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Transmission Disequilibrium Testing (TDT) was performed using the Unphased program v3.0.8 [29].
Twelve SNPs were studied in depth, selected based upon allele frequency and linkage disequilibrium testing.
In addition, the linkage disequilibrium (LD) option in PROC HAPLOTYPE was specified which generated a likelihood ratio test for linkage disequilibrium testing a null hypothesis of no association between the SNPs within a given haplotype region.
The use of case/parent trios and transmission disequilibrium testing (in FBAT) controlled for ethnic admixture in this cohort.
For linkage disequilibrium testing, HaploView v4.2 was employed [ 42] with HapMap version 3 data from release 28 [ 43].
Transmission disequilibrium testing (TDT) of data from trio families was performed using the TDTPHASE program, part of the UNPHASED suite.
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Finally, the transmission disequilibrium test showed evidence for linkage between B2A2 haplotype and schizophrenia.
Head-to-head comparisons with the relevance-chain, multifactor dimensionality reduction, and the pedigree disequilibrium test (PDT) methods were obtained.
A total of 224 family trios (672 participants in total) were enrolled in this family-based transmission disequilibrium test.
To generate the FBAT statistic, three important characteristics of the original transmission disequilibrium test (TDT) are incorporated.
These estimates are then used to construct a rare-variant transmission disequilibrium test (rvTDT) in the case-parent data.
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