Informatics and clinical genome sequencing: opening the black box

Moorthie, Sowmiya; Hall, Alison; Wright, Caroline F.

doi:10.1038/gim.2012.116

Cited by 32 publications

(23 citation statements)

References 55 publications

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“…Genome sequencing comprises a set of interrelated activities that follow on from the generation of the sequence of the base pairs across the entire genome/exome. These activities include (a) the identification of defined variants in the sequence as compared with some reference sequence, (b) the selection of those areas of the genome that contain variants that are pertinent to the clinical or research question and (c) the interpretation and analysis of the data within those selected areas 8. It is at the final stage when the sequence variations are interpreted that judgements are made about the meaning of the variants that exist in the analysed sequence 9…”

Section: Pertinent Versus Incidental: the Status Of Genetic Findings mentioning

confidence: 99%

Revealing the results of whole-genome sequencing and whole-exome sequencing in research and clinical investigations: some ethical issues: Table 1

et al. 2014

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The introduction of new sequencing technologies wholegenome sequencing (WGS) and whole-exome sequencing (WES) that are much less finely targeted than previous genetic tests has resulted in ethical debate about what should be done with clinically significant findings that may arise during the sequencing process. In this piece we argue that, in addition to whether the finding has been intentionally sought or arises incidentally, the ethical issues concerning what should be done with WES and WGS findings are also influenced by whether sequencing occurs in a clinical or research setting. We argue that decisions about the disclosure of WGS and WES findings generated in the clinical context are much less ethically contentious than decision making about the feedback of research results. We conclude by calling for greater transparency about the purpose of sample collection, more explicit protocols for transitioning between research and clinical contexts and patients and research participants to be warned of the potential for incidental findings to be generated, their potential significance and the actions that might be taken as a result.

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Section: Pertinent Versus Incidental: the Status Of Genetic Findings mentioning

confidence: 99%

Revealing the results of whole-genome sequencing and whole-exome sequencing in research and clinical investigations: some ethical issues: Table 1

et al. 2014

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“…In addition to these considerations, bioinformatics challenges are numerous and the field is thus a highly dynamic area of research (Table 2) (30 ). Multiple open source or commercial software solutions invariably exist for any single analysis step, each with their own characteristics, strengths, and weaknesses (19 ). Often individual software applications are tailored to a particular sequencing platform, sequence length, or sequencing protocol (31,32 ).…”

Section: Alignment and Variant Detection (Secondary Analysis)mentioning

confidence: 99%

Bioinformatics for Clinical Next Generation Sequencing

2015

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BACKGROUND:Next generation sequencing (NGS)-based assays continue to redefine the field of genetic testing. Owing to the complexity of the data, bioinformatics has become a necessary component in any laboratory implementing a clinical NGS test.CONTENT: The computational components of an NGSbased work flow can be conceptualized as primary, secondary, and tertiary analytics. Each of these components addresses a necessary step in the transformation of raw data into clinically actionable knowledge. Understanding the basic concepts of these analysis steps is important in assessing and addressing the informatics needs of a molecular diagnostics laboratory. Equally critical is a familiarity with the regulatory requirements addressing the bioinformatics analyses. These and other topics are covered in this review article.

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“…The available amalgamated data is simply not reliable enough be used as is. 31,37,38 Individual molecular diagnostic laboratories use a combination of proprietary databases and human geneticists to overcome this interpretation problem. However, because their approach is only partly automated and usually focused on a narrow set of genes, it is not well suited for an EHR.…”

Section: Practicalities and Challenges Of Genomic Data Interpretationmentioning

confidence: 99%

Storing and interpreting genomic information in widely deployed electronic health record systems

Ury¹

2013

Genetics in Medicine

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Informatics and clinical genome sequencing: opening the black box

Cited by 32 publications

References 55 publications

Revealing the results of whole-genome sequencing and whole-exome sequencing in research and clinical investigations: some ethical issues: Table 1

Revealing the results of whole-genome sequencing and whole-exome sequencing in research and clinical investigations: some ethical issues: Table 1

Bioinformatics for Clinical Next Generation Sequencing

Storing and interpreting genomic information in widely deployed electronic health record systems

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