Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis.

For a better interpretation of variants, evidence-based databases, such as ClinVar, compile data on the presumed relationships between variants and phenotypes. In this study, we aimed to analyze the pattern of sequencing depth in variants from whole-exome sequencing data in the 1000 Genomes project phase 3, focusing on the variants present in the ClinVar database that were predicted to affect protein-coding regions. We demonstrate that the distribution of the sequencing depth varies across different sequencing centers (pair-wise comparison, p < 0.001). Most importantly, we found that the distribution pattern of sequencing depth is specific to each facility, making it possible to correctly assign 96.9% of the samples to their sequencing center. Thus, indicating the presence of a systematic bias, related to the methods used in the different facilities, which generates significant variations in breadth and depth in whole-exome sequencing data in clinically relevant regions. Our results show that methodological differences, leading to significant heterogeneity in sequencing depth, may potentially influence the accuracy of genetic diagnosis. Furthermore, our findings highlight how it is still challenging to integrate results from different sequencing centers, which may also have an impact on genomic research.

Dysregulation of NEUROG2 plays a key role in focal cortical dysplasia.

OBJECTIVE: Focal cortical dysplasias (FCDs) are an important cause of drug-resistant epilepsy. In this work, we aimed to investigate whether abnormal gene regulation, mediated by microRNA, could be involved in FCD type II. METHODS: We used total RNA from the brain tissue of 16 patients with FCD type II and 28 controls. MicroRNA expression was initially assessed by microarray. Quantitative polymerase chain reaction, in situ hybridization, luciferase reporter assays, and deep sequencing for genes in the mTOR pathway were performed to validate and further explore our initial study. RESULTS: hsa-let-7f (p = 0.039), hsa-miR-31 (p = 0.0078), and hsa-miR34a (p = 0.021) were downregulated in FCD type II, whereas a transcription factor involved in neuronal and glial fate specification, NEUROG2 (p < 0.05), was upregulated. We also found that the RND2 gene, a NEUROG2-target, is upregulated (p < 0.001). In vitro experiments showed that hsa-miR-34a downregulates NEUROG2 by binding to its 5'-untranslated region. Moreover, we observed strong nuclear expression of NEUROG2 in balloon cells and dysmorphic neurons and found that 28.5% of our patients presented brain somatic mutations in genes of the mTOR pathway. INTERPRETATION: Our findings suggest a new molecular mechanism, in which NEUROG2 has a pivotal and central role in the pathogenesis of FCD type II. In this way, we found that the downregulation of hsa-miR-34a leads to upregulation of NEUROG2, and consequently to overexpression of the RND2 gene. These findings indicate that a faulty coupling in neuronal differentiation and migration mechanisms may explain the presence of aberrant cells and complete dyslamination in FCD type II. Ann Neurol 2018;83:623-635.

Systematic review and meta-analysis of complementary treatments for women with symptomatic endometriosis.

BACKGROUND: Despite advances in treatments for endometriosis, some symptoms persist owing to the chronic inflammation observed in this disease. OBJECTIVE: To identify resources, methods, and/or complementary treatments to alleviate the pain symptoms of endometriosis, and to identify adverse effects of treatments. SEARCH STRATEGY: Lilacs, Scielo, PEDro, Scopus, Pubmed, CENTRAL Cochrane, Science Direct, and Google Scholar were searched for studies published in Portuguese, English, and Spanish to July 31, 2017, using the terms "physical therapy" OR "complementary treatment" AND "endometriosis". SELECTION CRITERIA: Randomized controlled trials relating to complementary pelvic pain treatment and adverse effects. DATA COLLECTION AND ANALYSIS: Eight studies were identified; two studies were included in the meta-analysis. MAIN RESULTS: The complementary interventions studied were acupuncture, exercise, electrotherapy, and yoga. All were inconclusive in affirming benefit, but demonstrated a positive trend in the treatment of symptoms of endometriosis. Meta-analysis of acupuncture showed a significant benefit in pain reduction as compared with placebo (P=0.007). CONCLUSIONS: Numerous complementary treatments have been used to alleviate the symptoms of endometriosis, but only acupuncture has demonstrated a significant improvement in outcomes. Nevertheless, other approaches demonstrated positive trends toward improving symptoms; this should encourage investigators to design controlled studies to support their applicability.