        
PLINK Results


Chr

Locus

BP

TDTHET

Pvalue (Perm)

\widehat{t}

\hat{{\pi}_{1}}

TDTHET SumStat

SumStat Pvalue (Perm)

TDT

Pvalue (Perm01)

OR

\widehat{t}

Max(T) Pvalue (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}

 The headings for each of the columns are defined as follows:
 Chr = Human chromosome on which locus is located.
 Locus = Particular SNP genotyped in idiopathic scoliosis trios.
 BP = Base pair position of Locus. This position is based on the human reference sequence (NCBI Build 36.1/HG18).
 TDTHET = Value of the TDTHET statistic for particular locus genotype data in idiopathic scoliosis trios.
 Pvalue (Perm) = Pvalue of corresponding TDTHET statistic, based on 100,000 random permutations. For a description of how the permutation pvalue is computed, see Methods, Pvalues by permutation.
 \widehat{t} = EMAlgorithm estimate of the probability, t, that a heterozygous parent transmits a "1" allele.
 \hat{{\pi}_{1}} = EMAlgorithm estimate of the probability, π_{1}, that a trio is linked to the locus in question.
 TDTHET SumStat = ∑_{
k
}TDTHET (k), where k indexes the set of all loci on a chromosome and TDTHET (k) is the value of the TDTHET statistic at the particular locus. For example, in Table 3, k = 1 or 2, corresponding to locus RS1400180 or RS10510181, respectively. The TDTHET statistic for each locus is 14.78 (k = 1) and 9.15 (k = 2). Therefore, for Chromosome 3, TDTHET SumStat = 14.78 + 9.15 = 23.93.
 SumStat Pvalue (Perm) = Permutation Pvalue corresponding the TDTHET SumStat value. For a further description, see Methods, Simulations, Multilocus.

(PLINK Results)
 TDT = Value of the TDT statistic as computed by PLINK.
 Pvalue (Perm01) = Permutation pvalue computed by PLINK. Purcell et al. [74] label this pvalue "Emp1". It is the Pointwise empirical pvalue.
 OR = Odds Ratio for the disease allele.
 \widehat{t}=\frac{T}{T+NT} = 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., [81–83]).
 Max(T) Pvalue (Perm02) = Permutation pvalue computed by PLINK that controls the familywise type I error rate. For more information, see Methods, Idiopathic Scoliosis Candidate Loci.