Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method

BACKGROUND: Systematic evaluation and study of single nucleotide polymorphisms (SNPs) made possible by high throughput genotyping technologies and bioinformatics promises to provide breakthroughs in the understanding of complex diseases. Understanding how the millions of SNPs in the human genome are involved in conferring susceptibility or resistance to disease, or in rendering a drug efficacious or toxic in the individual is a major goal of the relatively new fields of pharmacogenomics. Esophageal squamous cell carcinoma is a high-mortality cancer with complex etiology and progression involving both genetic and environmental factors. We examined the association between esophageal cancer risk and patterns of 61 SNPs in a case-control study for a population from Shanxi Province in North Central China that has among the highest rates of esophageal squamous cell carcinoma in the world. METHODS: High-throughput Masscode mass spectrometry genotyping was done on genomic DNA from 574 individuals (394 cases and 180 age-frequency matched controls). SNPs were chosen from among genes involving DNA repair enzymes, and Phase I and Phase II enzymes. We developed a novel adaptation of the Decision Forest pattern recognition method named Decision Forest for SNPs (DF-SNPs). The method was designated to analyze the SNP data. RESULTS: The classifier in separating the cases from the controls developed with DF-SNPs gave concordance, sensitivity and specificity, of 94.7%, 99.0% and 85.1%, respectively; suggesting its usefulness for hypothesizing what SNPs or combinations of SNPs could be involved in susceptibility to esophageal cancer. Importantly, the DF-SNPs algorithm incorporated a randomization test for assessing the relevance (or importance) of individual SNPs, SNP types (Homozygous common, heterozygous and homozygous variant) and patterns of SNP types (SNP patterns) that differentiate cases from controls. For example, we found that the different genotypes of SNP GADD45B E1122 are all associated with cancer risk. CONCLUSION: The DF-SNPs method can be used to differentiate esophageal squamous cell carcinoma cases from controls based on individual SNPs, SNP types and SNP patterns. The method could be useful to identify potential biomarkers from the SNP data and complement existing methods for genotype analyses

Domain Altering SNPs in the Human Proteome and Their Impact on Signaling Pathways

Single nucleotide polymorphisms (SNPs) constitute an important mode of genetic variations observed in the human genome. A small fraction of SNPs, about four thousand out of the ten million, has been associated with genetic disorders and complex diseases. The present study focuses on SNPs that fall on protein domains, 3D structures that facilitate connectivity of proteins in cell signaling and metabolic pathways. We scanned the human proteome using the PROSITE web tool and identified proteins with SNP containing domains. We showed that SNPs that fall on protein domains are highly statistically enriched among SNPs linked to hereditary disorders and complex diseases. Proteins whose domains are dramatically altered by the presence of an SNP are even more likely to be present among proteins linked to hereditary disorders. Proteins with domain-altering SNPs comprise highly connected nodes in cellular pathways such as the focal adhesion, the axon guidance pathway and the autoimmune disease pathways. Statistical enrichment of domain/motif signatures in interacting protein pairs indicates extensive loss of connectivity of cell signaling pathways due to domain-altering SNPs, potentially leading to hereditary disorders

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline—NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications

Stretching the spines of gymnasts: a review

Gymnastics is noted for involving highly specialized strength, power, agility and flexibility. Flexibility is perhaps the single greatest discriminator of gymnastics from other sports. The extreme ranges of motion achieved by gymnasts require long periods of training, often occupying more than a decade. Gymnasts also start training at an early age (particularly female gymnasts), and the effect of gymnastics training on these young athletes is poorly understood. One of the concerns of many gymnastics professionals is the training of the spine in hyperextension-the ubiquitous 'arch' seen in many gymnastics positions and movements. Training in spine hyperextension usually begins in early childhood through performance of a skill known as a back-bend. Does practising a back-bend and other hyperextension exercises harm young gymnasts? Current information on spine stretching among gymnasts indicates that, within reason, spine stretching does not appear to be an unusual threat to gymnasts' health. However, the paucity of information demands that further study be undertaken

Comparative genomics of the tardigrades <i>Hypsibius dujardini</i> and <i>Ramazzottius varieornatus</i>

Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda

Adaptação cultural de instrumento que avalia atividades do trabalho e sua relação com sintomas osteomusculares Adaptación cultural de un instrumento que evalúa actividades del trabajo y su relación con síntomas osteomusculares Cross-cultural adaptation of an instrument to measure work-related activities that may contribute to osteomuscular symptoms

OBJETIVO: Traduzir e adaptar culturalmente o questionário Work-related activities that may contribute to job-related pain and/or injury para o português falado no Brasil e verificar a validade de conteúdo desta nova versão. MÉTODOS: A adaptação cultural seguiu normas internacionalmente aceitas com as etapas de tradução, síntese, retro-tradução, avaliação por um comitê de especialistas e pré-teste. Esta versão do instrumento foi aplicada em 40 trabalhadores. RESULTADOS: O procedimento de adaptação cultural foi realizado com sucesso. O comitê de especialistas verificou a validade de conteúdo e realizou algumas modificações. No pré-teste, 7,5% dos indivíduos indicaram sugestões para um item do questionário e 17,5% demonstraram dificuldades no entendimento da instrução. Informações adicionais foram incluídas para tornar o instrumento final mais compreensível. CONCLUSÕES: A versão brasileira deste instrumento foi obtida com sucesso.<br>OBJETIVO: Traducir y adaptar culturalmente el cuestionario Work-related activities that may contribute to job-related pain and/or injury al portugués hablado en el Brasil y verificar la validez de contenidos de esta nueva versión. MÉTODOS: La adaptación cultural siguió normas internacionalmente aceptadas con las etapas de traducción, síntesis, retro-traducción, evaluación por un comité de especialistas y pre test. Esta versión del instrumento fue aplicada a 40 trabajadores. RESULTADOS: El procedimiento de adaptación cultural fue realizado con éxito. El comité de especialistas verificó la validez de contenido y realizó algunas modificaciones. En el pre test, el 7,5% de los individuos indicaron sugerencias para un item del cuestionario y el 17,5% demostraron dificultades en el entendimiento de la instrucción. Las informaciones adicionales fueron incluidas para conseguir que el instrumento final sea más comprensible. CONCLUSIONES: La versión brasileña de este instrumento fue obtenida con éxito.<br>OBJECTIVE: To translate the Work-Related Activities Questionnaire into Brazilian Portuguese and to evaluate its cross-cultural adaptation among a sample of Brazilian workers. METHODS: International standard recommendations were followed to translate and back-translate the instrument, and to establish the cross-cultural adaptation of the instrument using content experts and pretest. A field testing of the instrument was conducted with 40 Brazilian workers. RESULTS: The procedure used to establish the cross-cultural adaptation of the instrument was found to be adequate. The panels of experts evaluated the initial content validity of the items of the instrument and suggested necessary revisions to achieve an acceptable content validity. In the pretest, 7.5% of individuals suggested changes in one of the items of the instrument. In addition, 17.5% of the individuals reported having difficulty understanding the instructions to complete the instrument. These findings led to further revision of the instrument. CONCLUSION: The Brazilian version of the instrument was adequately cross-culturally adapted and validated

Assessing the Unidimensionality of Psychological Scales: Using Multiple Criteria from Factor Analysis

Psychometric testing, Construct validity, Quality of Life, Test dimensionality, Rational criteria combinations and indices, Unidimensionality methodology,

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs