scholarly journals Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping

2018 ◽  
Vol 9 ◽  
Author(s):  
Yuxuan Yuan ◽  
Zbyněk Milec ◽  
Philipp E. Bayer ◽  
Jan Vrána ◽  
Jaroslav Doležel ◽  
...  
Keyword(s):  
Large Scale ◽  
Structural Variation ◽  
Optical Mapping ◽  
Subterranean Clover

scholarly journals Single-molecule analysis reveals widespread structural variation in multiple myeloma

2015 ◽  
Vol 112 (25) ◽  
pp. 7689-7694 ◽  
Author(s):  
Aditya Gupta ◽  
Michael Place ◽  
Steven Goldstein ◽  
Deepayan Sarkar ◽  
Shiguo Zhou ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Tumor Progression ◽  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Plasma Cells ◽  
Optical Mapping ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Whole Genome Analysis

Multiple myeloma (MM), a malignancy of plasma cells, is characterized by widespread genomic heterogeneity and, consequently, differences in disease progression and drug response. Although recent large-scale sequencing studies have greatly improved our understanding of MM genomes, our knowledge about genomic structural variation in MM is attenuated due to the limitations of commonly used sequencing approaches. In this study, we present the application of optical mapping, a single-molecule, whole-genome analysis system, to discover new structural variants in a primary MM genome. Through our analysis, we have identified and characterized widespread structural variation in this tumor genome. Additionally, we describe our efforts toward comprehensive characterization of genome structure and variation by integrating our findings from optical mapping with those from DNA sequencing-based genomic analysis. Finally, by studying this MM genome at two time points during tumor progression, we have demonstrated an increase in mutational burden with tumor progression at all length scales of variation.

scholarly journals OptiDiff: structural variation detection from single optical mapping reads

2022 ◽  
Author(s):  
Mehmet Akdel ◽  
Dick de Ridder
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Optical Mapping ◽  
Cost Effective ◽  
Sequencing Data ◽  
Mapping Technology ◽  
Cost Effective Alternative ◽  
Algorithmic Approaches ◽  
Broad Interest

Detecting structural variation (SV) in eukaryotic genomes is of broad interest due to its often dramatic phenotypic effects, but remains a major, costly challenge based on DNA sequencing data. A cost-effective alternative in detecting large-scale SV has become available with advances in optical mapping technology. However, the algorithmic approaches to identifying SVs from optical mapping data are limited. Here, we propose a novel, open-source SV detection tool, OptiDiff, which employs a single molecule based approach to detect and classify homozygous and heterozygous SVs at coverages as low as 20x, showing better performance than the state of the art.

scholarly journals Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level

2017 ◽  
Author(s):  
Yuxuan Yuan ◽  
Zbyněk Milec ◽  
Philipp E. Bayer ◽  
Jan Vrána ◽  
Jaroslav Doležel ◽  
...  
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Optical Mapping ◽  
Subterranean Clover ◽  
Structural Variations ◽  
Recognition Sequence ◽  
Nucleotide Level ◽  
Total Size ◽  
Short Reads ◽  
A Genome

AbstractWhole genome sequencing has been widely used to detect structural variations (SVs). However, the limited single molecule size makes it difficult to characterize large-scale SVs in a genome because they cannot fully cover such vast and complex regions. Recently, optical mapping in nanochannels has provided novel resolution to detect large-scale SVs by comparing the physical location of the nickase recognition sequence in genomes. Other than in humans, SVs discovered in plants by optical mapping have not been validated. To assess the accuracy of SV calling in plants by optical mapping, we selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The SVs discovered by BioNano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

CONTRIBUTION OF DNA COPY-NUMBER VARIATION (CNV) TO CANCER SUSCEPTIBILITY AND LARGE-SCALE GENOME ALTERATIONS IN OSTEOSARCOMA (OS)

2008 ◽  
Vol 31 (4) ◽  
pp. 19
Author(s):  
I Pasic ◽  
A Shlien ◽  
A Novokmet ◽  
C Zhang ◽  
U Tabori ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Large Scale ◽  
Structural Variation ◽  
Age Of Onset ◽  
Cancer Susceptibility ◽  
Small Sample Size ◽  
Snp Array ◽  
Tumour Suppressor Gene ◽  
Small Sample ◽  
International Hapmap Project

