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High-Throughput Genotyping on Archived Dried Blood Spot Samples

机译:存档干血斑样品的高通量基因分型

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摘要

Aims: The aim of this study was to investigate if dried blood spot (DBS) samples stored in the Danish Neonatal Screening Biobank (DNSB) and the Danish National Birth Cohort (DNBC) repository are useful for Illumina single-nucleotide polymorphism (SNP) genotyping. Genomic DNA (gDNA) was extracted from just one 3.2 mm DBS punch. The extract was subsequently whole-genome amplified to meet the required amounts of DNA for genotyping. For evaluation of the biobank samples, we included variable factors: time of storage, gDNA, and whole-genome amplified DNA (wgaDNA) concentrations and the Illumina quality metric (GenCall score). Results: The custom 1152 SNP genotyping assay had a 68.5% locus success rate, which was close to the expected 70%. An effect of storage condition was seen in the DNSB samples stored from 1982 to 1987, whereas none was seen in the samples stored from 1988 to 1990. The genotyping quality of the DNBC samples was affected by type of filter paper. Conclusion: We here demonstrate that high-throughput Illumina genotyping can be performed successfully on wgaDNA made of gDNA extracted from only one 3.2 mm DBS disk. This validates the vast potential of existing biobanks in the study of the role of gene interactions in complex diseases.
机译:目的:本研究的目的是调查丹麦新生儿筛查生物库(DNSB)和丹麦国家出生队列(DNBC)库中存储的干血斑(DBS)样本是否可用于Illumina单核苷酸多态性(SNP)基因分型。基因组DNA(gDNA)仅从一个3.2 mm DBS打孔机中提取。随后将提取物进行全基因组扩增,以满足基因分型所需的DNA量。为了评估生物库样品,我们包括了可变因素:储存时间,gDNA和全基因组扩增DNA(wgaDNA)浓度以及Illumina质量指标(GenCall评分)。结果:定制的1152 SNP基因分型分析的基因座成功率为68.5%,接近预期的70%。 1982年至1987年储存的DNSB样品中观察到了储存条件的影响,而1988年至1990年储存的样品中没有观察到存储条件。DNBC样品的基因分型质量受滤纸类型的影响。结论:我们在这里证明,高通量的Illumina基因分型可以成功地对仅从一个3.2 mm DBS盘中提取的gDNA制成的wgaDNA进行。这证实了现有生物库在基因相互作用在复杂疾病中的作用研究中的巨大潜力。

著录项

  • 来源
    《Genetic Testing》 |2009年第2期|173-179|共7页
  • 作者单位

    Department of Clinicai Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark Department of Clinical Biochemistry and Immunology Statens Serum Institut Artillerivej 5 DK-2300 Copenhagen Denmark;

    NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark;

    NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia;

    Department of Clinicai Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark;

    Department of Clinicai Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark;

  • 收录信息 美国《科学引文索引》(SCI);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
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  • 入库时间 2022-08-17 13:21:27

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