The association between variants in the CFTR gene and nonobstructive male infertility: A meta-analysis

The association of genetic variants and congenital bilateral absence of the vas deferens (CBAVD) has been well acknowledged. By contrast, the link between nonobstructive azoospermia (NOA) or oligospermia and alterations in the cystic fibrosis transmembrane conductive regulator (CFTR) remains inconclusive. To clarify the problem, a meta-analysis was performed out after systematically searching Pubmed, Web of Science, Embase and the Chinese national knowledge infrastructure (CNKI) database. As we know, the ∆F508 and IVS8-5T gene mutations are the most studied genetic variants in CFTR gene. We reviewed the data from male patients who underwent the aforementioned genetic test. Our study revealed that the IVS8-5T mutation may be positively associated with the risk of nonobstructive male infertility (odds ratio (OR) 1.69; 95% CI: 1.12–2.55). This association strengthened when concerning NOA (OR: 2.62; 95% CI: 1.49–4.61). However, the ∆F508 mutation seemed to be a smaller contributing factor to this risk (OR: 1.63; 95% CI: 0.86–3.08). Our study aims to clarify the association between the ∆F508 and IVS8-5T gene mutations and nonobstructive male infertility. Therefore, screening for the IVS8-5T mutation in the CFTR gene may be recommended for men with NOA or severe oligozoospermia seeking assisted reproductive technology (ART).     

Transgender pediatric surgical patients—Important perioperative considerations

Transgender describes a variety of identities in which an individual's gender identity is different from expected based on the sex assigned at birth. In the United States, it is estimated that over 1 million adults and 150 000 youth identify as transgender, with increasing numbers being seen in healthcare and surgical settings. These numbers will continue to rise as visibility and acceptance grow. Current guidelines recommend transition‐related surgeries be reserved for older adolescents and adults. However, this is not the only circumstance in which the pediatric anesthesiologist may find themselves caring for a transgender patient. In order to provide the safest and most affirming care, it is crucial that the pediatric anesthesiologist develop a working knowledge of this unique and vulnerable population, including the potential impacts of gender‐affirming treatment on their perioperative care.     

Origin and epidemic status of porcine epidemic diarrhea virus variants in China

From 2010, porcine epidemic diarrhea virus (PEDV) variants caused sequential outbreaks of disease in Asia and the United States. In this retrospective study, 49 complete spike (S) gene sequences were obtained from PEDV strains collected in China from 2014 to 2016. We observed that variant PEDV strains with novel insertions, deletions, and multiple S gene recombination types were present in China. In addition, mixed infections involving different variant strains were observed in some areas. Based on phylogenetic and recombination analyses, we determined that the newly emerged PEDV variants potentially originated via recombination between the earliest Chinese G1 genogroup strain, JS‐2004‐2 and earlier Korean pandemic strains. These findings provide important information for understanding ongoing PEDV outbreaks and suggest that novel variants make it more difficult to prevent PEDV infection.     

MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation,universal nomenclature collation,and reference genome conversion

Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user‐friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one‐stop mtDNA variant annotation and analysis Web service. mvTool is built upon the MSeqDR infrastructure ( https://mseqdr.org ), with contributions of expert curated data from MITOMAP ( https://www.mitomap.org ) and HmtDB ( https://www.hmtdb.uniba.it/hmdb ). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS‐ and HGVS‐based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mitogenomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum et al., 2013). mvTools also provides mtDNA somatic variants annotations. “mvTool API” is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel, and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php .     

Inferring the effect of genomic variation in the new era of genomics

Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene‐variant–disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next‐generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as “synergistic heterozygosity,” digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large‐scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.     

The contribution of molecular pathology to the classification of thyroid tumors

Significant molecular advances have been undertaken for the past two decades in the field of thyroid follicular neoplasms, including a detailed genomic profile of papillary thyroid carcinoma (PTC) by The Cancer Genome Atlas (TCGA) project. These molecular discoveries led to a better understanding of the pathogenesis of thyroid neoplasms and resulted in reclassification of certain types of thyroid tumors. This review discusses how, 1) the molecular profiles of follicular-patterned lesions led to the reclassification of the follicular variant of PTC into non-invasive follicular thyroid neoplasm with papillary like nuclei, 2) the genotyping of Hürthle cell neoplasm provided the rationale to classify these tumors independently from follicular adenomas and carcinomas, and 3) BRAF and RAS molecular signatures have the potential of subclassifying PTC and poorly differentiated thyroid carcinoma into clinically relevant molecular subtypes.     

Structural and sequence variants in patients with Silver‐Russell syndrome or similar features—Curation of a disease database

Silver‐Russell syndrome (SRS) is a clinically and molecularly heterogeneous disorder involving prenatal and postnatal growth retardation, and the term SRS‐like is broadly used to describe individuals with clinical features resembling SRS. The main molecular subgroups are loss of methylation of the distal imprinting control region (H19/IGF2:IG‐DMR) on 11p15.5 (50%) and maternal uniparental disomy of chromosome 7 (5%–10%). Through a comprehensive literature search, we identified 91 patients/families with various structural and small sequence variants, which were suggested as additional molecular defects leading to SRS/SRS‐like phenotypes. However, the molecular and phenotypic data of these patients were not standardized and therefore not comparable, rendering difficulties in phenotype–genotype comparisons. To overcome this challenge, we curated a disease database including (epi)genetic phenotypic data of these patients. The clinical features are scored according to the Netchine‐Harbison clinical scoring system (NH‐CSS), which has recently been accepted as standard by consensus. The structural and sequence variations are reviewed and where necessary redescribed according to recent recommendations. Our study provides a framework for both research and diagnostic purposes through facilitating a standardized comparison of (epi)genotypes with phenotypes of patients with structural/sequence variants.