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

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.

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%...

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...

RNA-seq

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...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

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

Sort by

Same author

Causal links among gut microbiota, immune-inflammatory and compensatory immune-regulatory systems, and schizophrenia.

Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology·2026

Same author

A multicenter cross-sectional study of gambling disorder among patients with methamphetamine use disorder in drug rehabilitation centers: prevalence, correlates, and network analysis.

Annals of general psychiatry·2025

Same author

Oral microbiota among treatment-naïve adolescents with depression: A case-control study.

Journal of affective disorders·2025

Same author

The role of personality traits and life stress in alcohol use disorder: Insights from NGF gene polymorphisms of Han Chinese population in Taiwan.

Progress in neuro-psychopharmacology & biological psychiatry·2024

Same author

Nerve growth factor gene polymorphisms may be associated with heroin dependence in women but do not mediate specific personality traits.

European archives of psychiatry and clinical neuroscience·2024

Same author

Neurogenetic underpinnings of nicotine use severity: Integrating the brain transcriptomes and GWAS variants via network approaches.

Psychiatry research·2024

Search research articles

Related Experiment Video

Updated: May 7, 2026

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

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

Published on: April 4, 2018

Variant callers for next-generation sequencing data: a comparison study.

Xiangtao Liu¹, Shizhong Han, Zuoheng Wang

¹Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America ; VA CT Health Care Center, West Haven, Connecticut, United States of America.

|October 3, 2013

Summary

This summary is machine-generated.

This study evaluated four variant callers for next-generation sequencing (NGS) data, finding GATK superior for accuracy and sensitivity in human disease genetics. Multiple-sample calling improved overall performance.

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

Related Experiment Videos

Last Updated: May 7, 2026

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

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

Published on: April 4, 2018

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

Area of Science:

Genomics
Bioinformatics
Human Disease Genetics

Background:

Next-generation sequencing (NGS) drives human disease genetic studies.
Variant calling pipelines are crucial for analyzing NGS data.
Caller performance and strategy significantly impact variant detection accuracy.

Purpose of the Study:

To evaluate and compare the performance of four leading variant callers (SAMtools, GATK, glftools, Atlas2).
To assess single-sample versus multiple-sample variant-calling strategies.
To determine the optimal bioinformatics pipeline for human disease genetic analysis using NGS data.

Main Methods:

Developed and applied four single-sample and three multiple-sample variant-calling pipelines using BWA aligner.
Utilized whole exome sequencing data from 20 individuals.
Validated results using Illumina HumanExome Beadchip and Sanger sequencing for high-discordance regions; compared sensitivity on simulated whole genome data.

Main Results:

High consistency observed across single-sample callers (pairwise overlap ~0.9).
GATK demonstrated superior rediscovery rate (0.9969), specificity (0.99996), and Ti/Tv ratio.
Multiple-sample calling enhanced sensitivity; GATK outperformed SAMtools and glfSingle on simulated data, especially with low coverage.
Exome sequencing variant genotypes showed higher accuracy than exome arrays.

Conclusions:

GATK offers significant advantages for general-purpose NGS analyses in human disease genetics.
The developed GATK pipelines provide robust and high-performing variant calling.
Accurate variant identification is critical for advancing genetic research and clinical applications.