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Table 2 Summarized individual genotyping results for SNPs and TDT results.

From: Association study in the 5q31-32 linkage region for schizophrenia using pooled DNA genotyping

SNP ID

Position

Gene nameâ–²

Type*

Pooling p-value

Total sample (N trios)

Frequency children

Frequency parents

T/NT

χ2

Individual genotyping total sample p-value

Individual genotyping 300 trios pool p-value

rs17169180

135188954

LOC153328

C/A

0.008

613

0.14

0.15

142/176

3.64

0.06

0.20

rs1859430

135258412

IL9

T/C

0.04

599

0.19

0.20

177/203

1.78

0.18

0.14

rs30747

135366739

TGFBI

C/A

0.04

590

0.05

0.05

60/58

0.03

0.85

0.28

rs7715300

135456919

TGFBI

C/A

0.03

612

0.06

0.08

64/108

11.26

0.001

0.18

rs2906066

141560461

-

T/C

0.05

589

0.14

0.13

122/145

1.98

0.16

0.57

rs7443175

141675612

SPRY4

T/C

0.03

612

0.23

0.25

239/200

3.46

0.06

0.36

rs6897690

141681136

SPRY4

A/G

0.008

615

0.22

0.24

255/209

4.56

0.03

0.0006

rs153423

141794129

-

C/T

0.05

611

0.21

0.20

180/202

1.27

0.26

0.46

  1. â–² Gene names are given for the intragenic SNPs and SNPs within 30 kb of a gene (column 3,"Gene name").
  2. * Minor allele is always presented first and its frequencies in children and in parents are given in columns 7 and 8 ("Frequency children", "Frequency parents"). Transmission/non-transmission counts from heterozygous parents for the minor allele in each case are in column 9 ("T/NT"). P-values from Transmission Disequilibrium Test (TDT) for the total sample and the pool sample are given in the column 11 ("Individual genotyping total sample p-value") and column 12 ("Individual genotyping 300 trios pool p-value"). Predicted pooling p-values are presented in column 5, ("Pooling p-value"). Pooling p-value is also provided for rs2906066, although it is not on the array, because it is in complete LD with rs2961720 which produced that p-value. All markers were in Hardy-Weinberg equilibrium.