Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

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%...

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

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,...

Next-generation Sequencing

Next-generation Sequencing

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....

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

Genomics

Genomics

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...

Genome Copying Errors

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Evaluating sequence-to-function deep learning models for ancestry-stratified regulatory variant effect prediction using multi-ancestry blood eQTLs.

bioRxiv : the preprint server for biology·2026

Same author

Testing behavioral economics principles in mailed FIT outreach: a randomized trial.

Cancer causes & control : CCC·2026

Same author

A TAD-informed aging-brain xQTL atlas of multi-modal and cell-type-resolved regulatory variation.

medRxiv : the preprint server for health sciences·2026

Same author

Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort.

PLoS genetics·2026

Same author

Placental toxic metal concentrations and preterm birth: Modification by social stressors.

Reproductive toxicology (Elmsford, N.Y.)·2026

Same author

Can ovarian cancer screening work? A secondary analysis of the UK collaborative trial of ovarian cancer screening.

British journal of cancer·2026

Search research articles

Related Experiment Video

Updated: Jun 5, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

CNV-Profile Regression: A New Approach for Copy Number Variant Association Analysis in Whole Genome Sequencing Data.

Yaqin Si, Wenbin Lu, Shannon Holloway

Biorxiv : the Preprint Server for Biology

|December 9, 2024

Summary

This study introduces a new framework to analyze copy number variants (CNVs) and their impact on disease risk. The method effectively identifies causal CNVs, offering improved precision for Alzheimer's Disease (AD) risk assessment.

More Related Videos

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Related Experiment Videos

Last Updated: Jun 5, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Area of Science:

Genetics
Genomic analysis
Disease risk assessment

Background:

Copy number variants (CNVs) are DNA alterations impacting disease risk.
Assessing CNV effects is challenging due to undefined loci, dosage/length dependency, and the need for joint analysis of regional CNVs.

Purpose of the Study:

To develop a novel framework for association analysis of copy number variants (CNVs).
To model an individual's entire CNV profile within a genomic region to capture length and dosage variations.
To enable joint estimation of CNV effects and bypass the need for predefined CNV loci.

Main Methods:

A new framework representing individuals' CNVs using a CNV profile curve.
Lasso penalty for selecting trait-associated CNVs.
Weighted L2-fusion penalty to encourage similar effects of adjacent CNVs.

Main Results:

Simulations demonstrate improved identification of causal CNVs with controlled false positive rates and precise effect-size estimates.
Application to Alzheimer's Disease Sequencing Project data identified additional CNVs associated with Alzheimer's Disease (AD).
Identified CNVs overlap with known AD-risk genes and are enriched in neuron-related biological processes.

Conclusions:

The proposed framework offers a robust method for CNV association analysis, improving disease risk assessment.
This approach enhances the identification of genetic variants contributing to complex diseases like Alzheimer's Disease.
The findings provide new insights into the genetic architecture of Alzheimer's Disease.