CGDSNPdb: a database resource for error-checked and imputed mouse SNPs

The Center for Genome Dynamics Single Nucleotide Polymorphism Database (CGDSNPdb) is an open-source value-added database with more than nine million mouse single nucleotide polymorphisms (SNPs), drawn from multiple sources, with genotypes assigned to multiple inbred strains of laboratory mice. All SNPs are checked for accuracy and annotated for properties specific to the SNP as well as those implied by changes to overlapping protein-coding genes. CGDSNPdb serves as the primary interface to two unique data sets, the ‘imputed genotype resource’ in which a Hidden Markov Model was used to assess local haplotypes and the most probable base assignment at several million genomic loci in tens of strains of mice, and the Affymetrix Mouse Diversity Genotyping Array, a high density microarray with over 600 000 SNPs and over 900 000 invariant genomic probes. CGDSNPdb is accessible online through either a web-based query tool or a MySQL public login

An imputed genotype resource for the laboratory mouse

We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 49 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data. The strong linkage disequilibrium found in dense sets of SNP markers in the laboratory mouse provides the basis for accurate imputation. Using genotypes from eight independent SNP resources, we empirically validated the quality of the imputed genotypes and demonstrate that they are highly reliable for most inbred strains. The imputed SNP resource will be useful for studies of natural variation and complex traits. It will facilitate association study designs by providing high density SNP genotypes for large numbers of mouse strains. We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains. The data are available for bulk download or query at http://cgd.jax.org/

A customized and versatile high-density genotyping array for the mouse

We designed a high-density mouse genotyping array containing 623,124 SNPs that capture the known genetic variation present in the laboratory mouse. The array also contains 916,269 invariant genomic probes that are targeted to functional elements and regions known to harbor segmental duplications. The array opens the door to the characterization of genetic diversity, copy number variation, allele specific gene expression and DNA methylation and will extend the successes of human genome-wide association studies to the mouse

Mutation discovery in mice by whole exome sequencing

We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we show that whole exome sequencing is a robust approach for discovery of putative mutations, irrespective of strain background. We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis

Messenger RNA Oxidation Occurs Early in Disease Pathogenesis and Promotes Motor Neuron Degeneration in ALS

BACKGROUND: Accumulating evidence indicates that RNA oxidation is involved in a wide variety of neurological diseases and may be associated with neuronal deterioration during the process of neurodegeneration. However, previous studies were done in postmortem tissues or cultured neurons. Here, we used transgenic mice to demonstrate the role of RNA oxidation in the process of neurodegeneration. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated that messenger RNA (mRNA) oxidation is a common feature in amyotrophic lateral sclerosis (ALS) patients as well as in many different transgenic mice expressing familial ALS-linked mutant copper-zinc superoxide dismutase (SOD1). In mutant SOD1 mice, increased mRNA oxidation primarily occurs in the motor neurons and oligodendrocytes of the spinal cord at an early, pre-symptomatic stage. Identification of oxidized mRNA species revealed that some species are more vulnerable to oxidative damage, and importantly, many oxidized mRNA species have been implicated in the pathogenesis of ALS. Oxidative modification of mRNA causes reduced protein expression. Reduced mRNA oxidation by vitamin E restores protein expression and partially protects motor neurons. CONCLUSION/SIGNIFICANCE: These findings suggest that mRNA oxidation is an early event associated with motor neuron deterioration in ALS, and may be also a common early event preceding neuron degeneration in other neurological diseases

Effects of marital status on overall and cancer-specific survival in laryngeal cancer patients: a population-based study

Abstract Marital status has long been recognized as an important prognostic factor for many cancers, however its’ prognostic effect for patients with laryngeal cancer has not been fully examined. We retrospectively analyzed 8834 laryngeal cancer patients in the Surveillance Epidemiology and End Results database from 2004 to 2010. Patients were divided into four groups: married, widowed, single, and divorced/separated. The difference in overall survival (OS) and cancer-specific survival (CSS) of the various marital subgroups were calculated using the Kaplan–Meier curve. Multivariate Cox regression analysis screened for independent prognostic factors. Propensity score matching (PSM) was also conducted to minimize selection bias. We included 8834 eligible patients (4817 married, 894 widowed, 1732 single and 1391 divorced/separated) with laryngeal cancer. The 5-year OS and CSS of married, widowed, single, and separated/divorced patients were examined. Univariate and multivariate analyses found marital status to be an independent predictor of survival. Subgroup survival analysis showed that the OS and CSS rates in widowed patients were always the lowest in the various American Joint Committee on Cancer stages, irrespective of sex. Widowed patients demonstrated worse OS and CSS in the 1:1 matched group analysis. Among patients with laryngeal cancer, widowed patients represented the highest-risk group, with the lowest OS and CSS

A Subject-Sensitive Perceptual Hash Based on MUM-Net for the Integrity Authentication of High Resolution Remote Sensing Images

Data security technology is of great significance to the application of high resolution remote sensing image (HRRS) images. As an important data security technology, perceptual hash overcomes the shortcomings of cryptographic hashing that is not robust and can achieve integrity authentication of HRRS images based on perceptual content. However, the existing perceptual hash does not take into account whether the user focuses on certain types of information of the HRRS image. In this paper, we introduce the concept of subject-sensitive perceptual hash, which can be seen as a special case of conventional perceptual hash, for the integrity authentication of HRRS image. To achieve subject-sensitive perceptual hash, we propose a new deep convolutional neural network architecture, named MUM-Net, for extracting robust features of HRRS images. MUM-Net is the core of perceptual hash algorithm, and it uses focal loss as the loss function to overcome the imbalance between the positive and negative samples in the training samples. The robust features extracted by MUM-Net are further compressed and encoded to obtain the perceptual hash sequence of HRRS image. Experiments show that our algorithm has higher tamper sensitivity to subject-related malicious tampering, and the robustness is improved by about 10% compared to the existing U-net-based algorithm; compared to other deep learning-based algorithms, this algorithm achieves a better balance between robustness and tampering sensitivity, and has better overall performance