SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

BackgroundOncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.ResultsIn reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100x more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.ConclusionThese new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.Peer reviewe

Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results

Pulmonary Lesions caused by the Nematode Rhabdias fuscovenosa in a Grass Snake, Natrix natrix

In June 2005, a free-ranging grass snake, Natrix natrix infected with Rhabdias fuscovenosa was collected for histologic examination of the lungs. Gross lesions were not noted; however, histologic examination revealed vacuolar degeneration of the respiratory epithelium, hemorrhage, smooth muscle degeneration, faveolae necrosis and obstruction, and intralesional nematodes. Eosinophils were the most common inflammatory cell observed in the areas of necrosis and interstitium. Herein we describe histopathologic changes due to R. fuscovenosa in a free-ranging grass snake

Influence of Intermittent Heating during Maceration on the Antioxidant Capacity of Some Grape Seeds and Skins

Ethanolic extracts from seeds and skins of three red grape varieties, namely, 'Cabernet Sauvignon', 'Merlot' and 'Burgund' from a Romanian winery, were prepared by maceration using different temperature conditions. The stable free radicals DPPH (2, 2-diphenyl- 1-picrylhydrazyl) and Tempol (4-hydroxy-2,2,6,6-tetramethylpiperidin-N-oxyl) were used in order to evaluate the antioxidant capacity of the extracts. The variation in time of free radical concentration was followed by double integration of the EPR spectra of the samples obtained after maceration under different conditions (room temperature and intermittent heating). Results showed that the antioxidant capacity depends on the nature of analysed samples (either being seeds or skins) and grape variety. The results also show that the intermittent heating during maceration leads to a decrease of the antioxidant capacity of samples

SDR-Enabled Multichannel Real-Time Measurement System for In Situ EMF Exposure Evaluation

The spatial and temporal variability of the signals emitted by modern communication devices produced a paradigm shift in approaching the human exposure to electromagnetic fields (EMF). This inherent variability requires in situ, agile EMF measurement solutions capable of performing real-time isotropic measurements. The aim of this paper is to describe a new real-time, highly flexible multichannel EMF measurement system that consists of a sensor connected to state-of-the-art software-defined radio (SDR) equipment. In this paper an electric field sensor is proposed, but we also provide information on the extension of the probe to electric and magnetic fields. In the receiver section, the proposed solution is compared in terms of performances (sensitivity and accuracy), costs, and requirements, with standard solutions based on spectrum analyzers or a digital oscilloscope. Finally, the proposed solution was tested considering the signals emitted in various operating scenarios by a mobile device operating in the LTE-A and IEEE 802.11ax mobile communication standards. The results confirm the versatility and efficiency of the proposed solution for in situ EMF measurements of signals emitted by the new generation communication devices

A preliminary study on ultra high frequency electromagnetic fields effect on black locust chlorophylls

Chlorophylls were quantitatively studied in the leaves of black locust (Robinia pseudoacacia L.) seedlings exposed to electromagnetic fields of high frequency. Exposure system was designed and built up to make possible simultaneous exposure of seedling lots (3 months old) to low power density electromagnetic fields corresponding to a frequency of 400 MHz. After three weeks of daily exposures (1, 2, 3 and 8 hours), chlorophyll levels were measured using adequate spectral device. Statistical analysis of experimental results was performed by means of t-test to identify significant modifications induced by electromagnetic treatment in exposed samples in comparison to the control. Chlorophyll-a as well as chlorophyll-b level was found to decrease except the exposure time of two hours, where a considerable enhancement was noticed. It was revealed that the ratio of the two main types of chlorophyll was decreasing logarithmically to the increase of daily exposure time