Introduction: OS, a common Li-Fraumeni syndrome (LFS)-associated neoplasm, is a common bone malignancy of children and adolescents. Sporadic OS is also characterized by young age of onset and high genomic instability, suggesting a genetic contribution to disease. This study examined the contribution of novel DNA structural variation elements, CNVs, to OS susceptibility. Given our finding of excessive constitutional DNA CNV in LFS patients, which often coincide with cancer-related genes, we hypothesized that constitutional CNV may also provide clues about the aetiology of LFS-related sporadic neoplasms like OS. Methods: CNV in blood DNA of 26 patients with sporadic OS was compared to that of 263 normal control samples from the International HapMap project, as well as 62 local controls. Analysis was performed on DNA hybridized to Affymetrix genome-wide human SNP array 6.0 by Partek Genomic Suite. Results: There was no detectable difference in average number of CNVs, CNV length, and total structural variation (product of average CNV number and length) between individuals with OS and controls. While this data is preliminary (small sample size), it argues against the presence of constitutional genomic instability in individuals with sporadic OS. Conclusion: We found that the majority of tumours from patients with sporadic OS show CN loss at chr3q13.31, raising the possibility that chr3q13.31 may represent a “driver” region in OS aetiology. In at least one OS tumour, which displays CN loss at chr3q13.31, we demonstrate decreased expression of a known tumour suppressor gene located at chr3q13.31. We are investigating the role ofchr3q13.31 in development of OS.

scholarly journals MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment

2018 ◽  
Vol 35 (15) ◽  
pp. 2671-2673 ◽  
Author(s):  
Josephine Burgin ◽  
Corentin Molitor ◽  
Fady Mohareb
Keyword(s):  
Large Scale ◽  
Optical Mapping ◽  
Java Virtual Machine ◽  
Supplementary Information ◽  
Desktop Computer ◽  
Draft Assembly ◽  
Simple Alternative ◽  
Mapping Analysis ◽  
Cross Platform ◽  
Genomic Map

Abstract Summary Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualization are limited to use on a Windows operating system or are developed initially for visualizing large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualize and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research. Availability and implementation MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals svtools: population-scale analysis of structural variation

2019 ◽  
Vol 35 (22) ◽  
pp. 4782-4787 ◽  
Author(s):  
David E Larson ◽  
Haley J Abel ◽  
Colby Chiang ◽  
Abhijit Badve ◽  
Indraniel Das ◽  
...  
Keyword(s):  
Large Scale ◽  
Structural Variation ◽  
Human Genetics ◽  
Mobile Element ◽  
Supplementary Information ◽  
Joint Analysis ◽  
Human Populations ◽  
Scale Analysis ◽  
Human Genomes ◽  
Variant Detection

Abstract Summary Large-scale human genetics studies are now employing whole genome sequencing with the goal of conducting comprehensive trait mapping analyses of all forms of genome variation. However, methods for structural variation (SV) analysis have lagged far behind those for smaller scale variants, and there is an urgent need to develop more efficient tools that scale to the size of human populations. Here, we present a fast and highly scalable software toolkit (svtools) and cloud-based pipeline for assembling high quality SV maps—including deletions, duplications, mobile element insertions, inversions and other rearrangements—in many thousands of human genomes. We show that this pipeline achieves similar variant detection performance to established per-sample methods (e.g. LUMPY), while providing fast and affordable joint analysis at the scale of ≥100 000 genomes. These tools will help enable the next generation of human genetics studies. Availability and implementation svtools is implemented in Python and freely available (MIT) from https://github.com/hall-lab/svtools. Supplementary information Supplementary data are available at Bioinformatics online.

