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Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
Caroline Vincent, Valentine Usongo, Chrystal Berry, Denise M Tremblay, Sylvain Moineau, Khadidja Yousfi, Florence Doualla-Bell, Eric Fournier, Céline Nadon, Lawrence Goodridge, Sadjia Bekal
Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S...
August 2018: Food Microbiology
Tingting Zhang, Wensong Wei, Bin Zhao, Ranran Wang, Mingliu Li, Liming Yang, Jianhua Wang, Qun Sun
This study investigated the possibility of using visible and near-infrared (VIS/NIR) hyperspectral imaging techniques to discriminate viable and non-viable wheat seeds. Both sides of individual seeds were subjected to hyperspectral imaging (400-1000 nm) to acquire reflectance spectral data. Four spectral datasets, including the ventral groove side, reverse side, mean (the mean of two sides' spectra of every seed), and mixture datasets (two sides' spectra of every seed), were used to construct the models. Classification models, partial least squares discriminant analysis (PLS-DA), and support vector machines (SVM), coupled with some pre-processing methods and successive projections algorithm (SPA), were built for the identification of viable and non-viable seeds...
March 8, 2018: Sensors
Inyoung Kim, Saemi Choi, Sun Kim
BACKGROUND: Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become huge, e.g., TCGA, and the data types to be analyzed have come in many varieties, including mutations, copy number variations, and transcriptome. We also need to consider a complex relationship with regulators of genes, particularly Transcription Factors(TF)...
February 19, 2018: BMC Bioinformatics
Xiaojing Pei, Tiancheng Lai, Guangyu Tao, Hu Hong, Feng Liu, Na Li
To be able to detect simultaneously multiple single-nucleotide variants (SNVs) with both ultra-high specificity and low-abundance detectability is of pivotal importance for molecular diagnostics and biological researches. In this contribution, we for the first time developed a multiplex SNV detection method that combines the masking tactic with fluorescent nanoparticle (FNP) counting based on the sandwich design. The method presents the rivaling performance due to the advantageous features: the masking reagent was designed to hybridize with the extremely large amount of the wild-type sequence to render the assay a high specificity; FNP count-ing provides a sensitive multiplexed SNV detection; the sandwich design facilitates an easy separation to make the detection free of interferences from the matrix...
March 5, 2018: Analytical Chemistry
Fei Liu, Lanhan Ye, Jiyu Peng, Kunlin Song, Tingting Shen, Chu Zhang, Yong He
Fast detection of heavy metals is very important for ensuring the quality and safety of crops. Laser-induced breakdown spectroscopy (LIBS), coupled with uni- and multivariate analysis, was applied for quantitative analysis of copper in three kinds of rice (Jiangsu rice, regular rice, and Simiao rice). For univariate analysis, three pre-processing methods were applied to reduce fluctuations, including background normalization, the internal standard method, and the standard normal variate (SNV). Linear regression models showed a strong correlation between spectral intensity and Cu content, with an R 2 more than 0...
February 27, 2018: Sensors
Dirk Walter, Patrick N Harter, Florian Battke, Ria Winkelmann, Markus Schneider, Katharina Holzer, Christine Koch, Jörg Bojunga, Stefan Zeuzem, Martin Leo Hansmann, Jan Peveling-Oberhag, Oliver Waidmann
Data on intratumoral heterogeneity of small intestine neuroendocrine tumors (SI-NETs) and related liver metastasis are limited. The aim of this study was to characterize genetic heterogeneity of 5 patients with SI-NETs. Therefore, formalin-fixed, paraffin-embedded tissue samples of primary and metastatic lesions as well as benign liver of five patients with synchronously metastasized, well differentiated SI-NETs were analyzed with whole exome sequencing. For one patient, chip based 850k whole DNA methylome analysis was performed of primary and metastatic tumor tissue as well as control tissue...
February 28, 2018: Scientific Reports
Matthieu Egloff, Lam-Son Nguyen, Karine Siquier-Pernet, Valérie Cormier-Daire, Geneviève Baujat, Tania Attié-Bitach, Christine Bole-Feysot, Patrick Nitschke, Michel Vekemans, Laurence Colleaux, Valérie Malan
Several hypotheses have been proposed to explain the phenotypic variability between parent and offspring carrying the same genomic imbalance, including unmasking of a recessive variant by a chromosomal deletion. Here, 19 patients with neurodevelopmental disorders harboring a rare deletion inherited from a healthy parent were investigated by whole-exome sequencing to search for SNV on the contralateral segment. This strategy allowed us to identify a candidate variant in two patients in the NUP214 and NCOR1 genes...
