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Genetics cross validation

Teivi Laurimäe, Liina Kinkar, Epp Moks, Thomas Romig, Rihab A Omer, Adriano Casulli, Gérald Umhang, Guna Bagrade, Malik Irshadullah, Mitra Sharbatkhori, Hossein Mirhendi, Francisco Ponce-Gordo, Silvia V Soriano, Antonio Varcasia, Mohammad Rostami-Nejad, Vanessa Andresiuk, Urmas Saarma
Tapeworms of the species complex of Echinococcus granulosus sensu lato (s. l.) are the cause of a severe zoonotic disease - cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterinary communities for accurate and effective communication of the role of different species in this complex on human and animal health. E. granulosus s. l. displays high genetic diversity and has been divided into different species and genotypes...
May 21, 2018: Parasitology
Can Peng, Yijin Yan, Veronica J Kim, Staci E Engle, Jennifer N Berry, J Michael McIntosh, Rachael L Neve, Ryan M Drenan
Nicotinic acetylcholine receptors (nAChRs), prototype members of the cys-loop ligand gated ion channel family, are key mediators of cholinergic transmission in the central nervous system. Despite their importance, technical gaps exist in our ability to dissect the function of individual subunits in the brain. To overcome these barriers, we designed CRISPR/Cas9 small guide RNA sequences (sgRNAs) for production of loss-of-function alleles in mouse nAChR genes. These sgRNAs were validated in vitro via deep sequencing...
May 19, 2018: European Journal of Neuroscience
Manje Gowda, Yoseph Beyene, Dan Makumbi, Kassa Semagn, Michael S Olsen, Jumbo M Bright, Biswanath Das, Stephen Mugo, L M Suresh, Boddupalli M Prasanna
In sub-Saharan Africa, maize is the key determinant of food security for smallholder farmers. The sudden outbreak of maize lethal necrosis (MLN) disease is seriously threatening the maize production in the region. Understanding the genetic basis of MLN resistance is crucial. In this study, we used four biparental populations applied linkage mapping and joint linkage mapping approaches to identify and validate the MLN resistance-associated genomic regions. All populations were genotyped with low to high density markers and phenotyped in multiple environments against MLN under artificial inoculation...
2018: Molecular Breeding: New Strategies in Plant Improvement
Min Chul Choi, Jin Sik Bae, Sang Geun Jung, Hyun Park, Won Duk Joo, Seung Hun Song, Chan Lee, Ji Ho Kim, Ki Chan Lee, Sunghoon Lee, Je Ho Lee
OBJECTIVE: The aim of the present study was to assess the frequency of germline mutations in patients with peritoneal carcinoma (PC) or the fallopian tube carcinoma (FTC), using a multi-gene panel. METHODS: Twenty-six patients diagnosed with either PC or FTC between January 2013 and December 2016 were recruited consecutively. Germline DNA was sequenced using a 6-gene next generation sequencing (NGS) panel following genetic counseling. Surgico-medical information was obtained from hospital records...
March 26, 2018: Journal of Gynecologic Oncology
Francesco Cucco, Alexandra Clipson, Hannah Kennedy, Joe Sneath Thompson, Ming Wang, Sharon Barrans, Moniek van Hoppe, Eguzkine Ochoa Ruiz, Josh Caddy, Debbie Hamid, Thomas Cummin, Cathy Burton, Andrew J Davies, Peter Johnson, Ming-Qing Du
DNA samples from formalin-fixed paraffin-embedded tissues are highly degraded with variable quality, and this imposes a big challenge for targeted sequencing due to false positives, largely caused by PCR errors and cytosine deamination. To eliminate false positives, a common practice is to validate the detected variants by Sanger sequencing or perform targeted sequencing in duplicate. Technically, PCR errors could be removed by molecular barcoding of template DNA prior to amplification as in the HaloPlexHS design...
May 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
Piet A van Rijn, Mieke A Maris-Veldhuis, Jan Boonstra, René G P van Gennip
African Horse Sickness Virus (AHSV) (Orbivirus genus, Reoviridae family) causes high mortality in naïve domestic horses with enormous economic and socio-emotional impact. There are nine AHSV serotypes showing limited cross neutralization. AHSV is transmitted by competent species of Culicoides biting midges. AHS is a serious threat beyond the African continent as endemic Culicoides species in moderate climates transmit the closely related prototype bluetongue virus. There is a desperate need for safe and efficacious vaccines, while DIVA (Differentiating Infected from Vaccinated) vaccines would accelerate control of AHS...
