scholarly journals Canine Genetics and Genomics

2021 ◽  
Author(s):  
Edo D’Agaro ◽  
Andrea Favaro ◽  
Davide Rosa
Keyword(s):  
Heart Disease ◽  
Next Generation Sequencing ◽  
Genomic Data ◽  
Behavioral Traits ◽  
Canine Genetics ◽  
Genome Wide ◽  
Tremendous Progress ◽  
Dog Breed ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

In the past fifteen years, tremendous progress has been made in dog genomics. Several genetic aspects of cancer, heart disease, hip dysplasia, vision and hearing problems in dogs have been investigated and studied in detail. Genome-wide associative studies have made it possible to identify several genes associated with diseases, morphological and behavioral traits. The dog genome contains an extraordinary amount of genetic variability that distinguishes the different dog breeds. As a consequence of the selective programs, applied using stringent breed standards, each dog breed represents, today, a population isolated from the others. The availability of modern next generation sequencing (NGS) techniques and the identification of millions of single functional mutations (SNPs) has enabled us to obtain new and unknown detailed genomic data of the different breeds.

scholarly journals Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

2017 ◽  
Author(s):  
Claire Marchal ◽  
Takayo Sasaki ◽  
Daniel Vera ◽  
Korey Wilson ◽  
Jiao Sima ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Replication Timing ◽  
Nucleotide Polymorphisms ◽  
Robust Methods ◽  
Next Generation ◽  
Single Nucleotide ◽  
Cellular Processes ◽  
Genome Wide ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACTCycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease. Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a rapid, robust and relatively inexpensive protocol to analyze genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing RT allelic asynchrony, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.

scholarly journals Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 92 ◽  
Author(s):  
Shannon J. McKie ◽  
Anthony Maxwell ◽  
Keir C. Neuman
Keyword(s):  
Next Generation Sequencing ◽  
Dna Cleavage ◽  
Next Generation ◽  
Dna Breaks ◽  
Genome Wide ◽  
Extension Activity ◽  
Nucleotide Resolution ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) platforms have been adapted to generate genome-wide maps and sequence context of binding and cleavage of DNA topoisomerases (topos). Continuous refinements of these techniques have resulted in the acquisition of data with unprecedented depth and resolution, which has shed new light on in vivo topo behavior. Topos regulate DNA topology through the formation of reversible single- or double-stranded DNA breaks. Topo activity is critical for DNA metabolism in general, and in particular to support transcription and replication. However, the binding and activity of topos over the genome in vivo was difficult to study until the advent of NGS. Over and above traditional chromatin immunoprecipitation (ChIP)-seq approaches that probe protein binding, the unique formation of covalent protein–DNA linkages associated with DNA cleavage by topos affords the ability to probe cleavage and, by extension, activity over the genome. NGS platforms have facilitated genome-wide studies mapping the behavior of topos in vivo, how the behavior varies among species and how inhibitors affect cleavage. Many NGS approaches achieve nucleotide resolution of topo binding and cleavage sites, imparting an extent of information not previously attainable. We review the development of NGS approaches to probe topo interactions over the genome in vivo and highlight general conclusions and quandaries that have arisen from this rapidly advancing field of topoisomerase research.

scholarly journals Detection and validation of six pathogenic variants in Chinese inherited heart disease patients using clinical whole-exome sequencing

2021 ◽  
Author(s):  
Lichao Cao ◽  
Fei Ye ◽  
Shuqi Xie ◽  
Ying Ba ◽  
Ying Zeng ◽  
...  
Keyword(s):  
Heart Disease ◽  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Sanger Sequencing ◽  
Targeted Next Generation Sequencing ◽  
Pathogenic Variants ◽  
Whole Exome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The targeted next-generation sequencing (NGS) was employed in detecting the pathogenic mutations in inherited heart disease patients in the present study. Two main methods, the NGS and the classic Sanger sequencing, were used in this study. And, the whole-exome sequencing (WES) was specifically used in this study.

scholarly journals SnakeChunks: modular blocks to build Snakemake workflows for reproducible NGS analyses

2017 ◽  
Author(s):  
Claire Rioualen ◽  
Lucie Charbonnier-Khamvongsa ◽  
Jacques van Helden
Keyword(s):  
Next Generation Sequencing ◽  
Life Sciences ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Rna Seq ◽  
Genome Wide ◽  
Domains Of Life ◽  
Supplementary Material ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractSummaryNext-Generation Sequencing (NGS) is becoming a routine approach for most domains of life sciences, yet there is a crucial need to improve the automation of processing for the huge amounts of data generated and to ensure reproducible results. We present SnakeChunks, a collection of Snakemake rules enabling to compose modular and user-configurable workflows, and show its usage with analyses of transcriptome (RNA-seq) and genome-wide location (ChIP-seq) data.AvailabilityThe code is freely available (github.com/SnakeChunks/SnakeChunks), and documented with tutorials and illustrative demos (snakechunks.readthedocs.io)[email protected], [email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6303 ◽  
Author(s):  
Yafei Mao
Keyword(s):  
Next Generation Sequencing ◽  
Evolutionary Biology ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genomic Data ◽  
Whole Genome ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Generation Sequencing

Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.

scholarly journals GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

2018 ◽  
Author(s):  
Yafei Mao ◽  
Noriyuki Satoh
Keyword(s):  
Next Generation Sequencing ◽  
Evolutionary Biology ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genomic Data ◽  
Whole Genome ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Generation Sequencing

ABSTRACTUnderstanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for robust and accurate tools to detect WGD. Here, we present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. We have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.

scholarly journals Can Genomics Remove Uncertainty from Adoption? Social Workers’ and Medical Advisors’ Accounts of Genetic Testing

2021 ◽  
Author(s):  
Michael Arribas-Ayllon ◽  
Katherine Shelton ◽  
Angus Clarke
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Social Workers ◽  
Genetic Information ◽  
Medical Professionals ◽  
High Quality ◽  
Genome Wide ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Wide Testing

Abstract Genetic testing is controversial in adoption with professionals taking different positions on whether children should be protected from genetic information or whether it can be used to assist adoption. In this article, we argue that advances in ‘genome-wide’ testing add further complications to these debates. Although next-generation sequencing (NGS) and microarray-based technologies can offer high-quality molecular diagnoses for a variety of conditions, they also increase the burden of interpretation. For these reasons, adoption professionals will need to understand the relevance and complexity of biomedical information. Our study explores the accounts of social workers’ and medical advisors’ knowledge and reasoning about genetic testing in adoption. Twenty participants, including social workers, managers, medical advisors and paediatricians, were recruited from adoption services in England and Wales. A key finding revealed that medical professionals reported increasing pressure to test children prior to adoption, whilst social workers justified testing on the basis that it reduced uncertainty and therefore assisted adoption. Professionals’ accounts of genetic testing suggest that social workers may not be aware of the potential indeterminacy of microarray and NGS technologies. This has important implications for adoption because increases in genomic uncertainty can stigmatise children and disadvantage their prospects for adoption.

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