什么时候 SNP 不是 SNP？

IF 2.2 4区工程技术 Q3 BIOCHEMICAL RESEARCH METHODS

BioTechniques Pub Date : 2024-09-12 DOI:10.1080/07366205.2024.2387993

Shapour Jalilzadeh,Valerie Walker,Gary P Leggatt,Eli Hatchwell

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引用次数: 0

摘要

基因组复制是结构变化和基因创新的重要来源。在人类中，最新和高度相同的序列（同源性大于 90%，长度大于 1 kb）被称为片段重复（SD）。由于短线程测序数据映射的局限性，SDs 内的单核苷酸变异或单核苷酸多态性尚未得到系统评估。在一项关于家族性肾结石病的研究中，单核苷酸变异体 rs62486260 被标记出来，但尚不清楚它是真实的还是因 SD 的存在而产生的假象。我们介绍了利用分段特异性长 PCR 检测和用于 Sanger 测序的短 PCR 进行研究的硅学和湿实验室方法。我们的结论是，rs62486260 是一个假象。我们的方法可用于处理其他此类情况。

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When is an SNP not an SNP?

Genomic duplications are important sources of structural change and gene innovation. In humans, the most recent and highly identical sequences (>90% homology, >1 kb long) are known as segmental duplications (SDs). Single-nucleotide variants or single-nucleotide polymorphisms within SDs have not been systematically assessed due to limitations around mapping short-read sequencing data. Single-nucleotide variant rs62486260 was flagged in a study of familial renal stone disease but it was unclear whether it was real or an artifact resulting from the presence of a SD. We describe in silico and wet-lab approaches to investigate this, using segment-specific long-PCR assays, followed by short PCR for Sanger sequencing. Our conclusion was that rs62486260 is an artifact. Our approach can be generalized to deal with other such situations.

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来源期刊

BioTechniques 工程技术-生化研究方法

CiteScore

4.40

自引率

0.00%

发文量

审稿时长

3.3 months

期刊介绍： BioTechniques is a peer-reviewed, open-access journal dedicated to publishing original laboratory methods, related technical and software tools, and methods-oriented review articles that are of broad interest to professional life scientists, as well as to scientists from other disciplines (e.g., chemistry, physics, computer science, plant and agricultural science and climate science) interested in life science applications for their technologies. Since 1983, BioTechniques has been a leading peer-reviewed journal for methods-related research. The journal considers: Reports describing innovative new methods, platforms and software, substantive modifications to existing methods, or innovative applications of existing methods, techniques & tools to new models or scientific questions Descriptions of technical tools that facilitate the design or performance of experiments or data analysis, such as software and simple laboratory devices Surveys of technical approaches related to broad fields of research Reviews discussing advancements in techniques and methods related to broad fields of research Letters to the Editor and Expert Opinions highlighting interesting observations or cautionary tales concerning experimental design, methodology or analysis.