Additional file 2: of Identification of mutations in the PI3K-AKT-mTOR signalling pathway in patients with macrocephaly and developmental delay and/or autism

Bi-allelic PTEN mutations in patient 3. The file consists of WES reads and clonal sequencing data to show that patient 3 has two mutations in different PTEN alleles. (DOCX 936 kb

Additional file 2: of cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

Descriptions and abbreviations of the 127 tissues/cell types. (XLSX 14 kb

Confirmation of association of <i>HLA</i> locus, and <i>TNFSF4</i>, <i>STAT4</i>, <i>TNFAIP3</i>, <i>IRF5</i>, <i>BLK</i> with SLE.

<p>Shown are association results comparing SLE patients with controls collected in Hong Kong analyzed by Plink (−log₁₀(<i>P</i>-value) of SNPs). The best SNP in Chromosome 11 is around <i>ETS1</i> gene (rs6590330), which is in high LD with rs1128334. And the best SNP in Chromosome 10 is in <i>WDFY4</i> (rs877819).</p

Quantile-Quantile plot of expected (x-axis) and observed (y-axis) −log₁₀(<i>P</i> value) distribution in our GWAS analysis.

<p>(A) Considering all the available SNPs. (B) SNPs in and around <i>HLA locus</i>, and <i>TNFSF4</i>, <i>STAT4</i>, <i>TNFAIP3</i>, <i>IRF5</i>, <i>BLK</i>, as well as <i>BANK1</i> were excluded from analysis.</p

Linkage disequilibrium and sequence conservation of SNPs in <i>ETS1</i>.

<p>Shown are LD for significant SNPs in and around <i>ETS1</i> detected by GWAS (A), and replicated SNPs in the 3′-UTR and downstream of the gene (B), and sequence conservation for sequences around SNP rs1128334 among different species (C).</p

SNPs showed significant association with SLE in a joint analysis of four independent Asian cohorts.

<p>SNPs showed significant association with SLE in a joint analysis of four independent Asian cohorts.</p

Principal component analysis of Chinese samples collected in Hong Kong, Taiwan, and Beijing.

<p>The red dots denote SLE patient samples collected in Hong Kong used in our GWAS study and the blue dots are unaffected samples from Beijing (A), Taiwan (B), and Hong Kong (C). The data on Taiwan samples was received from deCODE Genetics; the data on Han Chinese in Beijing is available from HapMap. The data on Hong Kong controls were from other studies in the University of Hong Kong that were genotyped by the same platform. Repeat of Eigenstrat analysis for 20 times using randomly chosen 100,000 SNPs each time from all the available SNPs produced similar results.</p

Confirmation of susceptibility genes in the Hong Kong Chinese population by GWAS.

<p>A1: minor allele; F_A: minor allele frequency in cases; F_U: minor allele frequency in controls.</p

SNPs in and around <i>ETS1</i> and <i>WDFY4</i> that showed significant association with SLE in the GWAS data.

<p>SNPs in and around <i>ETS1</i> and <i>WDFY4</i> that showed significant association with SLE in the GWAS data.</p

Replication of disease association for <i>WDFY4</i> SNPs in the Hong Kong samples.

<p>Replication of disease association for <i>WDFY4</i> SNPs in the Hong Kong samples.</p