在从单细胞DNA测序数据的基因树上整合SNV和CNA
Liting Zhang1, Hank W Bass2, Jerome Irianto3
1Department of Computer Science, Florida State University, Tallahassee, Florida 32306, USA.
Genome research
|November 22, 2023
概括
SCsnvcna是一种新的计算工具,通过将单核酸变异 (SNV) 放置在从副本数异常 (CNA) 信号推断出来的基因组上,构建瘤进化树. 这种方法通过使用独立的细胞集来检测SNV和CNA来克服技术上的挑战,从而改善了家族遗传分析.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 癌症研究 癌症研究
背景情况:
- 单细胞DNA测序对于理解瘤进化和突变获取至关重要.
- 现有的全基因组放大方法通常有利于单核酸变异 (SNV) 或拷贝数异常 (CNA) 检测,而不是两者兼而有之.
- 这种限制阻碍了全面的遗传树推断和SNV-CNA相互作用的研究.
研究的目的:
- 引入SCsnvcna,这是一个计算工具,旨在通过整合SNV和CNA数据来构建家族遗传树.
- 为了应对检测同一细胞群中的SNV和CNA的技术挑战.
- 通过使用独立的SNV和CNA数据集,提供一种更实用的方法来分析瘤演变.
主要方法:
- SCsnvcna使用贝叶斯概率模型推断进化树.
- 它利用基因型约束和细胞流行率来优化SNV在CNA衍生后代上的位置.
- 该方法适用于SNV和CNA数据采集的独立单元组.
主要成果:
- 在使用七种最先进的方法进行全面的模拟和比较时,SCsnvcna表现出了稳健性和准确性.
- 该工具始终实现较低的错误率,并有效地扩展不同树叶节点,SNV和SNV细胞数量.
- 对结直肠癌数据集的应用证实了SNV细胞和SNV放置一致性,并完善了ATP7B的放置.
结论:
- SCsnvcna提供了一个实用且准确的解决方案,用于从独立的SNV和CNA数据中构建家族遗传树.
- 该工具增强了复杂多瘤样本的分析,为瘤进化提供了精细的见解.
- SCsnvcna推进了在癌症中单核酸变异和拷贝数异常之间的相互作用的研究.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.8K
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...
5.8K
Phylogenetic Trees
45.4K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.4K
Single Nucleotide Polymorphisms-SNPs
15.2K
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,...
15.2K
Phylogeny
44.2K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
44.2K
Comparing Copy Number Variations and SNPs
17.7K
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%...
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%...
17.7K
Gene Evolution - Fast or Slow?
7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.1K


