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 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 Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments

2021 ◽  
Author(s):  
Brian P. Anton ◽  
Alexey Fomenkov ◽  
Victoria Wu ◽  
Richard J. Roberts
Keyword(s):  
Single Molecule ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Specific Sequence ◽  
Genome Wide ◽  
Cost Effective Alternative ◽  
Simple Column ◽  
Sequencing Platforms

ABSTRACTSingle-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that “write” these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

scholarly journals Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0247541
Author(s):  
Brian P. Anton ◽  
Alexey Fomenkov ◽  
Victoria Wu ◽  
Richard J. Roberts
Keyword(s):  
Single Molecule ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Specific Sequence ◽  
Genome Wide ◽  
Cost Effective Alternative ◽  
Simple Column ◽  
Sequencing Platforms

Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that “write” these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

scholarly journals The High Capacity Expanding Lifeboat HiCEL – Meeting the Modern SAR Challenge

2018 ◽  
Author(s):  
J R E Wright ◽  
G E Payne
Keyword(s):  
Large Scale ◽  
High Capacity ◽  
Cost Effective ◽  
Second World War ◽  
Concept Design ◽  
Small Vessels ◽  
Large Numbers ◽  
Cost Effective Alternative ◽  
Operational Envelope ◽  
Second World

The Mediterranean migrant crisis has resulted in the highest population displacement since the Second World War. In 2016 alone, over one million made the journey across the sea. Since 2013 over 15,000 have died as a result of this journey. Small vessels such as wooden fishing boats and RIBs are commonly used by smugglers as transport. These are often unseaworthy and filled with numbers of passengers far exceeding their intended capacity. When failure occurs, rescues are typically conducted by the nearest available vessel. These vessels are often ill-equipped for a large-scale Search and Rescue (SAR) operation making it highly dangerous for all involved.  The size and quantity of lifeboats available are often insufficient for the large numbers of people to be rescued; as a result, repeat journeys are required, making the rescue process slow, inefficient and hazardous. This paper outlines a novel solution to this problem. A concept design is presented for a rapidly expandable lifeboat capable of holding large numbers of passengers, whilst still fitting into the operational envelope of common davits. The unique inflatable design can be deployed quickly from a range of vessels and aeroplanes offering an immediate platform from which disembarkation onto a suitable vessel can be achieved. CONOPS are outlined along with the required capabilities of the design. Drop stitch technology is identified as a viable means of manufacturing the large inflatable platforms. Finally, the paper discusses an alternative solution, retrofitting existing enclosed lifeboats with the solution to offer a more cost-effective alternative.  

scholarly journals Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly

2020 ◽  
Author(s):  
Xuefang Zhao ◽  
Ryan L. Collins ◽  
Wan-Ping Lee ◽  
Alexandra M. Weber ◽  
Yukyung Jun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Human Genetics ◽  
Clinical Diagnostics ◽  
Added Value ◽  
Mendelian Disease ◽  
Segmental Duplications ◽  
Genomic Context ◽  
Long Read

AbstractVirtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and emerging clinical diagnostic approaches utilize short-reads (srWGS), which present constraints for genome-wide discovery of structural variants (SVs). Alternative long-read single molecule technologies (lrWGS) offer significant advantages for genome assembly and SV detection, while these technologies are currently cost prohibitive for large-scale disease studies and clinical diagnostics (∼5-12X higher cost than comparable coverage srWGS). Moreover, only dozens of such genomes are currently publicly accessible by comparison to millions of srWGS genomes that have been commissioned for international initiatives. Given this ubiquitous reliance on srWGS in human genetics and genomics, we sought to characterize and quantify the properties of SVs accessible to both srWGS and lrWGS to establish benchmarks and expectations in ongoing medical and population genetic studies, and to project the added value of SVs uniquely accessible to each technology. In analyses of three trios with matched srWGS and lrWGS from the Human Genome Structural Variation Consortium (HGSVC), srWGS captured ∼11,000 SVs per genome using reference-based algorithms, while haplotype-resolved assembly from lrWGS identified ∼25,000 SVs per genome. Detection power and precision for SV discovery varied dramatically by genomic context and variant class: 9.7% of the current GRCh38 reference is defined by segmental duplications (SD) and simple repeats (SR), yet 91.4% of deletions that were specifically discovered by lrWGS localized to these regions. Across the remaining 90.3% of the human reference, we observed extremely high concordance (93.8%) for deletions discovered by srWGS and lrWGS after error correction using the raw lrWGS reads. Conversely, lrWGS was superior for detection of insertions across all genomic contexts. Given that the non-SD/SR sequences span 90.3% of the GRCh38 reference, and encompass 95.9% of coding exons in currently annotated disease associated genes, improved sensitivity from lrWGS to discover novel and interpretable pathogenic deletions not already accessible to srWGS is likely to be incremental. However, these analyses highlight the added value of assembly-based lrWGS to create new catalogues of functional insertions and transposable elements, as well as disease associated repeat expansions in genomic regions previously recalcitrant to routine assessment.

scholarly journals Implications for industrial application of bioflocculant demand alternatives to conventional media: waste as a substitute

