Investigation of the MC1R Gene Sequence Variation Using Oxford Nanopore Sequencing.

IF 3 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

ELECTROPHORESIS Pub Date : 2025-05-02 DOI:10.1002/elps.8141

Wojciech Branicki, Aleksandra Pisarek-Pacek, Kamila Marszałek, Agata Jarosz, Magdalena Kukla-Bartoszek, Magdalena Zubańska, Agnieszka Bronikowska, Katarzyna Węgrzyn, Bożena Wysocka, Magdalena Spólnicka, Ewelina Pośpiech

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引用次数: 0

Abstract

The MC1R gene, which is responsible for most cases of red hair, affects other hair and skin colours and contributes to differences in pain sensitivity and consists of a single exon with a very high level of allelic heterogeneity. In this research, we show that the Oxford Nanopore Technology (ONT) offers a good alternative to study the MC1R sequence variation. MinION was used to sequence the 1590 bp MC1R exon and minimal promoter in a cohort of 126 subjects, including 65 red-haired individuals, using the FLO-MIN106 (R9.4) chemistry. Assigned DNA variants were validated using Ion Torrent technology provided with Ion Xpress Plus Fragment Library Kit and the Personal Genome Machine^TM (PGM^TM). We show that the use of the latest sequencing kit V14 together with the FLO-MIN114 (R10.4.1) flow cell has eliminated the systematic errors observed with the previous chemistry and allowed reliable detection of short indels important for phenotypic inference. Importantly, the use of the algorithm implemented in the EPI2ME software enabled convenient and accurate read-based phase determination which can be useful in data interpretation.

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利用牛津纳米孔测序技术研究MC1R基因序列变异。

MC1R基因是大多数红发病例的原因，它影响其他头发和皮肤的颜色，并导致疼痛敏感性的差异，它由一个具有非常高水平等位基因异质性的单外显子组成。在这项研究中，我们发现牛津纳米孔技术（ONT）为研究MC1R序列变异提供了一个很好的选择。使用FLO-MIN106 （R9.4）化学方法，MinION对126名受试者（包括65名红发个体）的1590 bp MC1R外显子和最小启动子进行测序。使用Ion Xpress Plus Fragment Library Kit和Personal Genome MachineTM （PGMTM）提供的Ion Torrent技术验证分配的DNA变体。我们表明，使用最新的测序试剂盒V14和FLO-MIN114 （R10.4.1）流式细胞消除了以前化学观察到的系统误差，并允许可靠地检测对表型推断重要的短索引。重要的是，使用EPI2ME软件中实现的算法实现了方便和准确的基于读取的相位测定，这在数据解释中很有用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

ELECTROPHORESIS 生物-分析化学

CiteScore

6.30

自引率

13.80%

发文量

244

审稿时长

1.9 months

期刊介绍： ELECTROPHORESIS is an international journal that publishes original manuscripts on all aspects of electrophoresis, and liquid phase separations (e.g., HPLC, micro- and nano-LC, UHPLC, micro- and nano-fluidics, liquid-phase micro-extractions, etc.). Topics include new or improved analytical and preparative methods, sample preparation, development of theory, and innovative applications of electrophoretic and liquid phase separations methods in the study of nucleic acids, proteins, carbohydrates natural products, pharmaceuticals, food analysis, environmental species and other compounds of importance to the life sciences. Papers in the areas of microfluidics and proteomics, which are not limited to electrophoresis-based methods, will also be accepted for publication. Contributions focused on hyphenated and omics techniques are also of interest. Proteomics is within the scope, if related to its fundamentals and new technical approaches. Proteomics applications are only considered in particular cases. Papers describing the application of standard electrophoretic methods will not be considered. Papers on nanoanalysis intended for publication in ELECTROPHORESIS should focus on one or more of the following topics: • Nanoscale electrokinetics and phenomena related to electric double layer and/or confinement in nano-sized geometry • Single cell and subcellular analysis • Nanosensors and ultrasensitive detection aspects (e.g., involving quantum dots, "nanoelectrodes" or nanospray MS) • Nanoscale/nanopore DNA sequencing (next generation sequencing) • Micro- and nanoscale sample preparation • Nanoparticles and cells analyses by dielectrophoresis • Separation-based analysis using nanoparticles, nanotubes and nanowires.