scholarly journals A chaotic viewpoint-based approach to solve haplotype assembly using hypergraph model

2020 ◽  
Author(s):  
Mohammad Hossein Olyaee ◽  
Alireza Khanteymoori ◽  
Khosrow Khalifeh
Keyword(s):  
Huge Amount ◽  
Chaos Game Representation ◽  
Haplotype Assembly ◽  
Hypergraph Partitioning ◽  
Sequencing Technologies ◽  
Hypergraph Model ◽  
Polyploid Form ◽  
High Throughput Dna Sequencing ◽  
The Cost ◽  
Weighted Hypergraph

AbstractDecreasing the cost of high-throughput DNA sequencing technologies, provides a huge amount of data that enables researchers to determine haplotypes for diploid and polyploid organisms. Although various methods have been developed to reconstruct haplotypes in diploid form, their accuracy is still a challenging task. Also, most of the current methods cannot be applied to polyploid form. In this paper, an iterative method is proposed, which employs hypergraph to reconstruct haplotype. The proposed method by utilizing chaotic viewpoint can enhance the obtained haplotypes. For this purpose, a haplotype set was randomly generated as an initial estimate, and its consistency with the input fragments was described by constructing a weighted hypergraph. Partitioning the hypergraph specifies those positions in the haplotype set that need to be corrected. This procedure is repeated until no further improvement could be achieved. Each element of the finalized haplotype set is mapped to a line by chaos game representation, and a coordinate series is defined based on the position of mapped points. Then, some positions with low qualities can be assessed by applying a local projection. Experimental results on both simulated and real datasets demonstrate that this method outperforms most other approaches, and is promising to perform the haplotype assembly.

scholarly journals Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 65
Author(s):  
Patricia Haug ◽  
Samuel Koller ◽  
Jordi Maggi ◽  
Elena Lang ◽  
Silke Feil ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Screening ◽  
De Novo ◽  
Efficient Tool ◽  
Sequencing Technologies ◽  
Whole Exome ◽  
Screening And Identification ◽  
High Throughput Dna Sequencing ◽  
New Mutations

Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.

scholarly journals From Genetics to Genomics of Epilepsy

2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Silvio Garofalo ◽  
Marisa Cornacchione ◽  
Alfonso Di Costanzo
Keyword(s):  
Dna Sequencing ◽  
Dna Microarrays ◽  
Molecular Cytogenetics ◽  
Entire Genome ◽  
Sequencing Technologies ◽  
Genomic Approach ◽  
Molecular Karyotype ◽  
High Throughput Dna Sequencing ◽  
Laboratory Technology ◽  
Near Future

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.

scholarly journals A phylogenetic transform enhances analysis of compositional microbiota data

2016 ◽  
Author(s):  
Justin D Silverman ◽  
Alex Washburne ◽  
Sayan Mukherjee ◽  
Lawrence A David
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Dominant Role ◽  
Phylogenetic Information ◽  
Abundance Data ◽  
Sequencing Technologies ◽  
Environmental Selection ◽  
Health And Disease ◽  
High Throughput Dna Sequencing ◽  
Spurious Results

ABSTRACTHigh-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbiota surveys reflect the relative abundance of bacterial taxa and not their absolute levels. It is well known that applying common statistical methods, such as correlation or hypothesis testing, to relative abundance data can lead to spurious results. Here, we introduce the PhILR transform, a data transform that utilizes microbial phylogenetic information. This transform enables off-the-shelf statistical tools to be applied to microbiota surveys free from artifacts usually associated with analysis of relative abundance data. Using environmental and human-associated microbial community datasets as benchmarks, we find that the PhILR transform significantly improves the performance of distance-based and machine learning-based statistics, boosting the accuracy of widely used algorithms on reference benchmarks by 90%. Because the PhILR transform relies on bacterial phylogenies, statistics applied in the PhILR coordinate system are also framed within an evolutionary perspective. Regression on PhILR transformed human microbiota data identified evolutionarily neighboring bacterial clades that may have differentiated to adapt to distinct body sites. Variance statistics showed that the degree of covariation of bacterial clades across human body sites tended to increase with phylogenetic relatedness between clades. These findings support the hypothesis that environmental selection, not competition between bacteria, plays a dominant role in structuring human-associated microbial communities.

scholarly journals LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

2021 ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Plant Genome ◽  
Plant Genomics ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Tissue Samples ◽  
Sequencing Technologies ◽  
The Cost ◽  
New Generation

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

scholarly journals Population Genomic- and Phylogenomic-Enabled Advances to Increase Insight Into Pathogen Biology and Epidemiology

