In general pedigrees, PDT [ 9], which breaks a pedigree into case-parent trios and discordant sib-pairs, and then sum up their contributions, has been often used in the field of genomic research.
Hardy-Weinberg testing as well as calculation of descriptive statistics was performed in both Pedstats (v.0.6.4) and Haploview v.3.32 [41] for both the Trios and the adult case control cohort.
All data underwent general quality checks which consisted of Mendelian error analysis (families with >5%) for the trios along with HWE analysis for both trios and case control data (cut-off 0.001).
Four hundred and twenty-four case-parents obesity trios and an independent sample of 453 extremely obese children and adolescents and 435 normal-weight and lean adult controls were genotyped by the Affymetrix Genome-Wide Human SNP Array 6.0.
We have currently completed study procedures for 106 affected sib-pair, 457 case-parent trio and 23 multiplex families.
Replications studies have been carried out in samples that varied not only in ethnic origin but also in structure (nuclear families, trios and cases) and ascertainment criteria.
Finally, we performed a joint analysis of all case-parents trios (discovery and replication sample) to increase the precision of the estimator, resulting in an OR of 1.190 for the deletion allele (95% CI = 1.016 1.394; one-sided P = 0.015).
The average numbers of these subsets per SNP in the SLIC sample were: 153 case-parents trios, 54 case-mother duos, 12 case-father duos and 18 cases.
A comparison between the 931 case subjects from the family trios and 2431 control subjects identified an additional nonoverlapping 32 SNPs (P<0.001).
Methods: We used hierarchical Bayesian modeling of rare-variant genetic architecture to estimate mean effect sizes and risk-gene proportions, analyzing the largest available collection of whole exome sequence data for SCZ (1,077 trios, 6,699 cases, and 13,028 controls), and data for four NDDs (ASD, ID, DD, and EPI; total 10,792 trios, and 4,058 cases and controls).
