相关实验视频

Updated: May 10, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

用黄金标准数据集对整个exome测序的变异调用软件进行基准测试

Matthew Wong¹, Bryan Liew¹, Melissa Hum¹

¹Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore.

Scientific reports

|April 21, 2025

概括

四个用户友好的变异调用软件被用于对整个外因子序列 (WES) 数据进行基准测试. 这就是Illumina Illumina.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
临床遗传学临床遗传学

背景情况:

精确的变异调用从整个外因组测序 (WES) 数据对于遗传疾病研究至关重要.
新兴的非编程软件为小型实验室和诊所民主化了WES数据分析.
本研究评估了用户友好的变量调用工具,以提高可访问性和性能.

研究的目的:

为了对四个非编程类型的调用软件进行比较,用于WES数据分析.
评估所选软件的准确性,灵敏性和运行时间.
引导临床医生和生物学家选择合适的变异分析工具.

主要方法:

基于Illumina基础空间序列中心,CLC基因组学工作台,Partek流和Varsome临床的基准测试.
使用了三个"瓶中的基因组" (GIAB) WES数据集 (HG001,HG002,HG003).
使用变量调用评估工具 (VCAT) 对比GIAB高信任区域的变量.

主要成果:

伊卢米纳的DRAGEN Enrichment实现了SNV的精度/回忆率>99%,而INDEL的精度/回忆率为96%.
帕特克Flow显示了最低的内部呼叫性能.
Illumina 和 CLC 的运行时间最短 (6-36 分钟),而 Partek Flow 的运行时间最长 (3.6-29.7 小时).

结论:

Illumina的软件为WES变种呼叫提供了精度,灵敏度和速度的最佳平衡.
对于缺乏生物信息学专业知识的实验室来说,非编程软件选项是可行的.
该研究为选择用户友好的变种调用工具提供了必要的数据.

关键词:

基准测试 (benchmarking) 是一种比较的方法.这是GIAB.没有编程的软件软件.变体调用变体调用整体外基因组测序的测序

更多相关视频

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

相关概念视频

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

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%...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...