May 11, 2018: Vaccine
Charu Bahl, Navneet Singh, Digambar Behera, Siddharth Sharma
AIM: Genetic variations present within Wnt and AhR pathway might be related to the lung cancer susceptibility. METHODS: A total of 555 subjects were genotyped using PCR-RFLP technique for polymorphic sites in DKK4, DKK3, DKK2, sFRP3, sFRP4, Axin2 and AhR. Multifactor dimensionality reduction method and classification and regression tree analysis was used. RESULTS: Overall sFRP4rs1802073 which has a cross validation consistency of 10/10, prediction error = 0...
November 2017: Personalized Medicine
Dorothee Wozny, Katharina Kramer, Iris Finkemeier, Ivan F Acosta, Maarten Koornneef
Genes controlling differences in seed longevity between two barley (Hordeum vulgare) accessions were identified by combining quantitative genetics 'omics' technologies in Near Isogenic Lines (NILs). The NILs were derived from crosses between the spring barley landraces L94 from Ethiopia and Cebada Capa from Argentina. A combined transcriptome and proteome analysis on mature, non-aged seeds of the two parental lines and the L94 NILs by RNA-sequencing and total seed proteomic profiling identified the UDP-glycosyltransferase MLOC_11661...
May 9, 2018: Plant, Cell & Environment
G S Campos, F A Reimann, L L Cardoso, C E R Ferreira, V S Junqueira, P I Schmidt, J Braccini Neto, M J I Yokoo, B P Sollero, A A Boligon, F F Cardoso
The objective of the present study was to evaluate the accuracy and bias of direct and blended genomic predictions using different methods and cross-validation techniques for growth traits (weight and weight gains) and visual scores (conformation, precocity, muscling and size) obtained at weaning and at yearling in Hereford and Braford breeds. Phenotypic data contained 126,290 animals belonging to the Delta G Connection genetic improvement program, and a set of 3,545 animals genotyped with the 50K chip and 131 sires with the 777K...
May 7, 2018: Journal of Animal Science
Preeti Patel, Vijay K Patel, Avineesh Singh, Talha Jawaid, Mehnaz Kamal, Harish Rajak
BACKGROUND: Histone deacetylase 1 (HDAC1) over expression is responsible for carcinogenesis by promoting epigenetic silence of tumour suppressor genes. Thus, HDAC1 inhibitors has came out as the potential therapeutic leads against multiple human cancers, as they can block the activity of particular HDACs, renovate the expression of several tumour suppressor genes and bring about cell differentiation, cell cycle arrest and apoptosis. METHODS: The present research work comprises of atom-based 3D-QSAR, docking, molecular dynamic simulations and DFT (density functional theory) studies on a diverse series of hydroxamic acid derivatives as selective HDAC1 inhibitors...
May 1, 2018: Current Computer-aided Drug Design
Shuchen Feng, Melinda Bootsma, Sandra L McLellan
The human microbiome contains many organisms that could potentially be used as indicators of human fecal pollution. Here we report the development of two novel human-associated genetic marker assays that target organisms within the family Lachnospiraceae Next-generation sequencing of the V6 region of the 16S rRNA gene from sewage and animal stool samples identified 40 human-associated marker candidates with a robust signal in sewage and low or no occurrence in nonhuman hosts. Two were chosen for quantitative PCR (qPCR) assay development using longer sequences (V2 to V9 regions) generated from clone libraries...
May 4, 2018: Applied and Environmental Microbiology
Sheng Wang, Xuanze Chen, Lei Chang, Miao Ding, Ruiying Xue, Haifeng Duan, Yujie Sun
Fluorescent probes with multimodal and multilevel imaging capabilities are highly valuable as imaging with such probes not only can obtain new layers of information but also enable cross-validation of results under different experimental conditions. In recent years, the development of genetically-encoded reversibly photoswitchable fluorescent proteins (RSFPs) has greatly promoted the application of various kinds of live-cell nanoscopy approaches, including reversible saturable optical fluorescence transitions (RESOLFT) and stochastic optical fluctuation imaging (SOFI)...
May 3, 2018: Analytical Chemistry
Gregor Gorjanc, John M Hickey
Summary: AlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic...
