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Secondly, stage-specific cancer genes fully located within the aberrant segments are then identified according to the reference annotation dataset. Thirdly, a pathway evolution network is constructed based on the impacted pathways functions and their overlapped genes. The involved significant functions and evolution paths uncovered by this network enabled investigation of the real progression of cancers, and thus facilitated the determination of appropriate clinical settings that will help to assess risk in cancer patients. Those findings at individual levels can be integrated to identify robust biomarkers in cancer progressions. Copyright © 2020 Aouiche, Chen and Shang.[This corrects the article DOI 10.3389/fgene.2019.01259.]. Copyright © 2020 Wang and Yan.Small supernumerary marker chromosomes (SMCs) are rare cytogenetic abnormalities. De novo small SMCs, particularly those combined with uniparental disomy (UPD), are assumed to result from incomplete trisomy rescue. Recently, a one-off cellular event designated as chromothripsis was reported as a mechanism for trisomy rescue in micronuclei. This Perspective article aims to highlight a possible association among trisomy rescue, chromothripsis, and SMCs. We propose that chromothripsis-mediated incomplete trisomy rescue in micronuclei underlies various chromosomal rearrangements including SMCs, although other mechanisms such as U-type exchange may also yield SMCs. These assumptions are primarily based on observations of previously reported patients with complex rearrangements and our patient with a small SMC. Given the high frequency of trisomic cells in human preimplantation embryos, chromothripsis-mediated trisomy rescue may be a physiologically important phenomenon. Nevertheless, trisomy rescue has a potential to produce UPD, SMCs, and other chromosomal rearrangements. The concepts of trisomy rescue, chromothripsis, and micronuclei provide novel insights into the mechanism for the maintenance and modification of human chromosomes. Copyright © 2020 Matsubara, Yanagida, Nagai, Kagami and Fukami.The RNA polymerase II transcription subunit 12 homolog (MED12) is a member of the mediator complex, which plays a critical role in RNA transcription. Mutations in MED12 cause X-linked intellectual disability and other anomalies collectively grouped as MED12-related disorders. While MED12 mutations have been most commonly reported in male patients, we present the case of a 1-year-old girl with clinical characteristics similar to MED12-related disorders. To explore the clinical characteristics of the condition and its possible pathogenesis, we analyzed the patient's clinical data; genetic testing by whole-exome sequencing revealed a de novo heterozygous mutation (c.1249-1G &gt; C) in MED12. Further cDNA experiments revealed that the patient had an abnormal splicing at the skipping of exon9, which may have produced a truncated protein. qPCR showed decreased MED12 gene expression level in the patient, and an X-chromosome inactivation test confirmed a skewed inactivation of the X-chromosome. The lymphoblast transcription levels of the genes involved in the Gli3-dependent sonic hedgehog (SHH) signaling pathway, namely, CREB5, BMP4, and NEUROG2, were found to be significantly elevated compared with those of her parents and sex- and age-matched controls. Our results support the view that MED12 mutations may dysregulate the SHH signaling pathway, which may have accounted for the aberrant craniofacial morphology of our patient. Copyright © 2020 Wang, Lin, Xue, Wang, Liu, Ou, Wu, Lan, Zhang, Yuan, Luo, Wang, Xi, Sun and Chen.Genomic selection increases the rate of genetic gain in breeding programs, which results in significant cumulative improvements in commercially important traits such as disease resistance. Genomic selection currently relies on collecting genome-wide genotype data accross a large number of individuals, which requires substantial economic investment. However, global aquaculture production predominantly occurs in small and medium sized enterprises for whom this technology can be prohibitively expensive. For genomic selection to benefit these aquaculture sectors, more cost-efficient genotyping is necessary. In this study the utility of low and medium density SNP panels (ranging from 100 to 9,000 SNPs) to accurately predict breeding values was tested and compared in four aquaculture datasets with different characteristics (species, genome size, genotyping platform, family number and size, total population size, and target trait). The traits show heritabilities between 0.19-0.49, and genomic prediction accuracies using the full density panel of 0.55-0.87. A consistent pattern of genomic prediction accuracy was observed across species with little or no accuracy reduction until SNP density was reduced below 1,000 SNPs (prediction accuracies of 0.44-0.75). Below this SNP density, heritability estimates and genomic prediction accuracies tended to be lower and more variable (93% of maximum accuracy achieved with 1,000 SNPs, 89% with 500 SNPs, and 70% with 100 SNPs). A notable drop in accuracy was observed between 200 SNP panels (0.44-0.75) and 100 SNP panels (0.39-0.66). Now that a multitude of studies have highlighted the benefits of genomic over pedigree-based prediction of breeding values in aquaculture species, the results of the current study highlight that these benefits can be achieved at lower SNP densities and at lower cost, raising the possibility of a broader application of genetic improvement in smaller and more fragmented aquaculture settings. Copyright © 2020 Kriaridou, Tsairidou, Houston and Robledo.Lactococcus petauri CF11 was originally isolated from the gut of healthy humans. To determine the underlying molecular and genetic mechanisms of the probiotic