用全基因组和全外基因组序列数据对人类Y染色体单元组分类器进行基准测试
Víctor García-Olivares1,2, Adrián Muñoz-Barrera1, Luis A Rubio-Rodríguez1
1Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
Computational and structural biotechnology journal
|October 11, 2023
概括
这项研究对使用高通量测序数据分类非重组人类Y染色体 (NRY) 单元组的命令行工具进行了基准测试. Yleaf和Y-LineageTracker显示出高准确度,Yleaf是全基因组和全外基因组测序应用的最佳选择.
科学领域:
- 遗传学 是一个遗传学.
- 人类学是人类学.
- 法医科学 法医科学 法医科学
背景情况:
- 人类Y染色体 (NRY) 的非重组区域对于遗传研究至关重要,能够准确地重建血统和检索祖先信息.
- 高通量测序 (HTS) 技术产生了大量的数据,这对于分析NRY地区至关重要.
研究的目的:
- 用不同的HTS数据类型对NRY单元组分类的各种命令行工具的性能进行比较.
- 根据测序数据指导研究人员选择NRY分析最合适的工具.
主要方法:
- 使用配对全基因组测序 (WGS) 和全外因组测序 (WES) 的命令行工具的评估Illumina来自50个无关的捐赠者的数据.
- 使用来自1000个基因组项目的54个个体的配对WGS/WES数据集进行验证.
- 对第三代HTS数据的工具性能评估来自捐赠者的子集和参考样本.
主要成果:
- Y-LineageTracker (98%) 和Yleaf (96%) 显示了NRY哈普洛组分类与WGS数据的最高准确性.
- 在WES数据上,Yleaf表现出卓越的性能,达到约90%的准确性.
- 在第三代HTS数据上,Yleaf,Y-LineageTracker和pathPhynder实现了88%的准确性.
结论:
- 全外基因组测序 (WES) 是NRY单基组确定的一种有效方法,为全基因组测序 (WGS) 提供了可行的替代方案.
- 在WGS和WES数据集中,Yleaf是NRY半组分类的推工具.
- 该研究为为第二代和第三代HTS数据选择最佳NRY分析工具提供了宝贵的资源.
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
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.5K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.5K
Modern Molecular Taxonomy
26
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
26
Human Genetics
588
Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
The complex relationship between genetics and psychology is observable through common biological components such...
588
Next-generation Sequencing
89.0K
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....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
89.0K
X and Y Chromosomes
26.2K
Among mammals, the gender of an organism is determined by the sex chromosomes. Humans have two sex chromosomes, X and Y. Every human diploid cell has 22 pairs of autosomes and one pair of sex chromosomes. A human female has two X chromosomes, while a male has one X chromosome and one Y chromosome.
The germline cells such as egg and sperm cells carry only half the number of chromosomes, i.e., 22 autosomes and one sex chromosome. All eggs have an X chromosome, while sperm cells can carry an X or...
The germline cells such as egg and sperm cells carry only half the number of chromosomes, i.e., 22 autosomes and one sex chromosome. All eggs have an X chromosome, while sperm cells can carry an X or...
26.2K