2019 ◽  
Vol 80 (10) ◽  
pp. 1807-1822
Author(s):  
Jibrin Ndejiko Mohammed ◽  
Wan Rosmiza Zana Wan Dagang
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Culture Conditions ◽  
Limiting Factor ◽  
Nutrient Sources ◽  
Cheap Alternative ◽  
Cost Effective Alternative ◽  
Pre Treatment ◽  
Microbial Flocculant ◽  
The Cost

Abstract The biodegradability and safety of the bioflocculants make them a potential alternative to non-biodegradable chemical flocculants for wastewater treatment. However, low yield and production cost has been reported to be the limiting factor for large scale bioflocculant production. Although the utilization of cheap nutrient sources is generally appealing for large scale bioproduct production, exploration to meet the demand for them is still low. Although much progress has been achieved at laboratory scale, Industrial production and application of bioflocculant is yet to be viable due to cost of the production medium and low yield. Thus, the prospects of bioflocculant application as an alternative to chemical flocculants is linked to evaluation and utilization of cheap alternative and renewable nutrient sources. This review evaluates the latest literature on the utilization of waste/wastewater as an alternative substitute for conventional expensive nutrient sources. It focuses on the mechanisms and metabolic pathways involved in microbial flocculant synthesis, culture conditions and nutrient requirements for bioflocculant production, pre-treatment, and also optimization of waste substrate for bioflocculant synthesis and bioflocculant production from waste and their efficiencies. Utilization of wastes as a microbial nutrient source drastically reduces the cost of bioflocculant production and increases the appeal of bioflocculant as a cost-effective alternative to chemical flocculants.

scholarly journals Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1444
Author(s):  
Nazeefa Fatima ◽  
Anna Petri ◽  
Ulf Gyllensten ◽  
Lars Feuk ◽  
Adam Ameur
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Single Molecule ◽  
Large Scale ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Human Samples

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

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

Measuring Satisfaction With Standard Survey Instruments and Single-Button Responses on Kiosks

2018 ◽  
Vol 62 (1) ◽  
pp. 1429-1433 ◽  
Author(s):  
Laura R. Rabbitt ◽  
Jacob A. Hasselgren ◽  
Cynthia Cook ◽  
Yevgeniy B. Sirotin
Keyword(s):  
User Satisfaction ◽  
Large Scale ◽  
Cost Effective ◽  
Strongly Correlated ◽  
Alternative Technologies ◽  
Large Scale Testing ◽  
System Usability Scale ◽  
Efficiency And Effectiveness ◽  
Survey Instruments ◽  
Cost Effective Alternative

User satisfaction with a technology is an essential usability metric. Unlike efficiency and effectiveness, which are generally recorded during use, satisfaction is often measured subsequently using questionnaires, such as the modified version of the system usability scale (MSUS). This makes satisfaction the most costly usability measure to acquire in large-scale testing. To mitigate this cost, we compared the performance of a four-button kiosk with a standard SUS instrument for measuring satisfaction. Three hundred and fifty four demographically diverse subjects used the kiosk and completed a SUS questionnaire immediately after using one of two different alternative technologies. Kiosk ratings took only 11.43 ( sd = 7.30) seconds on average to collect, much faster than 1200 seconds on average for the SUS. Kiosk ratings and MSUS scores were strongly correlated ( r = 0.62, p < .005), showing the same pattern of differences between the tested technologies. However, the index of dispersion for kiosk ratings was 71.74% larger than for MSUS scores. We conclude that satisfaction kiosks are a cost-effective alternative for measuring satisfaction in usability studies with large sample sizes.

scholarly journals SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes derived data

2021 ◽  
Author(s):  
Jessie J.F. Medeiros ◽  
Jose-Mario Capo-Chichi ◽  
Liran I. Shlush ◽  
John E. Dick ◽  
Andrea Arruda ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genetic Research ◽  
Cost Effective ◽  
Data Interpretation ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Targeted Next Generation Sequencing ◽  
Wide Scale ◽  
Molecular Inversion Probes ◽  
Derived Data

Single-molecule molecular inversion probes (smMIPs) provides a modular and cost-effective platform for high-multiplex targeted next-generation sequencing (NGS). Nevertheless, translating the raw smMIP-derived sequencing data into accurate and meaningful information currently requires proficient computational skills and a large amount of computational work, prohibiting wide-scale adoption of smMIP-based technologies. To enable easy, efficient, and accurate interrogation of smMIP-derived data, we developed SmMIP-tools, a computational toolset that combines the critical analytic steps for smMIP data interpretation into a single computational pipeline. Here, we describe in detail two of the software's major components. The first is a read processing tool that performs quality control steps, generates read-smMIP linkages and retrieves molecular tags. The second is an error-aware variant caller capable of detecting single nucleotide variants (SNVs) and short insertions and deletions (indels). Using a cell-line DNA dilution series and a cohort of blood cancer patients, we benchmarked SmMIP-tools and evaluated its performance against clinical sequencing reports. We anticipate that SmMIP-tools will increase accessibility to smMIP-technology, enabling cost-effective genetic research to push personalized medicine forward.

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