLA gene cluster [ 35, 36].
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Linkage analyses were performed for milk performance traits, somatic cell score (SCS), and LPL.
The authors have shown that this phenotype does in fact aggregate in families; therefore, linkage analyses are currently underway.
Estimation of heritability and linkage analyses were run by use of the SOLAR program (version 2.1.3).
Multipoint parametric and non-parametric (model-free) linkage analyses were used for the pedigrees.
Multipoint variance component linkage analyses were conducted using SOLAR version 4.0.7.
Quantitative trait linkage analyses were performed on each of these replicates.
Parametric and non-parametric multipoint linkage analyses were performed using the Allegro version 2.0 program [22].
Classical linkage analyses are generally not successful as many NDM mutations occur de novo or are not fully penetrant.
Multipoint parametric and non-parametric (model-free) multipoint linkage analyses were performed on the family of the subjects.
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