AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic marker as they represent the finest resolution of a DNA sequence (a single nucleotide), are generally abundant in populations and have a low mutation rate. Analysis of assembled EST sequence data provides a cost-effective means to identify large numbers of SNPs associated with functional genes. We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The database is freely accessible at http://autosnpdb.qfab.org.au/

Sequence analysis and characterization of active human alu subfamilies based on the 1000 genomes pilot project

© The Author(s) 2015. The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic young Alu insertion events, absent fromthe human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths.All the sequenced Alu lociwerederived from the Alu Y lineagewith no evidence of retrotransposition activity involving older Alu families (e.g., AluJandAluS). AluYa5 is currently themost active Alu subfamily in the human lineage, followed by AluYb8, andmany others including three newly identified subfamilieswe have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages

The variant call format and VCFtools

Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API

Extending reference assembly models

The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles. However, the models and analysis assumptions that underlie the current assembly need revising to fully represent human sequence diversity. Improved analysis tools and updated data reporting formats are also required

Structural characterization of vanadium oxide catalysts supported on nanostructured silica SBA-15 using X-ray absorption spectroscopy

The local structure of vanadium oxide supported on nanostructured SiO2 (VxOy/SBA-15) was investigated by in situ X-ray absorption spectroscopy (XAS). Because the number of potential parameters in XAS data analysis often exceeds the number of "independent" parameters, evaluating the reliability and significance of a particular fitting procedure is mandatory. The number of independent parameters (Nyquist) may not be sufficient. Hence, in addition to the number of independent parameters, a novel approach to evaluate the significance of structural fitting parameters in XAS data analysis is introduced. Three samples with different V loadings (i.e. 2.7 wt %, 5.4 wt %, and 10.8 wt %) were employed. Thermal treatment in air at 623 K resulted in characteristic structural changes of the V oxide species. Independent of the V loading, the local structure around V centers in dehydrated VxOy/SBA-15 corresponded to an ordered arrangement of adjacent V2O7 units. Moreover, the V2O7 units were found to persist under selective oxidation reaction conditions

ESGO/ESTRO/ESP guidelines for the management of patients with endometrial carcinoma

A European consensus conference on endometrial carcinoma was held in 2014 to produce multi-disciplinary evidence-based guidelines on selected questions. Given the large body of literature on the management of endometrial carcinoma published since 2014, the European Society of Gynaecological Oncology (ESGO), the European SocieTy for Radiotherapy and Oncology (ESTRO), and the European Society of Pathology (ESP) jointly decided to update these evidence-based guidelines and to cover new topics in order to improve the quality of care for women with endometrial carcinoma across Europe and worldwide

ESGO/ESTRO/ESP guidelines for the management of patients with endometrial carcinoma

A European consensus conference on endometrial carcinoma was held in 2014 to produce multidisciplinary evidence-based guidelines on selected questions. Given the large body of literature on the management of endometrial carcinoma published since 2014, the European Society of Gynaecological Oncology (ESGO), the European SocieTy for Radiotherapy & Oncology (ESTRO) and the European Society of Pathology (ESP) jointly decided to update these evidence-based guidelines and to cover new topics in order to improve the quality of care for women with endometrial carcinoma across Europe and worldwide. ESGO/ESTRO/ESP nominated an international multidisciplinary development group consisting of practicing clinicians and researchers who have demonstrated leadership and expertise in the care and research of endometrial carcinoma (27 experts across Europe). To ensure that the guidelines are evidence-based, the literature published since 2014, identified from a systematic search was reviewed and critically appraised. In the absence of any clear scientific evidence, judgment was based on the professional experience and consensus of the development group. The guidelines are thus based on the best available evidence and expert agreement. Prior to publication, the guidelines were reviewed by 191 independent international practitioners in cancer care delivery and patient representatives. The guidelines comprehensively cover endometrial carcinoma staging, definition of prognostic risk groups integrating molecular markers, pre- and intra-operative work-up, fertility preservation, management for early, advanced, metastatic, and recurrent disease and palliative treatment. Principles of radiotherapy and pathological evaluation are also defined

Potential health impacts of heavy metals on HIV-infected population in USA.

Noninfectious comorbidities such as cardiovascular diseases have become increasingly prevalent and occur earlier in life in persons with HIV infection. Despite the emerging body of literature linking environmental exposures to chronic disease outcomes in the general population, the impacts of environmental exposures have received little attention in HIV-infected population. The aim of this study is to investigate whether individuals living with HIV have elevated prevalence of heavy metals compared to non-HIV infected individuals in United States. We used the National Health and Nutrition Examination Survey (NHANES) 2003-2010 to compare exposures to heavy metals including cadmium, lead, and total mercury in HIV infected and non-HIV infected subjects. In this cross-sectional study, we found that HIV-infected individuals had higher concentrations of all heavy metals than the non-HIV infected group. In a multivariate linear regression model, HIV status was significantly associated with increased blood cadmium (p=0.03) after adjusting for age, sex, race, education, poverty income ratio, and smoking. However, HIV status was not statistically associated with lead or mercury levels after adjusting for the same covariates. Our findings suggest that HIV-infected patients might be significantly more exposed to cadmium compared to non-HIV infected individuals which could contribute to higher prevalence of chronic diseases among HIV-infected subjects. Further research is warranted to identify sources of exposure and to understand more about specific health outcomes