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相关概念视频

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
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相关实验视频

Updated: May 9, 2025

Infinium Assay for Large-scale SNP Genotyping Applications
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使用全基因组测序对TOMM40'523多T多态的基因组定型.

Ricardo A Vialle1,2, Lei Yu1, Yan Li1

  • 1Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.

medRxiv : the preprint server for health sciences
|May 2, 2025
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概括

一种新的计算方法准确地确定了TOMM40的基因型.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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科学领域:

  • 遗传学和基因组学 遗传学和基因组学
  • 计算生物学 计算生物学
  • 神经科学是一个神经科学.

背景情况:

  • TOMM40'523多T重复多态 (rs10524523) 与阿尔茨海默病 (AD) 和认知能力下降有关.
  • 这种多态的精确基因定型对于神经退行研究至关重要.
  • 目前用于从全基因组测序 (WGS) 数据中确定TOMM40'523的基因型的方法往往不足,需要额外的PCR和向测序.

研究的目的:

  • 开发和验证一个新的计算管道,用于直接从WGS数据中准确的TOMM40'523多T重复多态的基因定型.
  • 评估这一管道的性能与传统的PCR基基因型定型方法相比.

主要方法:

  • 使用XGBoost开发了一个集体机器学习模型,集成来自多个短串重复 (STR) 检测工具的预测.
  • 利用STR工具预测,k-mer计数和其他功能来增强聚-T重复长度估计.
  • 在四个队列研究中的1202名参与者中,比较了基于PCR的基因定型与计算管道的基因定型.

主要成果:

  • 整体计算模型在重复长度估计中显著优于单个STR工具.
  • 与PCR衍生的黄金标准相比,在重复长度估计 (R2 = 0.92) 和基因型精度 (93.2%) 中获得了高精度.
  • 通过复制TOMM40'523变体和认知衰退之间的已知关联来验证WGS衍生的基因型.

结论:

  • 从WGS数据中计算TOMM40'523的基因型定型是基于PCR的测试的可扩展和可靠的替代方案.
  • 这种基于WGS的方法可以在大型遗传研究中更广泛地调查TOMM40变异.
  • 开发的管道增强了现有的WGS数据对阿尔茨海默病和认知衰退研究的实用性.