转录组学和长期读取的基因组学的整合优先考虑了罕见疾病中的结构变异
Tanner D Jensen1, Bohan Ni2, Chloe M Reuter3
1Stanford University.
medRxiv : the preprint server for health sciences
|April 8, 2024
概括
长读测序显著改善了与孟德尔病相关的罕见结构变异 (SV) 的检测. 将基因表达数据与一个新的模型 (Watershed-SV) 集成,优先考虑功能性SV和并联重复扩展,用于诊断罕见的遗传疾病.
科学领域:
- 基因组学就是基因组学.
- 罕见疾病遗传学 罕见疾病遗传学
- 生物信息学是一种生物信息学.
背景情况:
- 罕见的结构变异 (SV) 难以检测和解释,但可能导致孟德尔病.
- 短读测序通常错过了复杂的SVs,使许多罕见疾病病例未被诊断出来.
研究的目的:
- 提高在未诊断的罕见疾病患者中罕见结构变异的检测和功能解释.
- 开发和验证一种新的计算模型,使用基因表达数据来优先考虑引起疾病的SVs.
主要方法:
- 来自68名未诊断疾病网络 (UDN) 参与者的长时间读取基因组的测序和分析.
- 优化了SV检测管道,并与571个对照基因组进行了比较.
- 将SV数据与基因表达特征集成,并开发流域-SV模型.
主要成果:
- 长读测序平均每基因组发现716个罕见的SV基因组,比短读方法增加2.4倍.
- 罕见的SV重叠增强剂和并联重复扩张 (TREs) 在基因表达异常值附近得到丰富.
- 流域-SV模型显著超过了基线方法,确定了每个UDN基因组中位数为8个高可信度的功能性SV.
结论:
- 长读测序与基因表达分析相结合,大大改善了在罕见疾病中功能性SV和TREs的识别和优先级.
- 水shed-SV模型通过整合各种基因组和转录组数据,为诊断遗传疾病提供了一种强大的方法.
- 这项研究确定了FAM177A1中潜在的因果化合物异构缺失,与罕见的神经发育障碍有关.
更多相关视频
11:35Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
Published on: August 21, 2016
13.0K
09:34Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
33.7K
相关概念视频
RNA-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
Genomics
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
Genome-wide Association Studies-GWAS
13.4K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.4K
