Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

19.2K
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%...
19.2K
Sanger Sequencing01:57

Sanger Sequencing

778.1K
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...
778.1K
RNA-seq03:21

RNA-seq

12.4K
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...
12.4K
Next-generation Sequencing03:00

Next-generation Sequencing

100.8K
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....
100.8K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

19.7K
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,...
19.7K

You might also read

Related Articles

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

Sort by
Same author

Palladium-catalyzed olefination and arylation of 2-substituted 1,2,3-triazole N-oxides.

Organic letters·2013
Same author

One-stop hybrid coronary revascularization versus coronary artery bypass grafting and percutaneous coronary intervention for the treatment of multivessel coronary artery disease: 3-year follow-up results from a single institution.

Journal of the American College of Cardiology·2013
Same author

Relative contributions of the thalamus and the paraventricular nucleus of the hypothalamus to the cardiac sympathetic afferent reflex.

American journal of physiology. Regulatory, integrative and comparative physiology·2013
Same author

Initial light soaking treatment enables hole transport material to outperform spiro-OMeTAD in solid-state dye-sensitized solar cells.

Journal of the American Chemical Society·2013
Same author

The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism.

The Plant journal : for cell and molecular biology·2013
Same author

Salvage intensity modulated radiotherapy using endorectal balloon after radical prostatectomy: clinical outcomes.

International journal of urology : official journal of the Japanese Urological Association·2013
Same journal

Protein dynamic simulations: From early inception to clinical translation over half a century.

Computational biology and chemistry·2026
Same journal

Integrated omics and virtual screening predict Tabularin as a dual inhibitor of the prognostic microRNAs mir-19a and mir-32 in colorectal cancer.

Computational biology and chemistry·2026
Same journal

In silico characterization of acetyl-CoA carboxylase from Staphylococcus aureus and Escherichia coli: A comparative analysis.

Computational biology and chemistry·2026
Same journal

An optimized cascaded transformer with progressive attention for lung and colon cancer diagnosis from histopathological images.

Computational biology and chemistry·2026
Same journal

From cross cancer transcriptomics to therapeutics: WGX-50 target hub genes in breast cancer and non-small cell lung carcinoma.

Computational biology and chemistry·2026
Same journal

Blood-based biomarker discovery through integrative transcriptomic and miRNA network analyses in schizophrenia, major depressive disorder, and bipolar disorder.

Computational biology and chemistry·2026
See all related articles

Related Experiment Video

Updated: Mar 25, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

12.2K

Copy number variants calling for single cell sequencing data by multi-constrained optimization.

Bo Xu1, Hongmin Cai1, Changsheng Zhang1

  • 1School of Computer Science & Engineering, South China University of Technology, Guangzhou, China.

Computational Biology and Chemistry
|March 1, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces a new computational method for detecting DNA copy number variations (CNVs) in single-cell sequencing data. The approach effectively models and corrects for amplification bias, improving the accuracy of CNV analysis in cancer research.

Keywords:
Copy number variantsPoisson distributionRead depthSparsityTotal variation

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.0K
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

17.5K

Related Experiment Videos

Last Updated: Mar 25, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

12.2K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.0K
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

17.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • DNA copy number variations (CNVs) are crucial for understanding genome evolution and cancer cell regulation.
  • Single-cell sequencing offers insights into cancer cell heterogeneity but faces challenges due to amplification bias and low data coverage.
  • Accurate modeling of sequencing data distribution and bias suppression are essential for reliable CNV analysis.

Purpose of the Study:

  • To develop a robust computational method for accurate CNV detection in single-cell sequencing data.
  • To address the challenges posed by amplification-induced bias and low genome coverage in single-cell DNA/RNA sequencing.
  • To improve the analysis of cancer cell evolution through precise CNV identification.

Main Methods:

  • Formulated CNV detection as a quadratic optimization problem with sparsity and smoothness constraints.
  • Modeled technical noise from amplification using a negative binomial distribution, a special case of Poisson distribution.
  • Employed an efficient alternating direction minimization method (ADMM) for numerical solutions.

Main Results:

  • The proposed method accurately reconstructs read depth signals, fitting CNV patterns more effectively.
  • Demonstrated superior performance on both synthetic and empirical single-cell sequencing datasets.
  • Successfully suppressed the influence of amplification bias on CNV detection.

Conclusions:

  • The developed method offers a significant advancement in CNV detection for single-cell sequencing data.
  • This approach holds high promise for advancing cancer research and understanding genome evolution at the single-cell level.
  • Accurate CNV analysis is critical for exploring gene expression heterogeneity and cancer cell evolution.