Representative histospots depicting microvessel area (MVA) and expression of angiogenesis markers.

<p>Panels (A) and (B) show cytokeratin staining for determination of the tumor area in red, DAPI-stained nuclei in blue and CD31-positive microvessel area in green. Panel A depicts a representative histospot from a European American sample, panel B shows a representative African American sample. (C) Proportion of African American and European American patients with large microvessel area (more than 0.6%, hatched bars) (D) Expression ranks of 11 VEGF-activated genes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Hu1" target="_blank">[19]</a> in African American and European American samples.</p

Association of ethnicity with TNBC subtypes [<b>9</b>].

<p>Correlations of gene expression with the mesenchymal stem cell (A), luminal androgen receptor positive (B) and basal 1 (C) subtypes were compared between African American (AA) and European American (EA) patient samples.</p

Gene sets positively associated with principal component 4 by enrichment analysis.

<p>Enrichment of gene sets from the Broad Molecular Signature Database (MSigDB) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Subramanian1" target="_blank">[34]</a>, Gene Ontology <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Ashburner1" target="_blank">[33]</a> and selected publications was assessed using Fisher's Exact test for 250 probes with the highest projection scores on principal component 4. P-values were FDR-adjusted for multiple testing.</p

Differential projection scores on principal component 4 by ethnicity.

<p>Differential projection scores on principal component 4 by ethnicity.</p

Clinical characteristics of the Yale TNBC cohort.

<p>Percentages refer to the total number of cases with available data.</p

Gene sets negatively associated with principal component 4 by enrichment analysis.

<p>Enrichment of gene sets from the Broad Molecular Signature Database (MSigDB) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Subramanian1" target="_blank">[34]</a>, Gene Ontology <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Ashburner1" target="_blank">[33]</a> and selected publications was assessed using Fisher's Exact test for 250 probes with the lowest projection scores on principal component 4. P-values were FDR-adjusted for multiple testing.</p

Associations of ethnicity with published gene expression signatures.

<p>Signatures of (A) <i>BRCA1</i> deficiency <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-VantVeer1" target="_blank">[37]</a> (B) genomic grade <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Sotiriou1" target="_blank">[17]</a> and (C) IGF1 ligand activation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071915#pone.0071915-Mu1" target="_blank">[18]</a> were compared between African American (AA) and European American (EA) patient samples.</p

No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (<i>CNTNAP2</i>), or in Other Contactin-Associated Proteins or Contactins

<div><p>Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (<i>CNTNAP2</i>) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in <i>CNTNAP2</i> and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the <i>CNTN</i> or <i>CNTNAP</i> genes, including <i>CNTNAP2</i>, placing marked limits on the scale of their plausible contribution to risk.</p></div

Additional file 2: Table S1. of Neurogenetic analysis of childhood disintegrative disorder

CDD families for genetic analysis. Table S2. Rare non-synonymous and synonymous variants from WES unique to probands or unaffected sibling controls. Table S3. Rates of variants from WES in CDD probands and unaffected sibling controls. Table S4. Genes represented once in the core probe set (Kang et al. 2011) and used for expression analysis. Table S5. Median expression values (Log2-transformed signal intensity) for CDD candidate genes by time period and brain region. Table S6. Difference in median expression values (Log2-transformed signal intensity) between non-neocortical and neocortical regions for gene sets by time period. Table S7. Pearson correlation coefficients for all pairwise combinations of CDD candidate genes. Table S8. Clinical characteristics of subjects studied by neuroimaging. Table S9. Features of CDD, LFASD, HFASD, and TD cohorts for neuroimaging analysis. Table S10. List of brain regions where TD:discovery exhibits significant faces > houses activation. Table S11. Mean % signal change (faces > houses) for each cohort in Fig. 4b. Table S12. Mean % signal change (faces > houses) for each cohort in Figure S2. Table S13. List of brain regions where CDD exhibits significant faces > houses activation. Table S14. Mean % signal change (faces > houses) for each cohort in Fig. 5b. Table S15. Clinical characteristics of subjects studied by eye tracking. Table S16. Features of CDD, LFASD, HFASD, and TD cohorts in eye-tracking analysis. Table S17. Whole-exome sequencing quality metrics. Table S18. Features of SSC probands with and without regression by IQ and autism severity. (XLSX 364 kb

Rates of singleton^* mutations: all genes.

<p>*singleton mutations met the following criteria: seen only once in either cases or controls exclusively, missense, nonsense, splice site, or start or stop codon disruptions with a frequency of less than 2% in this data, and less than 1% in all populations in the Exome Variant Server[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref038" target="_blank">38</a>] and SeattleSNP[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref039" target="_blank">39</a>] databases</p><p>Rates of singleton^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t002fn001" target="_blank">*</a>} mutations: all genes.</p