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,...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

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...

You might also read

Related Articles

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

Sort by

Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026

Same author

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

bioRxiv : the preprint server for biology·2026

Same author

Cryptic Diversity and Impacts of Domestication in the Black Soldier Fly (Hermetia illucens) Genome.

Genome biology and evolution·2026

Same author

Pangenome-guided sequence assembly via binary optimization.

Briefings in bioinformatics·2026

Same author

The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

Genome biology and evolution·2026

Same author

The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.

Frontiers in science·2026

Search research articles

Related Experiment Video

Updated: Jun 7, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.

Si Quang Le¹, Richard Durbin

¹Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom.

Genome Research

|October 29, 2010

Summary

This summary is machine-generated.

This study introduces new methods for discovering and genotyping single-nucleotide polymorphisms (SNPs) from low-coverage whole-genome sequencing data. These techniques leverage shared haplotype information to accurately identify genetic variants in populations.

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Related Experiment Videos

Last Updated: Jun 7, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

Genomics
Population Genetics
Bioinformatics

Background:

Decreasing sequencing costs enable whole-genome sequencing of multiple individuals.
Low-coverage sequencing of many samples is an efficient strategy for variant detection.
Combining data across samples is crucial for identifying shared sequence variants.

Purpose of the Study:

To present novel methods for discovering and genotyping single-nucleotide polymorphism (SNP) sites from low-coverage sequencing data.
To utilize shared haplotype (linkage disequilibrium) information for improved variant detection.
To explore the trade-off between sequencing depth and sample size in variant discovery.

Main Methods:

SNP candidate collection based on independent sequence calls per site.
Utilizing MARGARITA with genotype or phased haplotype data to infer ancestral recombination graphs (ARGs).
Refining SNP probabilities using marginal ancestral trees and Bayesian inference with population genetic priors.

Main Results:

Developed and validated methods for SNP discovery and genotyping from low-coverage sequencing data.
Demonstrated applicability using simulation data and real data from the 1000 Genomes Project.
Quantified the relationship between sequencing depth and the number of samples for variant detection.

Conclusions:

The proposed methods effectively discover and genotype SNPs from low-coverage whole-genome sequencing data.
Shared haplotype information significantly enhances variant detection accuracy.
The findings provide guidance on optimizing sequencing strategies for population-level genetic studies.