potential of CF11, we performed complete genome sequencing, annotation, and comparative genome analysis. The complete genome of L. petauri CF11 comprised of 1,997,720 bp, with a DNA G+C content of 38.21 mol% containing 1982 protein coding genes and 16 rRNA operons. We found that 1206 genes (56.05%) were assigned a putative function using the gene ontology (GO) resource. The gene products of CF11 were primarily concentrated in molecular function and biological processes, such as catalysis, binding, metabolism, and cellular processes. Furthermore, 1,365 (68.87%) genes were assigned an illative function using COGs. CF11 proteins were associated with carbohydrate transport and metabolism, and amino acid transport and metabolism. This indicates that CF11 bacteria can perform active energy exchange. We classified 1,111 (56.05%) genes into six KEGG functional categories; fructose-bisphosphate aldolase and the phosphoenol pyruvatephosphotransferase system (PTS), which are necessary in producing short-chain fatty acids (SCFAs), were excited in the carbohydrate metabolic pathway. This suggests that L. petauri CF11 produces SCFAs via glycolysis. The genomic island revealed that some regions contain fragments of antibiotic resistance and bacteriostatic genes. In addition, ANI analysis showed that L. petauri CF11 had the closest relationship with L. petauri 159469T, with an average nucleotide consistency of 98.03%. [https://www.selleckchem.com/products/msab.html Selleck MSAB] Taken together, the present study offers further insights into the functional and potential role of L. petauri CF11 in health care. Copyright © 2020 Ou, Ren, Fang, Wu, Jiang, Chen, Zhong, Wang and Zhang.MicroRNAs (miRNAs) are non-coding RNA molecules that regulate gene expression. Extensive research has explored the role of miRNAs in the risk for type 2 diabetes (T2D) and coronary heart disease (CHD) using single-omics data, but much less by leveraging population-based omics data. Here we aimed to conduct a multi-omics analysis to identify miRNAs associated with cardiometabolic risk factors and diseases. First, we used publicly available summary statistics from large-scale genome-wide association studies to find genetic variants in miRNA-related sequences associated with various cardiometabolic traits, including lipid and obesity-related traits, glycemic indices, blood pressure, and disease prevalence of T2D and CHD. Then, we used DNA methylation and miRNA expression data from participants of the Rotterdam Study to further investigate the link between associated miRNAs and cardiometabolic traits. After correcting for multiple testing, 180 genetic variants annotated to 67 independent miRNAs were associated with the studied traits. Alterations in DNA methylation levels of CpG sites annotated to 38 of these miRNAs were associated with the same trait(s). Moreover, we found that plasma expression levels of 8 of the 67 identified miRNAs were also associated with the same trait. Integrating the results of different omics data showed miR-10b-5p, miR-148a-3p, miR-125b-5p, and miR-100-5p to be strongly linked to lipid traits. Collectively, our multi-omics analysis revealed multiple miRNAs that could be considered as potential biomarkers for early diagnosis and progression of cardiometabolic diseases. Copyright © 2020 Mens, Maas, Klap, Weverling, Klatser, Brakenhoff, van Meurs, Uitterlinden, Ikram, Kavousi and Ghanbari.The choice of a genetic marker genotyping platform is important for genomic prediction in livestock and poultry. High-throughput sequencing can produce more genetic markers, but the genotype quality is lower than that obtained with single nucleotide polymorphism (SNP) chips. The aim of this study was to compare the accuracy of genomic prediction between high-throughput sequencing and SNP chips in broilers. In this study, we developed a new SNP marker screening method, the pre-marker-selection (PMS) method, to determine whether an SNP marker can be used for genomic prediction. We also compared a method which preselection marker based results from genome-wide association studies (GWAS). With the two methods, we analysed body weight at the12th week (BW) and feed conversion ratio (FCR) in a local broiler population. A total of 395 birds were selected from the F2 generation of the population, and 10X specific-locus amplified fragment sequencing (SLAF-seq) and the Illumina Chicken 60K SNP Beadchip were used for gene accuracy of GEBV, and that more accurate genomic prediction can be obtained from an increased number of genomic markers when using high-throughput sequencing in local broiler populations. Due to its lower genotyping cost, high-throughput sequencing could be a good alternative to SNP chips for genomic prediction in breeding programmes of local broiler populations. Copyright © 2020 Liu, Luo, Ma, Wang, Shu, Su and Qu.In recent years, there has been an explosive increase in the amount of bioinformatics data produced, but data are not information. The purpose of bioinformatics research is to obtain information with biological significance from large amounts of data. Multiple sequence alignment is widely used in sequence homology detection, protein secondary and tertiary structure prediction, phylogenetic tree analysis, and other fields. Existing research mainly focuses on the specific steps of the algorithm or on specific problems, and there is a lack of high-level abstract domain algorithm frameworks. As a result, multiple sequence alignment algorithms are complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm, which may lead to computing errors. Here, through in-depth study and analysis of the heuristic multiple sequence alignment algorithm (HMSAA) domain, a domain-feature model and an interactive model of HMSAA components have been established according to the generative programming method.