基因组构建对RNA-seq解释和诊断的影响
Rachel A Ungar1, Pagé C Goddard1, Tanner D Jensen1
1Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
American journal of human genetics
|June 4, 2024
概括
基因组构造选择显著影响转录组学分析,影响基因量化和异常检测. 这项研究提供了受影响基因的数据库,以确保可靠的罕见病诊断.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 转录学对于理解遗传变异和诊断疾病至关重要.
- 以前的研究表明,基因组构造会影响基因组分析结果.
- 基因组构建对转录组学的影响仍然不太了解.
研究的目的:
- 评估不同基因组构造 (hg19,hg38,CHM13) 如何影响转录组学.
- 评估对基因表达量化和异常值检测的影响.
- 为了识别基因和临床相关的变异受影响的基因组构建选择.
主要方法:
- 分析了386种罕见疾病和对照样本,使用转录学.
- 在hg19,hg38和CHM13基因组构建中比较基因表达量化.
- 评估表达异常调用并确定构建依赖和排他性基因.
主要成果:
- 61%的量化基因不受基因组构建的影响.
- 1492个基因显示了构建依赖量化.
- 有9,077个基因具有注释特异性表达,包括566个临床相关的和512个OMIM基因.
结论:
- 基因组构建选择明显影响转录组学,影响基因量化和异常检测.
- 有相当数量的基因,包括临床相关的基因,显示构造特定的表达模式.
- 建议将转录组学数据与构建影响数据库交叉引用,以提高诊断准确度.
相关概念视频
03:21RNA-seq
9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K
03:36Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
02:24Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
02:02Genomics
36.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.3K
03:00Next-generation Sequencing
88.6K
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....
88.6K