May 2, 2018: Bioinformatics
Elizabeth R Piette, Jason H Moore
Background: Machine learning methods and conventions are increasingly employed for the analysis of large, complex biomedical data sets, including genome-wide association studies (GWAS). Reproducibility of machine learning analyses of GWAS can be hampered by biological and statistical factors, particularly so for the investigation of non-additive genetic interactions. Application of traditional cross validation to a GWAS data set may result in poor consistency between the training and testing data set splits due to an imbalance of the interaction genotypes relative to the data as a whole...
2018: BioData Mining
Caroline Du, Julong Wei, Shibo Wang, Zhenyu Jia
Many statistical methods are available for genomic selection (GS) through which genetic values of quantitative traits are predicted for plants and animals using whole-genome SNP data. A large number of predictors with much fewer subjects become a major computational challenge in GS. Principal components regression (PCR) and its derivative, i.e., partial least squares regression (PLSR), provide a solution through dimensionality reduction. In this study, we show that PCR can perform better than PLSR in cross validation...
May 1, 2018: Heredity
Fernanda Rodrigues-Soares, Fernanda S G Kehdy, Julia Sampaio-Coelho, Poliana X C Andrade, Carolina Céspedes-Garro, Camila Zolini, Marla M Aquino, Mauricio L Barreto, Bernardo L Horta, Maria Fernanda Lima-Costa, Alexandre C Pereira, Adrián LLerena, Eduardo Tarazona-Santos
We present allele frequencies involving 39 pharmacogenetic biomarkers studied in Brazil, and their distribution on self-reported race/color categories that: (1) involve a mix of perceptions about ancestry, morphological traits, and cultural/identity issues, being social constructs pervasively used in Brazilian society and medical studies; (2) are associated with disparities in access to health services, as well as in their representation in genetic studies, and (3), as we report here, explain a larger portion of the variance of pharmaco-allele frequencies than geography...
May 1, 2018: Pharmacogenomics Journal
Esteban Pardo, José Mário T Morgado, Norberto Malpica
Multicolor in situ hybridization (mFISH) is a karyotyping technique used to detect major chromosomal alterations using fluorescent probes and imaging techniques. Manual interpretation of mFISH images is a time consuming step that can be automated using machine learning; in previous works, pixel or patch wise classification was employed, overlooking spatial information which can help identify chromosomes. In this work, we propose a fully convolutional semantic segmentation network for the interpretation of mFISH images, which uses both spatial and spectral information to classify each pixel in an end-to-end fashion...
April 30, 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Sermin Kesebir
Mood disorders comprise major depressive disorder (MDD), bipolar disorder (BD) and the milder forms of these two disorders. Reccurring MDD is also known as unipolar disorder. The distinction between unipolar and bipolar disorders was first suggested in 1957 by Leonard and was made official after support by several studies in 1980. Indeed, in 150 AD, Aretaeus of Cappadocia wrote "It seems to me that melancholia is the beginning and a part of mania". Additionally, Kraepelin, who proposed the first medical disease model in psychiatry a century ago, considered recurrent unipolar depression cases under the category of bipolar disorder and conceptualized spectrum disorders...
June 2018: Journal of Clinical Medicine Research
Guo-Min Zhang, Tian-Qing Zheng, Zhuo Chen, Yong-Li Wang, Ying Wang, Yu-Min Shi, Chun-Chao Wang, Li-Yan Zhang, Jun-Tao Ma, Ling-Wei Deng, Wan Li, Tian-Tian Xu, Cheng-Zhi Liang, Jian-Long Xu, Zhi-Kang Li
Grain minerals in rice, especially those in milled grains, are important sources of micro-nutrition elements, such as iron (Fe), zinc (Zn), manganese (Mn), copper (Cu), and selenium (Se), and of toxic heavy metal elements, especially cadmium (Cd), for populations consuming a rice diet. To date, the genetic mechanism underlying grain mineral concentrations (GMCs) in milled grain remains largely unknown. In this report, we adopted a set of 698 germplasms consisting of two subsets [ indica / Xian (X-set) and japonica / Geng (G-set)], to detect quantitative trait loci (QTL) affecting GMC traits of Fe, Zn, Cd, Mn, Cu, and Se in milled grains...
2018: Frontiers in Plant Science
Yasir Serag Alnor Gorafi, June-Sik Kim, Awad Ahmed Elawad Elbashir, Hisashi Tsujimoto
The multiple synthetic derivatives platform described in this study will provide an opportunity for effective utilization of Aegilops tauschii traits and genes for wheat breeding. Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61...
April 28, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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