scholarly journals Microsatellite Capture Sequencing

Genotyping ◽  
2018 ◽  
Author(s):  
Keisuke Tanaka ◽  
Rumi Ohtake ◽  
Saki Yoshida ◽  
Takashi Shinohara
Keyword(s):  
Capture Sequencing

scholarly journals The elusive parasite: comparing macroscopic, immunological, and genomic approaches to identifying malaria in human skeletal remains from Sayala, Egypt (third to sixth centuries AD)

2021 ◽  
Vol 13 (7) ◽  
Author(s):  
Alvie Loufouma Mbouaka ◽  
Michelle Gamble ◽  
Christina Wurst ◽  
Heidi Yoko Jäger ◽  
Frank Maixner ◽  
...  
Keyword(s):  
Diagnostic Tests ◽  
Sample Selection ◽  
Human Remains ◽  
Rapid Diagnostic Tests ◽  
Skeletal Remains ◽  
Pathological Changes ◽  
Human Skeletal Remains ◽  
The Past ◽  
A Site ◽  
Capture Sequencing

AbstractAlthough malaria is one of the oldest and most widely distributed diseases affecting humans, identifying and characterizing its presence in ancient human remains continue to challenge researchers. We attempted to establish a reliable approach to detecting malaria in human skeletons using multiple avenues of analysis: macroscopic observations, rapid diagnostic tests, and shotgun-capture sequencing techniques, to identify pathological changes, Plasmodium antigens, and Plasmodium DNA, respectively. Bone and tooth samples from ten individuals who displayed skeletal lesions associated with anaemia, from a site in southern Egypt (third to sixth centuries AD), were selected. Plasmodium antigens were detected in five of the ten bone samples, and traces of Plasmodium aDNA were detected in six of the twenty bone and tooth samples. There was relatively good synchronicity between the biomolecular findings, despite not being able to authenticate the results. This study highlights the complexity and limitations in the conclusive identification of the Plasmodium parasite in ancient human skeletons. Limitations regarding antigen and aDNA preservation and the importance of sample selection are at the forefront of the search for malaria in the past. We confirm that, currently, palaeopathological changes such as cribra orbitalia are not enough to be certain of the presence of malaria. While biomolecular methods are likely the best chance for conclusive identification, we were unable to obtain results which correspond to the current authentication criteria of biomolecules. This study represents an important contribution in the refinement of biomolecular techniques used; also, it raises new insight regarding the consistency of combining several approaches in the identification of malaria in past populations.

scholarly journals Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Komal Jain ◽  
Teresa Tagliafierro ◽  
Adriana Marques ◽  
Santiago Sanchez-Vicente ◽  
Alper Gokden ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Fold Increase ◽  
The United States ◽  
Genomic Research ◽  
Babesia Microti ◽  
Hybridization Capture ◽  
Mouse Tissues ◽  
Genome Analyses ◽  
Capture Sequencing

AbstractInadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.

Application of Virome Capture Sequencing in Shellfish Sold at Retail Level in Singapore

2021 ◽  
Author(s):  
Malcolm Turk Hsern Tan ◽  
Si Xian Ho ◽  
Justin Jang Hann Chu ◽  
Dan Li
Keyword(s):  
Capture Sequencing

scholarly journals BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

2014 ◽  
Vol 15 (2) ◽  
pp. R35 ◽  
Author(s):  
Andrea Riebler ◽  
Mirco Menigatti ◽  
Jenny Z Song ◽  
Aaron L Statham ◽  
Clare Stirzaker ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bayesian Approach ◽  
Sequencing Data ◽  
Affinity Capture ◽  
Capture Sequencing

scholarly journals Methyl-binding DNA capture Sequencing for Patient Tissues

10.3791/54131 ◽  
2016 ◽  
Author(s):  
Rohit R. Jadhav ◽  
Yao V. Wang ◽  
Ya-Ting Hsu ◽  
Joseph Liu ◽  
Dawn Garcia ◽  
...  
Keyword(s):  
Dna Capture ◽  
Capture Sequencing

scholarly journals Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals

2020 ◽  
Author(s):  
Harsha Doddapaneni ◽  
Sara Javornik Cregeen ◽  
Richard Sucgang ◽  
Qingchang Meng ◽  
Xiang Qin ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Oligonucleotide Probe ◽  
Threshold Value ◽  
Open Reading Frames ◽  
Clinical Samples ◽  
Viral Loads ◽  
Full Length Genome ◽  
Probe Set ◽  
Reading Frames ◽  
Capture Sequencing

AbstractThe newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

scholarly journals Scarcity of Recurrent Regulatory Driver Mutations in Colorectal Cancer Revealed by Targeted Deep Sequencing

2019 ◽  
Vol 3 (2) ◽  
Author(s):  
Rebecca C Poulos ◽  
Dilmi Perera ◽  
Deborah Packham ◽  
Anushi Shah ◽  
Caroline Janitz ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Excision Repair ◽  
Regulatory Elements ◽  
Driver Mutations ◽  
Gene Promoters ◽  
Driver Genes ◽  
Panel Testing ◽  
Target Capture ◽  
Target Capture Sequencing ◽  
Capture Sequencing

Abstract Background Genetic testing of cancer samples primarily focuses on protein-coding regions, despite most mutations arising in noncoding DNA. Noncoding mutations can be pathogenic if they disrupt gene regulation, but the benefits of assessing promoter mutations in driver genes by panel testing has not yet been established. This is especially the case in colorectal cancer, for which few putative driver variants at regulatory elements have been reported. Methods We designed a unique target capture sequencing panel of 39 colorectal cancer driver genes and their promoters, together with more than 35 megabases of regulatory elements focusing on gene promoters. Using this panel, we sequenced 95 colorectal cancer and matched normal samples at high depth, averaging 170× and 82× coverage, respectively. Results Our target capture sequencing design enabled improved coverage and variant detection across captured regions. We found cases with hereditary defects in mismatch and base excision repair due to deleterious germline coding variants, and we identified mutational spectra consistent with these repair deficiencies. Focusing on gene promoters and other regulatory regions, we found little evidence for base or region-specific recurrence of functional somatic mutations. Promoter elements, including TERT, harbored few mutations, with none showing strong functional evidence. Recurrent regulatory mutations were rare in our sequenced regions in colorectal cancer, though we highlight some candidate mutations for future functional studies. Conclusions Our study supports recent findings that regulatory driver mutations are rare in many cancer types and suggests that the inclusion of promoter regions into cancer panel testing is currently likely to have limited clinical utility in colorectal cancer.

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