February 26, 2018: European Journal of Human Genetics: EJHG
Chang Yu, Xuefeng Wang, Lifeng Huang, Ying Tong, Lili Chen, Hailong Wu, Qiang Xia, Xiaoni Kong
AIM: Accumulation of mitochondrial DNA (mtDNA) mutations has been proposed to contribute to initiation and progression of tumors. METHODS: By using high-through sequencing strategies, we measured 33 specimens including: 11 hepatocellular carcinoma (HCC) tissues, 11 corresponding adjacent tissues and 11 normal liver tissues. RESULTS: We identified 194 Single Nucleotide Variants (SNV, including insert and deletion) in 33 liver tissues. And 13 somatic novel mutations were detected, including 7 mutations in the coding region...
February 20, 2018: Gene Expression
Jiyu Peng, Fei Liu, Tingting Shen, Lanhan Ye, Wenwen Kong, Wei Wang, Xiaodan Liu, Yong He
Fast detection of toxic metals in crops is important for monitoring pollution and ensuring food safety. In this study, laser-induced breakdown spectroscopy (LIBS) was used to detect the chromium content in rice leaves. We investigated the influence of laser wavelength (532 nm and 1064 nm excitation), along with the variations of delay time, pulse energy, and lens-to-sample distance (LTSD), on the signal (sensitivity and stability) and plasma features (temperature and electron density). With the optimized experimental parameters, univariate analysis was used for quantifying the chromium content, and several preprocessing methods (including background normalization, area normalization, multiplicative scatter correction (MSC) transformation and standardized normal variate (SNV) transformation were used to further improve the analytical performance...
February 18, 2018: Sensors
Lorena Suarez-Kelly, Keiko Akagi, Julie W Reeser, Eric Samorodnitsky, Matthew Reeder, Amy Smith, Sameek Roychowdhury, David E Symer, William E Carson
Metaplastic breast carcinoma (MBC) is rare and has a poor prognosis. Here we describe genetic analysis of a 41-year-old female patient with MBC and neurofibromatosis type I (NF1). She initially presented with pT3N1a, grade 3 MBC, but lung metastases were discovered subsequently. To identify the molecular cause of her NF1, we screened for germline mutations disrupting NF1 or SPRED1, revealing a heterozygous germline single nucleotide variant (SNV) in exon 21 of NF1 at c.2709G>A, chr17: 29556342. By report, this variant disrupts pre-mRNA splicing of NF1 transcripts...
February 15, 2018: Cold Spring Harbor Molecular Case Studies
Alma Dorothea Jaeger, Christian Ehm, Dieter Lentz
Hydrodefluorination reactions (HDF) of per- and polyfluorinated olefins and arenes by cheap aluminum alkyl hydrides in non-coordinating solvents can be catalyzed by O and N donors. TONs with respect to the organocatalysts of up to 87 have been observed. Depending on substrate and concentration, high selectivities can be achieved. For the prototypical hexafluoropropene, however, low selectivities are observed (E/Z ~ 2). DFT studies show that the preferred HDF mechanism for this substrate in the presence of donor solvents proceeds from the dimer Me4Al2(μ-H)2·THF via nucleophilic vinylic substitution (SNV) like transition states with low selectivity and without formation of an intermediate, not via hydrometallation or σ-bond metathesis...
February 14, 2018: Chemistry: a European Journal
Fei He, Wanjun Zhou, Ren Cai, Tizhen Yan, Xiangmin Xu
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods...
February 13, 2018: Journal of Human Genetics
Upneet K Sokhi, Mark P Liber, Laura Frye, Sungho Park, Kyuho Kang, Tania Pannellini, Baohong Zhao, Rada Norinsky, Lionel B Ivashkiv, Shiaoching Gong
Enhancers regulate gene expression and have been linked with disease pathogenesis. Little is known about enhancers that regulate human disease-associated genes in primary cells relevant for pathogenesis. Here we use BAC transgenics and genome editing to dissect, in vivo and in primary immune cells, enhancers that regulate human TNFAIP3, which encodes A20 and is linked with autoimmune diseases. A20 expression is dependent on a topologically associating subdomain (sub-TAD) that harbors four enhancers, while another >20 enhancers in the A20 locus are redundant...
February 13, 2018: Nature Communications
Chihiro Udagawa, Yasushi Sasaki, Hiroshi Suemizu, Yasuyuki Ohnishi, Hiroshi Ohnishi, Takashi Tokino, Hitoshi Zembutsu
Although there has been progress moving from a 'one-size-fits-all' cytotoxic approach to personalized molecular medicine, the majority of patients with cancer receive chemotherapy using cytotoxic anticancer drugs. The sequencing analysis of 409 genes associated with cancer was conducted in the present study using 59 DNA sequences extracted from human cancer xenografts implanted into nude mice, of which sensitivity to 9 cytotoxic anticancer drugs [5-fluorouracil, nimustine, adriamycin, cyclophosphamide, cisplatin, mitomycin C (MMC), methotrexate, vincristine (VCR), and vinblastine] was examined...
