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Minimal information for reporting a genomics experiment.

ABSTRACT: Exome and genome sequencing has facilitated the identification of hundreds of genes and other regions that are recurrently mutated in hematologic neoplasms. The data sets from these studies theoretically provide opportunities. Quality differences between data sets can confound secondary analyses. We explore the consequences of these on the conclusions from some recent studies of B-cell lymphomas. We highlight the need for a minimum reporting standard to increase transparency in genomic research.

SUBMITTER: Dreval K

PROVIDER: S-EPMC10653092 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Minimal information for reporting a genomics experiment.

Dreval Kostiantyn K Boutros Paul C PC Morin Ryan D RD

Blood 20221201 24

Exome and genome sequencing has facilitated the identification of hundreds of genes and other regions that are recurrently mutated in hematologic neoplasms. The data sets from these studies theoretically provide opportunities. Quality differences between data sets can confound secondary analyses. We explore the consequences of these on the conclusions from some recent studies of B-cell lymphomas. We highlight the need for a minimum reporting standard to increase transparency in genomic research. ...[more]

PMID: 36219881

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Project description:BackgroundAccurate, high-confidence data is critical for assessing potential biothreat incidents. In a biothreat event, false-negative and -positive results have serious consequences. Worst case scenarios can result in unnecessary shutdowns or fatalities at an exorbitant monetary and psychological cost, respectively. Quantitative PCR assays for agents of interest have been successfully used for routine biosurveillance. Recently, there has been increased impetus for adoption of amplicon sequencing (AS) for biosurveillance because it enables discrimination of true positives from near-neighbor false positives, as well as broad, simultaneous detection of many targets in many pathogens in a high-throughput scheme. However, the high sensitivity of AS can lead to false positives. Appropriate controls and workflow reporting can help address these challenges.ObjectivesData reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection.MethodsWe present a set of standards, Amplicon Sequencing Minimal Information (ASqMI), developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program on Agent Detection Assays for making actionable calls in biosurveillance applications. In addition to the first minimum information guidelines for AS, we provide a controls checklist and scoring scheme to assure AS run quality and assess potential sample contamination.ResultsAdoption of the ASqMI guidelines will improve data quality, help track workflow performance, and ultimately provide decision makers confidence to trust the results of this new and powerful technology.ConclusionAS workflows can provide robust, confident calls for biodetection; however, due diligence in reporting and controls are needed. The ASqMI guideline is the first AS minimum reporting guidance document that also provides the means for end users to evaluate their workflows to improve confidence.HighlightsStandardized reporting guidance for actionable calls is critical to ensuring trustworthy data.

Dataset Information

Minimal information for reporting a genomics experiment.

Publications

Minimal information for reporting a genomics experiment.

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