DNA capture in nanopores for genome sequencing: challenges and opportunities

2012 ◽  
Vol 22 (27) ◽  
pp. 13423 ◽  
Author(s):  
Yuhui He ◽  
Makusu Tsutsui ◽  
Masateru Taniguchi ◽  
Tomoji Kawai
Keyword(s):  
Genome Sequencing ◽  
Challenges And Opportunities ◽  
Dna Capture

scholarly journals Whole Genome Sequencing as a Diagnostic Test: Challenges and Opportunities

2014 ◽  
Vol 60 (5) ◽  
pp. 724-733 ◽  
Author(s):  
Caitlin C Chrystoja ◽  
Eleftherios P Diamandis
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Test ◽  
Whole Genome ◽  
Clinical Implementation ◽  
Technological Advances ◽  
Challenges And Opportunities ◽  
Patient Health ◽  
Therapeutic Decision Making ◽  
The Cost

Abstract BACKGROUND Extraordinary technological advances and decreases in the cost of DNA sequencing have made the possibility of whole genome sequencing (WGS) as a highly accessible clinical test for numerous indications feasible. There have been many recent, successful applications of WGS in establishing the etiology of complex diseases and guiding therapeutic decision-making in neoplastic and nonneoplastic diseases and in various aspects of reproductive health. However, there are major, but not insurmountable, obstacles to the increased clinical implementation of WGS, such as hidden costs, issues surrounding sequencing and analysis, quality assurance and standardization protocols, ethical dilemmas, and difficulties with interpretation of the results. CONTENT The widespread use of WGS in routine clinical practice remains a distant proposition. Prospective trials will be needed to establish if, and for whom, the benefits of WGS will outweigh the likely substantial costs associated with follow-up tests, the risks of overdiagnosis and overtreatment, and the associated emotional distress. SUMMARY WGS should be carefully implemented in the clinic to allow the realization of its potential to improve patient health in specific indications. To minimize harm the use of WGS for all other reasons must be carefully evaluated before clinical implementation.

scholarly journals Clinical Tumor Sequencing: Opportunities and Challenges for Precision Cancer Medicine

2015 ◽  
pp. e175-e182 ◽  
Author(s):  
Senthilkumar Damodaran ◽  
Michael F. Berger ◽  
Sameek Roychowdhury
Keyword(s):  
Genome Sequencing ◽  
Clinical Care ◽  
Point Mutations ◽  
Genomic Testing ◽  
Genomic Alterations ◽  
Discovery Research ◽  
Challenges And Opportunities ◽  
Cancer Medicine ◽  
Next Generation Sequencing Ngs ◽  
Tumor Genome

Advances in tumor genome sequencing have enabled discovery of actionable alterations leading to novel therapies. Currently, there are approved targeted therapies across various tumors that can be matched to genomic alterations, such as point mutations, gene amplification, and translocations. Tools to detect these genomic alterations have emerged as a result of decreasing costs and improved throughput enabled by next-generation sequencing (NGS) technologies. NGS has been successfully utilized for developing biomarkers to assess susceptibility, diagnosis, prognosis, and treatment of cancers. However, clinical application presents some potential challenges in terms of tumor specimen acquisition, analysis, privacy, interpretation, and drug development in rare cancer subsets. Although whole-genome sequencing offers the most complete strategy for tumor analysis, its present utility in clinical care is limited. Consequently, targeted gene capture panels are more commonly employed by academic institutions and commercial vendors for clinical grade cancer genomic testing to assess molecular eligibility for matching therapies, whereas whole-exome and transcriptome (RNASeq) sequencing are being utilized for discovery research. This review discusses the strategies, clinical challenges, and opportunities associated with the application of cancer genomic testing for precision cancer medicine.

scholarly journals Challenges and opportunities for strain verification by whole-genome sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jenna E. Gallegos ◽  
Sergei Hayrynen ◽  
Neil R. Adames ◽  
Jean Peccoud
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Challenges And Opportunities

scholarly journals Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile

2021 ◽  
Vol 11 ◽  
Author(s):  
Helena M. B. Seth-Smith ◽  
Michael Biggel ◽  
Tim Roloff ◽  
Vladimira Hinic ◽  
Thomas Bodmer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Molecular Diagnostic ◽  
Whole Genome ◽  
Clostridioides Difficile ◽  
Challenges And Opportunities ◽  
Long Read ◽  
Illumina Sequence ◽  
Pcr Ribotyping

Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile.

scholarly journals Challenges and opportunities for strain verification by whole-genome sequencing

2019 ◽  
Author(s):  
Jenna E Gallegos ◽  
Sergei Hayrynen ◽  
Neil Adames ◽  
Jean Peccoud
Keyword(s):  
Whole Genome Sequencing ◽  
Cell Lines ◽  
Genome Sequencing ◽  
Life Sciences ◽  
Whole Genome ◽  
Next Generation ◽  
Bioinformatics Tools ◽  
Challenges And Opportunities ◽  
Reference Genomes ◽  
Mutant Collection

AbstractLaboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such materials are subject to mix-ups, contamination, and accumulation of secondary mutations, verification of strains and samples is not an established part of many experimental workflows. With the plummeting cost of next generation technologies, it is conceivable that whole genome sequencing (WGS) could be applied to routine strain and sample verification in the future. To demonstrate the need for strain validation by WGS, we sequenced haploid yeast segregants derived from a popular commercial mutant collection and identified several unexpected mutations. We determined that available bioinformatics tools may be ill-suited for verification and highlight the importance of finishing reference genomes for commonly-used laboratory strains.

Continuous hydrogenolysis of acetal-stabilized lignin in flow

2021 ◽  
Author(s):  
Wu Lan ◽  
Yuan Peng Du ◽  
Songlan Sun ◽  
Jean Behaghel de Bueren ◽  
Florent Héroguel ◽  
...  
Keyword(s):  
Steady State ◽  
Challenges And Opportunities

We performed a steady state high-yielding depolymerization of soluble acetal-stabilized lignin in flow, which offered a window into challenges and opportunities that will be faced when continuously processing this feedstock.

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