scholarly journals Restriction Enzyme Based Enriched L1Hs Sequencing (REBELseq): A Scalable Technique for Detection of Ta Subfamily L1Hs in the Human Genome

2020 ◽  
Vol 10 (5) ◽  
pp. 1647-1655
Author(s):  
Benjamin C. Reiner ◽  
Glenn A. Doyle ◽  
Andrew E. Weller ◽  
Rachel N. Levinson ◽  
Esin Namoglu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Postmortem Brain ◽  
Whole Genome ◽  
Mobile Dna ◽  
Neuronal Nuclei ◽  
Dna Elements ◽  
Long Interspersed Element ◽  
Generation Sequencing ◽  
Human Specific

Long interspersed element-1 retrotransposons (LINE-1 or L1) are ∼6 kb mobile DNA elements implicated in the origins of many Mendelian and complex diseases. The actively retrotransposing L1s are mostly limited to the L1 human specific (L1Hs) transcriptional active (Ta) subfamily. In this manuscript, we present REBELseq as a method for the construction of Ta subfamily L1Hs-enriched next-generation sequencing libraries and bioinformatic identification. REBELseq was performed on DNA isolated from NeuN+ neuronal nuclei from postmortem brain samples of 177 individuals and empirically-driven bioinformatic and experimental cutoffs were established. Putative L1Hs insertions passing bioinformatics cutoffs were experimentally validated. REBELseq reliably identified both known and novel Ta subfamily L1Hs insertions distributed throughout the genome. Differences in the proportion of individuals possessing a given reference or non-reference retrotransposon insertion were identified. We conclude that REBELseq is an unbiased, whole genome approach to the amplification and detection of Ta subfamily L1Hs retrotransposons.

scholarly journals Restriction Enzyme Based Enriched L1Hs sequencing (REBELseq)

2019 ◽  
Author(s):  
Benjamin C. Reiner ◽  
Glenn A. Doyle ◽  
Andrew E. Weller ◽  
Rachel N. Levinson ◽  
Esin Namoglu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Postmortem Brain ◽  
Whole Genome ◽  
Mobile Dna ◽  
Neuronal Nuclei ◽  
Dna Elements ◽  
Long Interspersed Element ◽  
Generation Sequencing ◽  
Human Specific

AbstractLong interspersed element-1 retrotransposons (LINE-1 or L1) are ~6 kb mobile DNA elements implicated in the origins of many Mendelian and complex diseases. The actively retrotransposing L1s are mostly limited to the L1 human specific Ta subfamily. In this manuscript, we present REBELseq as a method for the construction of differentially amplified next-generation sequencing libraries and bioinformatic identification of Ta subfamily long interspersed element-1 human specific elements. REBELseq was performed on DNA isolated from NeuN+ neuronal nuclei from postmortem brain samples of 177 individuals and empirically-driven bioinformatic and experimental cutoffs were established. REBELseq reliably identified both known and novel Ta subfamily L1 insertions distributed throughout the genome. Differences in the proportion of individuals possessing a given reference or non-reference retrotransposon insertion were identified. We conclude that REBELseq is an unbiased, whole genome approach to the amplification and detection of Ta subfamily L1 retrotransposons.

scholarly journals Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

scholarly journals Rapid whole-genome mutational profiling using next-generation sequencing technologies

2008 ◽  
Vol 18 (10) ◽  
pp. 1638-1642 ◽  
Author(s):  
D. R. Smith ◽  
A. R. Quinlan ◽  
H. E. Peckham ◽  
K. Makowsky ◽  
W. Tao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mutational Profiling ◽  
Generation Sequencing

High throughput crop genome genotyping by a combination of pool next generation sequencing and haplotype-based data processing

2021 ◽  
Author(s):  
Michael Schneider ◽  
Asis Shrestha ◽  
Agim Ballvora ◽  
Jens Leon
Keyword(s):  
Next Generation Sequencing ◽  
Allele Frequency ◽  
Frequency Estimation ◽  
Whole Genome ◽  
Next Generation ◽  
Conservation Genomics ◽  
High Coverage ◽  
Allele Frequency Estimation ◽  
Low Coverage ◽  
Generation Sequencing

Abstract BackgroundThe identification of environmentally specific alleles and the observation of evolutional processes is a goal of conservation genomics. By generational changes of allele frequencies in populations, questions regarding effective population size, gene flow, drift, and selection can be addressed. The observation of such effects often is a trade-off of costs and resolution, when a decent sample of genotypes should be genotyped for many loci. Pool genotyping approaches can derive a high resolution and precision in allele frequency estimation, when high coverage sequencing is utilized. Still, pool high coverage pool sequencing of big genomes comes along with high costs.ResultsHere we present a reliable method to estimate a barley population’s allele frequency at low coverage sequencing. Three hundred genotypes were sampled from a barley backcross population to estimate the entire population’s allele frequency. The allele frequency estimation accuracy and yield were compared for three next generation sequencing methods. To reveal accurate allele frequency estimates on a low coverage sequencing level, a haplotyping approach was performed. Low coverage allele frequency of positional connected single polymorphisms were aggregated to a single haplotype allele frequency, resulting in two to 271 times higher depth and increased precision. We compared different haplotyping tactics, showing that gene and chip marker-based haplotypes perform on par or better than simple contig haplotype windows. The comparison of multiple pool samples and the referencing against an individual sequencing approach revealed whole genome pool resequencing having the highest correlation to individual genotyping (up to 0.97), while transcriptomics and genotyping by sequencing indicated higher error rates and lower correlations.ConclusionUsing the proposed method allows to identify the allele frequency of populations with high accuracy at low cost. This is particularly interesting for conservation genomics in species with big genomes, like barley or wheat. Whole genome low coverage resequencing at 10x coverage can deliver a highly accurate estimation of the allele frequency, when a loci-based haplotyping approach is applied. Using annotated haplotypes allows to capitalize from biological background and statistical robustness.

scholarly journals DNA Methylation Landscape of 16 Canine Somatic Tissues by Methylation-Sensitive Restriction Enzyme-Based Next Generation Sequencing

2021 ◽  
Author(s):  
Jumpei Yamazaki ◽  
Yuki Matsumoto ◽  
Jaroslav Jelinek ◽  
Teita Ishizaki ◽  
Shingo Maeda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Companion Animals ◽  
Next Generation ◽  
Cpg Sites ◽  
Somatic Tissues ◽  
Methylation Sensitive Restriction Enzyme ◽  
Generation Sequencing

Abstract Background: DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Results: Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps from 16 somatic tissues. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (>70%, 52.5%-64.6% of all CpG sites analyzed) or unmethylated (<30%, 22.5%-28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Conclusions: Our study provides basic dataset for DNA methylation profiles in dogs.

scholarly journals Complete Genome Sequence of Matlo Bat Lyssavirus

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
Colyn S. Grobler ◽  
Jessica Coertse ◽  
Wanda Markotter
Keyword(s):  
South Africa ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Novel Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequencing Technologies ◽  
Generation Sequencing

ABSTRACT The genus Lyssavirus includes rabies virus as well as multiple diverse and recently described novel species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence of Matlo bat lyssavirus, which was isolated from a Natal long-fingered bat (Miniopterus natalensis) in South Africa.

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