Apr 9, 2020

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection

BioRxiv : the Preprint Server for Biology
X. LuoFeifei Xiao

Abstract

Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e., boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we therefore proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic correlation (i.e., LD). To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presents high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. W...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Biological Markers
Brain Diseases
Genes
Schizophrenia
Epilepsy
Neurons
Human Genetics
Weighing Patient
Alzheimer's Disease
Autistic Disorder

Related Feeds

Alzheimer's Disease: Transcription

Transcription involves copying (transcribing) the gene's DNA sequence into RNA. Impaired transcription is associated with the pathogenesis and progression of conditions such as Alzheimer's disease (AD). Here are the latest discoveries pertaining to transcription and this disease.

Alzheimer's Disease: Genes&Microglia (Preprints)

Genes and microglia are associated with the risk of developing and the progression of conditions such as Alzheimer's Disease (AD). Here are the latest preprints pertaining to this disease.

Alzheimer's Disease: Animal models

Alzheimer's disease is a chronic neurodegenerative disease which can be studied using various experimental systems. This feed focuses on animal models used for Alzheimer's disease research.

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Alzheimer's Disease: RNA Sequencing

RNA sequencing is used to reveal the presence and quantity of RNA in a given sample. In this feed, RNA sequencing investigates the genetic and molecular mechanisms related to the pathophysiology of Alzheimer's disease (AD). Here are the latest discoveries pertaining to RNA sequencing and this disease.

Autism

Autism spectrum disorder is associated with challenges with social skills, repetitive behaviors, and often accompanied by sensory sensitivities and medical issues. Here is the latest research.

Alzheimer's Disease: Genetics

Alzheimer's disease is a chronic neurodegenerative disease. Discover genetic and epigenetic aspects of Alzheimer’s disease, including genetic markers and genomic structural variations here.

Alzheimer's Disease: Genes&Microglia

Genes and microglia are associated with the risk of developing and the progression of conditions such as Alzheimer's Disease (AD). Here are the latest discoveries pertaining to this disease.

Related Papers

Current Genetics
Stephanie Lauer, David Gresham
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Agnieszka ŻmieńkoMarek Figlerowicz
© 2020 Meta ULC. All rights reserved