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

Next-generation Sequencing03:00

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 Sequencing01:57

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...
RNA-seq03:21

RNA-seq

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 microarray-based...
Comparing Copy Number Variations and SNPs02:26

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%...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Single Nucleotide Polymorphisms-SNPs01:05

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,...

You might also read

Related Articles

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

Sort by
Same author

NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.

Bioinformatics (Oxford, England)·2024
Same author

A foundational atlas of autism protein interactions reveals molecular convergence.

bioRxiv : the preprint server for biology·2023
Same author

Longitudinal fundus imaging and its genome-wide association analysis provide evidence for a human retinal aging clock.

eLife·2023
Same author

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation.

Genes and immunity·2022
Same author

Mid- and long-term outcomes of thoracic endovascular aortic repair in acute and subacute uncomplicated type B aortic dissection.

Journal of cardiac surgery·2022
Same author

ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes.

iScience·2022

Related Experiment Video

Updated: Jun 22, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing

Kevin Judd McKernan1, Heather E Peckham, Gina L Costa

  • 1Life Technologies, Beverly, Massachusetts 01915, USA. Kevin.McKernan@appliedbiosystems.com

Genome Research
|June 24, 2009
PubMed
Summary

This study presents a novel genome sequencing method with high accuracy, enabling the discovery of millions of genetic variations, including novel single nucleotide polymorphisms (SNPs) and structural variants, in an African individual.

More Related Videos

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

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

Related Experiment Videos

Last Updated: Jun 22, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

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

Area of Science:

  • Genomics
  • Human Genetics

Background:

  • Genome sequencing is crucial for understanding human genetic variation.
  • Accurate identification of genetic variants requires high-quality sequencing data and advanced analytical methods.

Purpose of the Study:

  • To describe genome sequencing of an African individual using a novel ligation-based assay.
  • To accurately identify single nucleotide polymorphisms (SNPs) and other genetic variations.
  • To provide insights into human genetic diversity and disease-associated variants.

Main Methods:

  • Utilized a novel ligation-based sequencing assay with enhanced error correction (>99.9% accuracy).
  • Generated billions of mate-paired reads for deep genome coverage (18x haploid, 300x clone coverage).
  • Employed advanced algorithms for SNP calling, haplotype phasing, and indel/structural variant detection.

Main Results:

  • Identified over 3.8 million SNPs, with 19% being novel.
  • Achieved high genome coverage (>98% with unique reads, 99.65% with mate-paired clones).
  • Detected numerous intra-read and inter-read indels, inversions, and gene fusions, including disease-associated variants.

Conclusions:

  • The novel sequencing assay significantly improves accuracy and variant detection capabilities.
  • The study highlights substantial undiscovered genetic variation in the human genome.
  • Findings offer guidance for future population and cancer genomics studies.