February 2018: Experimental and Therapeutic Medicine
W J Wu, K Q Liu, B J Li, C Dong, Z K Zhang, P H Li, R H Huang, W Wei, J Chen, H L Liu
The Sine oculis homeobox 1 (Six1) gene is important for skeletal muscle growth and fiber specification; therefore, it is considered as a promising candidate gene that may influence porcine growth and meat quality traits. Nevertheless, the association of Six1 with these processes, and the mechanisms regulating its expression, remain unclear. The objectives of this study were to identify variant sites of in Six1 in different pig breeds, conduct association analysis to evaluated the relationship between polymorphisms of theses variants and porcine production traits in Pietrainm × Duroc × Landrace × Yorkshire (P×D×L×Y) commercial pigs, and explore the potential regulatory mechanisms of Six1 affecting production traits...
February 8, 2018: Journal of Animal Science
Bingbing Xie, Zifeng Yuan, Yadong Yang, Zhidan Sun, Shuigeng Zhou, Xiangdong Fang
BACKGROUND: Breast cancer is one of the most frequently diagnosed cancers among women worldwide, characterized by diverse biological heterogeneity. It is well known that complex and combined gene regulation of multi-omics is involved in the occurrence and development of breast cancer. RESULTS: In this paper, we present the Multi-Omics Breast Cancer Database (MOBCdb), a simple and easily accessible repository that integrates genomic, transcriptomic, epigenomic, clinical, and drug response data of different subtypes of breast cancer...
February 10, 2018: Breast Cancer Research and Treatment
John Stephen Malamon, Andres Kriete
Late-onset Alzheimer's disease (LOAD) and age are significantly correlated such that one-third of Americans beyond 85 years of age are afflicted. We have designed and implemented a pilot study that combines systems biology approaches with traditional next-generation sequencing (NGS) analysis techniques to identify relevant regulatory pathways, infer functional relationships and confirm the dysregulation of these biological pathways in LOAD. Our study design is a most comprehensive systems approach combining co-expression network modeling derived from RNA-seq data, rigorous quality control (QC) standards, functional ontology, and expression quantitative trait loci (eQTL) derived from whole exome (WES) single nucleotide variant (SNV) genotype data...
February 9, 2018: Biology
Wulfran Cacheux, Virginie Dangles-Marie, Etienne Rouleau, Julien Lazartigues, Elodie Girard, Adrien Briaux, Pascale Mariani, Sophie Richon, Sophie Vacher, Bruno Buecher, Marion Richard-Molard, Emmanuelle Jeannot, Nicolas Servant, Fereshteh Farkhondeh, Odette Mariani, Thomas Rio-Frio, Sergio Roman-Roman, Emmanuel Mitry, Ivan Bieche, Astrid Lièvre
Anal squamous cell carcinomas (ASCC) are rare tumours in humans. The etiological role of HPV infection is now well established but little is known about the molecular landscape and signalling pathways involved in the pathogenesis of this cancer. Here we report the results from a whole exome sequencing of a homogeneous group of 20 treatment-naive ASCC. A total of 2422 somatic single nucleotide variations (SNV) were found, with an overall moderate rate of somatic mutations per tumour (median: 105 relevant SNV per tumour) but a high mutational load in 3 tumours...
January 2, 2018: Oncotarget
Jing-Wen Hao, Nai-Dong Chen, Cun-Wu Chen, Fu-Cheng Zhu, De-Liang Qiao, Yong-Jun Zang, Jun Dai, Xiang-Wen Song, Han Chen
A rapid, green, low cost and nondestructive attenuated total reflection near infrared (ATR NIR) method was developed to quantify the total polysaccharide and the main monosaccharides mannose and glucose in Dendrobium huoshanense. Total 100 D. huoshanense samples from different places were analyzed using ATR NIR method. Potential outlying samples were initially removed from the collected NIR data using the PCA-Mahalanobis distance method. Spectral data preprocessing was studied in the construction of a partial least squares (PLS) model and six different signal pretreatment methods, including multiplicative scattering correction (MSC), standard normal transformation (SNV), first and second derivatives, the combination of MSC with the first derivative, and the combination of SNV with the first derivative, were compared...
January 25, 2018: Journal of Pharmaceutical and Biomedical Analysis
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