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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

15.2K
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...
15.2K
DNA Microarrays02:34

DNA Microarrays

20.4K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
20.4K
Next-generation Sequencing03:00

Next-generation Sequencing

97.3K
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....
97.3K
Sanger Sequencing01:57

Sanger Sequencing

772.2K
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...
772.2K
Genomics02:02

Genomics

39.5K
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...
39.5K

You might also read

Related Articles

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

Sort by
Same author

Rare protein-coding variation and the genetic architecture of height in >1.4 million individuals.

medRxiv : the preprint server for health sciences·2026
Same author

Separating direct, indirect, and parent-of-origin genetic effects in the human population.

Cell genomics·2026
Same author

Benchmarking imputation accuracy in the presence or absence of a reference panel.

Molecular biology and evolution·2026
Same author

Population-scale repeat expansions elucidate disease risk and brain atrophy.

Nature·2026
Same author

Humans with function-disrupting variants in the myostatin gene (MSTN) have increased skeletal muscle mass and strength, and less adiposity.

Nature communications·2026
Same author

Rare coding variants in CHRNB3 associate with reduced daily cigarette smoking across ancestries.

Nature communications·2026
Same journal

Large-scale discovery and annotation of substructure patterns in mass spectrometry profiles.

Nature communications·2026
Same journal

Salmonella SopB suppresses post-transcriptionally regulated cytokine release to reduce early tissue inflammation and delay disease progression.

Nature communications·2026
Same journal

A human-specific microRNA controls the timing of excitatory synaptogenesis.

Nature communications·2026
Same journal

An HMA-like integrated domain in the wheat tandem kinase WTK4 recognises an RNase-like pathogen effector.

Nature communications·2026
Same journal

Learning regularities in noise engages both neural predictive activity and representational changes.

Nature communications·2026
Same journal

The H3K4 methyltransferase KMT2D is an essential cofactor for GATA1 at erythroid gene enhancers.

Nature communications·2026
See all related articles

Related Experiment Video

Updated: Dec 27, 2025

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

18.2K

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Olivier Delaneau1, Jonathan Marchini2,

  • 1Department of Statistics, University of Oxford, Oxford OX1 3TG, UK.

Nature Communications
|February 6, 2015
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method to estimate haplotypes from low-coverage sequencing data, improving genotype imputation for genome-wide association studies (GWAS). This enhances variant discovery, especially for low-frequency variants.

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

39.7K
Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

13.2K

Related Experiment Videos

Last Updated: Dec 27, 2025

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

18.2K
Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

39.7K
Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

13.2K

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • The 1000 Genomes Project (1000 GP) provides crucial data for genotype imputation in genome-wide association studies (GWAS).
  • Accurate haplotype estimation is vital for effective genotype imputation.

Purpose of the Study:

  • To develop an improved method for estimating haplotypes from low-coverage sequencing data.
  • To leverage single-nucleotide polymorphism (SNP) microarray data from the same samples to enhance haplotype phasing.
  • To create a new 1000 GP haplotype reference set for the human genetics community.

Main Methods:

  • Phasing SNP array data to create a haplotype scaffold.
  • Phasing low-coverage sequencing data onto the established haplotype scaffold.
  • Utilizing relatedness between sequenced and non-sequenced samples to improve imputation accuracy.

Main Results:

  • The developed method generates a new 1000 GP haplotype reference set.
  • Validation shows lower genotype discordance compared to existing methods.
  • Demonstrated improved imputation performance in downstream GWAS, particularly for low-frequency variants.

Conclusions:

  • The new haplotype phasing method enhances the accuracy of genotype imputation.
  • The improved reference set benefits GWAS by increasing power for variant detection, especially rare variants.
  • This advancement supports broader applications of genomic data in human genetic research.