2021 ◽  
Vol 111 (1) ◽  
pp. 8-11
Author(s):  
Remco Stam ◽  
Pierre Gladieux ◽  
Boris A. Vinatzer ◽  
Erica M. Goss ◽  
Neha Potnis ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Genomics ◽  
Cost Effective ◽  
Whole Genome ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Population Genomic ◽  
High Throughput Dna Sequencing ◽  
Opening Up ◽  
Insight Into

Population genetics has been a key discipline in phytopathology for many years. The recent rise in cost-effective, high-throughput DNA sequencing technologies, allows sequencing of dozens, if not hundreds of specimens, turning population genetics into population genomics and opening up new, exciting opportunities as described in this Focus Issue . Without the limitations of genetic markers and the availability of whole or near whole-genome data, population genomics can give new insights into the biology, evolution and adaptation, and dissemination patterns of plant-associated microbes.

scholarly journals HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

2016 ◽  
Vol 27 (5) ◽  
pp. 801-812 ◽  
Author(s):  
Peter Edge ◽  
Vineet Bafna ◽  
Vikas Bansal
Keyword(s):  
Haplotype Assembly ◽  
Sequencing Technologies

scholarly journals Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 858 ◽  
Author(s):  
Krehenwinkel ◽  
Pomerantz ◽  
Prost
Keyword(s):  
Dna Sequencing ◽  
Biodiversity Loss ◽  
Taxonomic Composition ◽  
Great Promise ◽  
Sequencing Platform ◽  
Biological Communities ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Sequencing Studies ◽  
High Throughput Dna Sequencing

We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development.

Fragment Re-Allocation Strategy Based on Hypergraph for NoSQL Database Systems

2016 ◽  
Vol 8 (3) ◽  
pp. 1-23 ◽  
Author(s):  
Zhikun Chen ◽  
Shuqiang Yang ◽  
Yunfei Shang ◽  
Yong Liu ◽  
Feng Wang ◽  
...  
Keyword(s):  
Database Systems ◽  
Communication Cost ◽  
Allocation Strategy ◽  
Hypergraph Partitioning ◽  
Computing Model ◽  
Operation Pattern ◽  
Nosql Database ◽  
High Scalability ◽  
Weighted Hypergraph ◽  
Allocation Strategies

NoSQL database is famed for the characteristics of high scalability, high availability, and high fault-tolerance. It is used to manage data for a lot of applications. The computing model has been transferred to “computing close to data”. Therefore, the location of fragment directly affects system's performance. Every site's load dynamical changes because of the increasing data and the ever-changing operation pattern. So system has to re-allocate fragment to improve system's performance. The general fragment re-allocation strategies of NoSQL database scatter the related fragments as possible to improve the operations' parallel degree. But those fragments may interact with each other in some application's operations. So the high parallel degree of operation may increase system's communication cost such as data are transferred by network. In this paper, the authors propose a fragment re-allocation strategy based on hypergraph. This strategy uses a weighted hypergraph to represent the fragments' access pattern of operations. A hypergraph partitioning algorithm is used to cluster fragments in the strategy. This strategy can improve system's performance according to reducing the communication cost while guaranteeing the parallel degree of operations. Experimental results confirm that the strategy will effectively contribute in solving fragment re-allocation problem in specific application environment of NoSQL database system, and it can improve system's performance.

scholarly journals A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples

2001 ◽  
Vol 11 (3) ◽  
pp. 441-447
Author(s):  
Jonathan Nakane ◽  
David Broemeling ◽  
Roger Donaldson ◽  
Andre Marziali ◽  
Thomas D. Willis ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Thermal Cycling ◽  
High Throughput ◽  
Dna Analysis ◽  
Detection Efficiency ◽  
Large Fraction ◽  
Cycle Sequencing ◽  
High Throughput Dna Sequencing ◽  
Reaction Volumes ◽  
The Cost

A large fraction of the cost of DNA sequencing and other DNA-analysis processes results from the reagent costs incurred during cycle sequencing or PCR. In particular, the high cost of the enzymes and dyes used in these processes often results in thermal cycling costs exceeding $0.50 per sample. In the case of high-throughput DNA sequencing, this is a significant and unnecessary expense. Improved detection efficiency of new sequencing instrumentation allows the reaction volumes for cycle sequencing to be scaled down to one-tenth of presently used volumes, resulting in at least a 10-fold decrease in the cost of this process. However, commercially available thermal cyclers and automated reaction setup devices have inherent design limitations which make handling volumes of <1 μL extremely difficult. In this paper, we describe a method for thermal cycling aimed at reliable, automated cycling of submicroliter reaction volumes.

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