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Supporting Information

Additional Supporting Information may be found in the online version of this article:

Appendix S1: Comparative analysis of Lhx6 and Lhx8 expression in the developing and adult brain of mouse and rat-LHX6 and LHX8 genetic association study samples and methods.

Appendix S2: Members of the TSGeneSEE consortium.

Figure S1: Pairwise LD tests (r2) in our German, Hungarian, Italian, and Polish samples, for all studied SNPs in the LHX6 and the LHX8 genes.

Table S1: Phenotypic details of TSGeneSEE (Hungarian, Italian, and Polish), and German sample. Patient numbers are shown in parentheses.

Table S2: Selection of tSNPs at LHX6 and LHX8 using the HapMap CEPH European population as reference (http://hapmap.ncbi.nlm.nih.gov/). The r2 threshold for tSNP selection was set to 0.8. Variation at LHX6 and LHX8 was captured by the selected tSNPs with a mean r2of 0.942 and 0.988, respectively.

Table S3a: Transmission test for linkage disequilibrium in four different populations (total of 222 trios) for single markers tested at LHX6 and LHX8 genes (test implemented and P-values determined by Haploview).

Table S3b: Transmission test for linkage disequilibrium in joint analysis of four different populations (total of 222 trios) for single markers tested at LHX6 and LHX8 genes (test implemented and P-values determined by Haploview). The TSGeneSEE sample corresponds to the Hungarian, Italian, and Polish samples analyzed jointly.

Table S4: Transmission test for linkage disequilibrium in four different populations (total of 222 trios) for a three SNP haplotype around SNP rs3808901 at the LHX6 gene (test implemented and P values determined by Haploview). The TSGeneSEE sample corresponds to the Hungarian. Italian. and Polish samples analyzed jointly.

Table S5: Allele frequencies of studied SNPs at LHX6 and LHX8 in all studied populations. Position refers to Build 36 of the genome.

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