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Table 3 Results of TDT-HET analysis on idiopathic scoliosis candidate loci

From: TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data

          PLINK Results
Chr Locus BP TDT-HET P-value (Perm) t ^ π 1 ^ TDT-HET SumStat SumStat P-value (Perm) TDT P-value (Perm01) OR t ^ Max(T) P-value (Perm02)
3 RS1400180 145968 14.78 1 6 × 10-4 0.80 0.30 23.93 1 0 × 10-5 14.35 2.8 × 10-4 1.44 0.59 0.001
3 RS10510181 166047 9.15 0.003 0.60 0.77    9.04 0.004 1.37 0.58 0.02
7 RS11770843 146426312 18.32 1.0 × 10-5 0.26 0.47 NA   17.29 1.6 × 10-4 1.56 0.61 3.3 × 10-4
21 RS1040315 40746722 18.41 2.0 × 10-5 0.76 0.38 40.94 0.00 19.10 3.0 × 10-5 1.54 0.61 1.2 × 10-4
21 RS2222973 40755754 22.53 0.00 0.36 0.87    22.25 2.0 × 10-5 0.60 0.38 7.0 × 10-5
  1. The headings for each of the columns are defined as follows:
  2. Chr = Human chromosome on which locus is located.
  3. Locus = Particular SNP genotyped in idiopathic scoliosis trios.
  4. BP = Base pair position of Locus. This position is based on the human reference sequence (NCBI Build 36.1/HG18).
  5. TDT-HET = Value of the TDT-HET statistic for particular locus genotype data in idiopathic scoliosis trios.
  6. P-value (Perm) = P-value of corresponding TDT-HET statistic, based on 100,000 random permutations. For a description of how the permutation p-value is computed, see Methods, P-values by permutation.
  7. t ^ = EM-Algorithm estimate of the probability, t, that a heterozygous parent transmits a "1" allele.
  8. π 1 ^ = EM-Algorithm estimate of the probability, π1, that a trio is linked to the locus in question.
  9. TDT-HET SumStat = ∑ k TDT-HET (k), where k indexes the set of all loci on a chromosome and TDT-HET (k) is the value of the TDT-HET statistic at the particular locus. For example, in Table 3, k = 1 or 2, corresponding to locus RS1400180 or RS10510181, respectively. The TDT-HET statistic for each locus is 14.78 (k = 1) and 9.15 (k = 2). Therefore, for Chromosome 3, TDT-HET SumStat = 14.78 + 9.15 = 23.93.
  10. SumStat P-value (Perm) = Permutation P-value corresponding the TDT-HET SumStat value. For a further description, see Methods, Simulations, Multi-locus.
  11. (PLINK Results)
  12. TDT = Value of the TDT statistic as computed by PLINK.
  13. P-value (Perm01) = Permutation p-value computed by PLINK. Purcell et al. [74] label this p-value "Emp1". It is the Point-wise empirical p-value.
  14. OR = Odds Ratio for the disease allele.
  15. t ^ = T T + N T = The maximum likelihood estimate of the probability, t, that a heterozygous parent transmits the disease allele. Here, T is the number of times a heterozygous parent transmits the disease allele, and NT = the number of times a heterozygous parent does not transmit the disease allele. It has been shown that, for the likelihood form of the TDT, this value is the maximum likelihood estimate of the transmission probability (see, e.g., [8183]).
  16. Max(T) P-value (Perm02) = Permutation p-value computed by PLINK that controls the family-wise type I error rate. For more information, see Methods, Idiopathic Scoliosis Candidate Loci.