评估分析前 DNA 完整性对基因组数据质量的影响。

IF 1.6 4区生物学

Biopreservation and Biobanking Pub Date : 2024-10-01 Epub Date: 2024-04-01 DOI:10.1089/bio.2023.0050

Sung-Mi Shim, Meehee Lee, Jae-Pil Jeon

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引用次数: 0

摘要

许多分子方法被用于生物库 DNA 样品的质量控制（QC）。自 2003 年以来，韩国国家生物库（NBK）利用传统的琼脂糖凝胶电泳和分光光度法为各种研究提供了超过 50 万份经过质量控制的基因组 DNA 样本。我们用不同范围的 DNA 质量指标（如基因组质量数（GQN））评估了 DNA 样本（n = 41）分析后的基因组数据质量，以制定基于证据的 DNA 质量标准最佳实践。我们使用单核苷酸多态性阵列、甲基化阵列和新一代测序等三种不同平台，使用不同质量的DNA样本（n = 41）（GQN值从4.0到10.0不等）检测了它们的质量指数。我们的数据分析显示，GQN 值和/或双链 DNA 浓度越高，基因组数据的质量越高。此外，所有分析过的 DNA 样本都成功生成了高质量的基因组数据。这项研究为基因组分析平台生物库DNA样本的质量控制提供了指导。

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Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality.

Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.

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来源期刊

Biopreservation and Biobanking Biochemistry, Genetics and Molecular Biology-General Biochemistry,Genetics and Molecular Biology

自引率

12.50%

发文量

114

期刊介绍： Biopreservation and Biobanking is the first journal to provide a unifying forum for the peer-reviewed communication of recent advances in the emerging and evolving field of biospecimen procurement, processing, preservation and banking, distribution, and use. The Journal publishes a range of original articles focusing on current challenges and problems in biopreservation, and advances in methods to address these issues related to the processing of macromolecules, cells, and tissues for research. In a new section dedicated to Emerging Markets and Technologies, the Journal highlights the emergence of new markets and technologies that are either adopting or disrupting the biobank framework as they imprint on society. The solutions presented here are anticipated to help drive innovation within the biobank community. Biopreservation and Biobanking also explores the ethical, legal, and societal considerations surrounding biobanking and biorepository operation. Ideas and practical solutions relevant to improved quality, efficiency, and sustainability of repositories, and relating to their management, operation and oversight are discussed as well.