Dataset Information

From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

ABSTRACT: Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA) it is paramount workflows and analytics are both fit for purpose.

SUBMITTER: Murray DC

PROVIDER: S-EPMC4406758 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

Murray Dáithí C DC Coghlan Megan L ML Bunce Michael M

PloS one 20150422 4

Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imper ...[more]

PMID: 25902146

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Project description:BackgroundGrowing demand for medical services has increased patient waiting time due to the limited number or unbalanced distribution of healthcare centers. Healthcare teleconsultation networks are one of the potentially powerful systems to overcome this problem. Medical pathology can hugely benefit from teleconsultation networks because having second opinions is precious for many cases; however, resource planning (i.e., assignment and distribution of pathology consultation requests) is challenging due to bulky medical images of patients. This results in high setup and operational costs. The aim of this study is to design an optimal teleconsultation network for pathology labs under the supervision of medical sciences universities in Tehran, Iran.MethodsTo avoid the setup cost, we first propose a modified hybrid peer-to-peer (P2P) overlay architecture for our telepathology network, using Iran's National Healthcare Information Network (SHAMS) as the underlying infrastructure. Then we apply optimization techniques to solve the request assignment and distribution problems in the network. Finally, we present a novel mathematical model with the objective of minimizing the variable operational costs of the system.ResultsThe efficiency of the proposed method was evaluated by a set of practical-sized network instances simulated based on the characteristics of SHAMS. The results show that the presented model and architecture can obtain optimal solutions for network instances up to 350 nodes, which covers our target network.ConclusionsWe believe that the proposed method can be beneficial for designing large-scale medical teleconsultation networks by adjusting the constraints according to the rules and conditions of each country. Our findings showed that teleconsultation networks in countries with strong information technology (IT) infrastructures are under the influence of consultation fees, while in countries with weak IT infrastructure, the transmission costs are more critical. To the best of our knowledge, no research has so far addressed resource planning in medical teleconsultation networks using optimization techniques. Besides, the target network, i.e., pathology labs under the supervision of medical sciences universities in Tehran and the SHAMS network, are discussed for the first time in this work.

Dataset Information

From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

Publications

From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

Similar Datasets

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