Additional file 4 of Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach

Additional file 4: Table S1. Detailed description of the study cohort

Additional file 2 of Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach

Additional file 2: Fig. S2. Comparison of the gene expression results between RNAseq and RT-qPCR

Additional file 7 of Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach

Additional file 7: Table S4. Enrichment analysis results for the RTT-MECP2 versus healthy controls, RTT versus MDS, RTT versus RTT-like, transcriptomic and proteomic data

Additional file 6 of Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach

Additional file 6: Table S3. RNAseq and proteomics differential expression results for RTT - MECP2 versus healthy controls

Additional file 3 of Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach

Additional file 3: Fig. S3. Comparison of genes from Genotype-Tissue Expression (GTEx) project and mean TPM (Transcripts per Kilobase Million) in fibroblast cultured cells in RNAseq and RT-qPCR

Additional file 9 of Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach

Additional file 9: Table S6. Summary for the DEG and DEP from RTT-MECP2 vs MDS and RTT-MECP2 versus RTT-like

Targeted Next Generation Sequencing in Patients with Inborn Errors of Metabolism

<div><p>Background</p><p>Next-generation sequencing (NGS) technology has allowed the promotion of genetic diagnosis and are becoming increasingly inexpensive and faster. To evaluate the utility of NGS in the clinical field, a targeted genetic panel approach was designed for the diagnosis of a set of inborn errors of metabolism (IEM). The final aim of the study was to compare the findings for the diagnostic yield of NGS in patients who presented with consistent clinical and biochemical suspicion of IEM with those obtained for patients who did not have specific biomarkers.</p><p>Methods</p><p>The subjects studied (n = 146) were classified into two categories: Group 1 (n = 81), which consisted of patients with clinical and biochemical suspicion of IEM, and Group 2 (n = 65), which consisted of IEM cases with clinical suspicion and unspecific biomarkers. A total of 171 genes were analyzed using a custom targeted panel of genes followed by Sanger validation.</p><p>Results</p><p>Genetic diagnosis was achieved in 50% of patients (73/146). In addition, the diagnostic yield obtained for Group 1 was 78% (63/81), and this rate decreased to 15.4% (10/65) in Group 2 (<i>X</i>² = 76.171; p < 0.0001).</p><p>Conclusions</p><p>A rapid and effective genetic diagnosis was achieved in our cohort, particularly the group that had both clinical and biochemical indications for the diagnosis.</p></div

Global genetic results.

<p>Genetic results (positive, under-study, and negative cases) shown as a percentages for each nosological group (aminoacidopathies (AA); organic acidurias (OA); free fatty acid oxidation defects (FFA); and neurometabolic (NM) and complex molecules (CM) defects) and for both diagnostic groups (Groups 1 and 2).</p

NKCC1 and KCC2 Cotransporters in the CSF of Rett Syndrome (RTT) Patients and Controls.

<p>(A) Immunoblot results in RTT patients and controls. Numbers refer to the patient ID numbers of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068851#pone-0068851-t001" target="_blank">Table 1</a>. Comparison of patients and age matched controls. (B) Mean Optic Densities of NKCC1 and KCC2 Cotransporter Proteins for Rett Patients and Controls suggesting discrepant cotransporter levels between Patients and Controls supported by the respective MANCOVA (<i>F</i> (1, 73) = 6.99, <i>p</i><.01, <i>η_p²</i> = .087). Error bars represent 95% Confidence Interval. *<i>p</i><.01.</p

Clinical and laboratory features of Rett Syndrome patients included in the study.

<p>DEL: Deletion. LP: Lumbar Puncture. AED: Anti epileptic drugs. VPA: Valproic Acid. CBZ: Carbamazepine. LEV: Levetiracetam. TPM: Topiramate.</p