National survey of viruses in pastures of subterranean clover. II. Statistical methodology for large scale quantitative ELISA

1993 ◽  
Vol 44 (8) ◽  
pp. 1863
Author(s):  
WJ Muller ◽  
K Helms ◽  
PM Waterhouse
Keyword(s):  
Large Scale ◽  
Time Course ◽  
Alfalfa Mosaic Virus ◽  
Subterranean Clover ◽  
Plant Sample ◽  
Statistical Methodology ◽  
Plate Design ◽  
Field Samples ◽  
Healthy Control ◽  
Sole Criterion

Statistical methodology was applied to a survey of time-course incidence of four viruses (alfalfa mosaic virus, clover yellow vein virus, subterranean clover mottle virus and subterranean clover red leaf virus) in improved pastures in southern regions of Australia, with samplings in each winter and spring over 3 years. The 100 samples per paddock collected at each time of sampling provided detection probabilities of 0.63 and 0.87 for 1% and 2% infection respectively. A microtitre plate design for ELISA was developed to include 60 field samples, 10 glasshouse-grown healthy control samples and 6 glasshouse-grown samples infected with the virus under examination. This design was used on 816 plates for each of the four viruses tested. The method used for identification of virus in sap of a plant sample from a particular paddock was that the ELISA reading was both significantly greater than healthy control readings, and an outlier in the distribution of readings of all sap samples from that paddock. It is argued that as the identification of uninfected samples as infected was highly unlikely, this double criterion method was superior to the use of each criterion separately. Use of significance above healthy control values as the sole criterion would have increased virus incidences by about 60%; use of outlier identification as the sole criterion would have increased virus incidences by about 30%. A generalized linear model with binomial errors and logit link was used for adjusting the virus incidences reported in the previous paper (Helms et al. 1993) for biases due to paddocks and/or districts not sampled on some occasions. This adjustment slightly increased overall incidences in all but one sampling and confirmed the time-course increase in incidence over the 3 years of the survey. The same model also proved to be the most appropriate for investigating the effects of year, season and district on virus incidence.

Large-Scale 3D Optical Mapping and Quantitative Analysis of Nanoparticle Distribution in Tumor Vascular Microenvironment

2020 ◽  
Vol 31 (7) ◽  
pp. 1784-1794 ◽  
Author(s):  
Dong-Jun Koo ◽  
Jinahn Choi ◽  
Minchul Ahn ◽  
Benjamin H. Ahn ◽  
Dal-Hee Min ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Large Scale ◽  
Optical Mapping ◽  
Nanoparticle Distribution

Virus diseases of annual pasture legumes: incidences, losses, epidemiology, and management

2012 ◽  
Vol 63 (5) ◽  
pp. 399 ◽  
Author(s):  
Roger A. C. Jones
Keyword(s):  
Large Scale ◽  
Current Knowledge ◽  
Subterranean Clover ◽  
Summer Rainfall ◽  
Virus Diseases ◽  
Pasture Legumes ◽  
Improvement Programs ◽  
Annual Medics ◽  
Grazed Swards ◽  
Pasture Legume

This paper reviews current knowledge concerning the occurrence, losses caused, epidemiology, and management of virus diseases of annual pasture legumes. The viruses commonly present are spread by contact, or aphid vectors either non-persistently or persistently. Whether they are seed-borne and their means of transmission are critical factors determining their incidences within pastures in climatic zones with dry summers or substantial summer rainfall. Large-scale national or state surveys of subterranean clover pastures revealed that some viruses reach high infection incidences. Contamination with seed-borne viruses was widespread in plots belonging to annual pasture legume improvement programs and seed stocks of subterranean clover, annual medics, and alternative annual pasture legumes, and in commercial annual medic seed stocks. Yield loss studies with grazed swards were completed for three common viruses: two in subterranean clover and one in annual medics. These studies demonstrated considerable virus-induced losses in herbage and seed yields, and established that virus infection causes deteriorated pastures with high weed contents even when foliar symptoms are mild. Comprehensive integrated disease management tactics involving phytosanitary, cultural, chemical, or host resistance measures were devised for these three viruses in infected pastures, and for seed-borne viruses in annual pasture legume improvement programs. Several other viruses are potentially important, but, with these, quantification of losses caused in grazed swards is lacking and information on incidences in pastures is currently insufficient. Critical research and development gaps that need addressing are identified.

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