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迈向基因组新生儿筛查:从干血斑开始进行外显子组测序的技术可行性。

Towards genomic-Newborn Screening: Technical feasibility of Exome Sequencing starting from dried blood spots.

作者信息

Mauri Alessia, Berardo Clarissa, Biganzoli Davide, Meta Andrea, Benedetti Sara, Rey Federica, Messa Letizia, Zuccotti Gian Vincenzo, Carelli Stephana, Alberti Luisella, Cereda Cristina

机构信息

Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy.

Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy.

出版信息

Mol Genet Metab Rep. 2024 Mar 20;39:101074. doi: 10.1016/j.ymgmr.2024.101074. eCollection 2024 Jun.

Abstract

Each year thousands of babies are born with rare genetic disorders not identified by current NBS panels, due to programs which are not yet optimal. Next-generation sequencing technologies have the potential to overcome many NBS drawbacks and provide large amounts of molecular data, broadening the number of diseases investigated. Here, we design and set up an NGS-based approach to evaluate the feasibility of NGS from dried blood spot starting from 34 DBSs. After assessing gDNA yield and integrity, libraries were performed using three target enrichment approaches, sequenced on NS500 platform, and analyzed on commercial platform. Specifically, we focus on virtual gene panels related to highly actionable neonatal/pediatric disorders. WES show that amount and quality of DBS-extracted gDNA are suitable for high-throughput sequencing. We obtain 500-1500 ng for each specimen, 1.7-1.8 260/280 wavelength, and DIN of 7 resulting DNA integrity, on par with traditional venous blood collection. A high read depth with 94.3% coverage uniformity is achieved for all samples. Data results on mean coverage are comparable among the different workflows tested and demonstrate that DBS from newborn collected at birth is a suitable material for the developing of gNBS programs.

摘要

由于目前的新生儿筛查(NBS)方案尚不完善,每年都有数千名患有罕见遗传疾病的婴儿出生,而这些疾病并未被当前的NBS检测出来。新一代测序技术有潜力克服许多NBS的缺点,并提供大量分子数据,从而扩大所研究疾病的数量。在此,我们设计并建立了一种基于二代测序(NGS)的方法,从34份干血斑(DBS)样本开始评估基于干血斑进行NGS检测的可行性。在评估基因组DNA(gDNA)产量和完整性后,使用三种靶向富集方法构建文库,在NS500平台上进行测序,并在商业平台上进行分析。具体而言,我们专注于与高度可干预的新生儿/儿科疾病相关的虚拟基因panel。全外显子测序(WES)表明,从DBS中提取的gDNA的量和质量适用于高通量测序。每个样本我们获得了500 - 1500 ng的gDNA,260/280波长比值为1.7 - 1.8,DNA完整性数值(DIN)为7,与传统静脉采血相当。所有样本均实现了高读深度,覆盖均匀性达94.3%。在测试的不同工作流程中,平均覆盖度的数据结果具有可比性,这表明出生时采集的新生儿DBS是开展基因组新生儿筛查(gNBS)项目的合适材料。

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