Dataset Information

Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange.

ABSTRACT: Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.

SUBMITTER: Lee JH

PROVIDER: S-EPMC7838410 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange.

Lee Jeong Hoon JH Kweon Solbi S Park Yu Rang YR

Scientific reports 20210126 1

Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA s ...[more]

PMID: 33500538

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Project description:BackgroundPatients and citizens need access to their health information to get a retrospective as well as a prospective view on their care and rehabilitation processes. However, patients' health information is stored in several health information systems and interoperability problems often hamper accessibility. In Sweden a national health information exchange (HIE) platform has been developed that enables information exchange between different health information systems. The aim of this study is to explore the opportunities and limitations of accessing and interacting with important health information through the Swedish national HIE platform.MethodsA single case study approach was used for this study as an in-depth understanding of the subject was needed. A fictive patient case with a pseudo-name was created based on an interview with a stroke coordinator in Stockholm County. Information access through the national health information exchange platform and available service contracts and application programming interfaces were studied using different scenarios.ResultsBased on the scenarios created in this study, patients would be able to access some health related information from their electronic health records using the national health information exchange platform. However, there is necessary information which is not retrievable as it is either stored in electronic health records and eHealth services which are not connected to the national health information exchange platform or there is no service contract developed for these types of information. In addition, patients are not able to share information with healthcare professionals.ConclusionThe national Swedish HIE platform provides the building blocks needed to allow patients online access to their health information in a fragmented and distributed health system. However, more complex interaction scenarios allowing patients to communicate with their health care providers or to update their health related information are not yet supported. Therefore it is of great importance to involve patients throughout the design and evaluation of eHealth services on both national and local levels to ensure that their needs for interoperability and information exchange are met.

Project description:BackgroundSparse relative effectiveness evidence is a frequent problem in Health Technology Assessment (HTA). Where evidence directly pertaining to the decision problem is sparse, it may be feasible to expand the evidence-base to include studies that relate to the decision problem only indirectly: for instance, when there is no evidence on a comparator, evidence on other treatments of the same molecular class could be used; similarly, a decision on children may borrow-strength from evidence on adults. Usually, in HTA, such indirect evidence is either included by ignoring any differences ('lumping') or not included at all ('splitting'). However, a range of more sophisticated methods exists, primarily in the biostatistics literature. The objective of this study is to identify and classify the breadth of the available information-sharing methods.MethodsForwards and backwards citation-mining techniques were used on a set of seminal papers on the topic of information-sharing. Papers were included if they specified (network) meta-analytic methods for combining information from distinct populations, interventions, outcomes or study-designs.ResultsOverall, 89 papers were included. A plethora of evidence synthesis methods have been used for information-sharing. Most papers (n=79) described methods that shared information on relative treatment effects. Amongst these, there was a strong emphasis on methods for information-sharing across multiple outcomes (n=42) and treatments (n=25), with fewer papers focusing on study-designs (n=23) or populations (n=8). We categorise and discuss the methods under four 'core' relationships of information-sharing: functional, exchangeability-based, prior-based and multivariate relationships, and explain the assumptions made within each of these core approaches.ConclusionsThis study highlights the range of information-sharing methods available. These methods often impose more moderate assumptions than lumping or splitting. Hence, the degree of information-sharing that they impose could potentially be considered more appropriate. Our identification of four 'core' methods of information-sharing allows for an improved understanding of the assumptions underpinning the different methods. Further research is required to understand how the methods differ in terms of the strength of sharing they impose and the implications of this for health care decisions.

Dataset Information

Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange.

Publications

Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange.

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