Applications of NGS

scientist reaching for sample in sequencing lab

What is NGS used for?

NGS is used to sequence vast amounts of genetic material, enabling researchers to take a broad, unbiased approach to scientific research in a variety of applications and biological systems.

Rather than profiling select markers, you can identify variants across thousands of regions, down to single-base resolution, in a single experiment. NGS expands the scope of your experimental studies to help find the answers to your boldest research questions.

Using NGS in key research areas

NGS can play an important role in pursuing the answer to a variety of biological questions using a wide array of published methods for diverse sample types. NGS enables the unbiased investigation of multiple biological “omes”, such as the proteome, transcriptome, epigenome, and genome. A combinatorial approach interrogating multiple omes at once, called multiomics, can also be achieved with NGS.

Popular NGS methods and applications include:

Cancer research

NGS is used to bulk-sequence tumors and identify genetic mutations in tumors, aiding in the development of targeted therapies and monitoring cancer progression through liquid biopsies.

Cancer Research Methods Guide

The Cancer Research Methods Guide is a 40+ page resource with simple workflows for a broad range of cancer research applications. This guide includes single-cell sequencing, spatial sequencing, methylation profiling, multiomics, cell-free RNA sequencing, and more.

Liquid Biopsy Methods Guide

This 20+ page eBook provides published, comprehensive workflows for thorough characterization of liquid biopsy samples using NGS and microarrays. Overviews of liquid biopsy analytes, research examples, diagrams, and more.

Microbiology and infectious diseases

NGS helps in pathogen identification, outbreak tracking, and studying antimicrobial resistance by sequencing the genomes of bacteria, viruses, and other microbes.

Methods Guide for Microbial Whole-Genome Sequencing

Sequence hundreds of organisms simultaneously, generate accurate reference genomes, and perform comparative genomic studies.

Genetic and rare diseases

NGS enables rapid sequencing of genomes or exomes to identify novel SNPs associated with rare diseases.

Key NGS applications in various fields

Applications	Areas of interest/fields	Recommended instruments
Gene expression profiling Examines gene expression of the subset of coding regions in the genome.	Cancer research Genetic disease research Cell & molecular biology Infectious disease research	Small and medium benchtop instruments MiSeq System NextSeq 1000 & 2000 Systems
Microbial genomics Discover novel microbes, monitor outbreaks, analyze food sources, and more.	Infectious disease research Microbiology	Small and medium benchtop instruments MiSeq System NextSeq 1000 & 2000 Systems
Targeted gene sequencing A useful tool for analyzing specific variants in a given sample.	Cancer research Cell & molecular biology Genetic disease	Small and medium benchtop instruments MiSeq System NextSeq 1000 & 2000 Systems
Small RNA sequencing A technique to detect and sequence small RNA species such as microRNAs.	Cell & molecular biology Cancer research	Small and medium benchtop instruments MiSeq System NextSeq 1000 & 2000 Systems
Enriched genome Used for analyzing specific genetic variants in a given sample.	Cancer research Cell & molecular biology Genetic disease research	Small and medium benchtop instruments MiSeq System NextSeq 1000 & 2000 Systems
Transcriptomics (bulk, single cell, spatial) The complete profiling of the transcriptome, including all RNA molecules found within individual cells or tissue, in bulk, or at spatial resolution.	Cancer research Cell & molecular biology Genetic disease research Infectious disease research Microbiology Agrigenomics	Medium benchtop instruments NextSeq 1000 & 2000 Systems
Immune repertoire (bulk and single cell) Used to identify unique receptor variants found in individuals susceptible to autoimmune disorders and other diseases.	Cancer research Genetic disease research Cell & molecular biology Infectious disease research	Medium benchtop instruments NextSeq 1000 & 2000 Systems

Featured workflows

The NGS workflow is easy to access and implement in a variety of sequencing methods and research fields. Below are a few example workflows for some of the most popular methods.

Prep

Illumina DNA Prep

Sequence

MiSeq System

NextSeq 1000 & NextSeq 2000 Systems

Analyze

BaseSpace Sequence Hub

DRAGEN Secondary Analysis

Prep

Illumina DNA Prep with Enrichment

Illumina DNA Prep with Exome 2.5 Enrichment

Sequence

NextSeq 1000 & NextSeq 2000 Systems

Benchtop sequencers

Analyze

Germline and somatic (tumor-only): DRAGEN Enrichment

Somatic tumor-only and tumor-normal: DRAGEN Somatic

Insights

Germline: Emedgene

Somatic: Connected Insights

Prep

Mechanical, enzymatic, or combinatorial methods with enrichment (optional) and QC

Low-throughput: microdissection, FACS

High-throughput: microfluidics, droplet-based, microwell approaches

Sequence

NextSeq 1000 & NextSeq 2000 Systems

Analyze

DRAGEN Single-Cell RNA Analysis

Insights

Partek

Connected Analytics: Bench

NGS applications and methods by instrument

Method	iSeq 100 System	MiniSeq System	MiSeq System	NextSeq 1000 and 2000 Systems
Key application Supported application *Small targeted panels < 50 genes, Large targeted panels > 50 genes
Small whole-genome sequencing (microbe, virus) Sequence the entire genome of a bacterium, virus, or other microbe.
Targeted DNA sequencing Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample.	Key application with small targeted panels*	Key application with small targeted panels*	Key application with small targeted panels*	Key application with small targeted panels*
mRNA sequencing Sensitive, accurate measurement of gene expression, after mRNA enrichment using poly-A capture.
Total RNA sequencing Analyze coding plus multiple forms of noncoding RNA for a comprehensive picture of the transcriptome.
16s rRNA sequencing A culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study.
Exome sequencing DNA technique analyzing coding regions of genes to identify genetic variants.
Shotgun metagenomics Sequence thousands of organisms in parallel. Identify unculturable or low-abundance microbes, or evaluate microbial diversity.
ATAC-Seq The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility across the genome.
Methylation sequencing Enhance epigenetic studies with high-coverage density and flexibility enabled by sequencing-based DNA methylation analysis.
Targeted proteomics Analyzes specific proteins to understand their function and interaction in biological systems.
Single-cell sequencing Discovery of distinct cellular niches that comprise a larger tissue.
Spatial analysis Obtain a comprehensive map of transcriptional activity within tissue sections.
Liquid biopsy research Examine cell-free circulating tumor DNA as a noninvasive cancer biomarker.
Immune repertoire sequencing Decodes immune cell receptors to understand immune system diversity and response.
Large whole-genome sequencing (human) Extensive sequencing of entire genome, revealing genetic information for research.

NGS technology

Discover the broad range of experiments you can perform with next-generation sequencing, and find out how Illumina NGS works.

Intro-to-NGS training courses

Our virtual courses provide an overview of NGS. You’ll learn about sequencing workflows, sample prep, data analysis, and more.

Whole-genome vs exome sequencing

Learn about the critical differences between whole-genome and whole-exome sequencing and when to use each method to efficiently make your next discoveries.

Planning NGS experiments

Learn about read length, coverage, quality scores, and other experimental considerations to help you plan your sequencing run.

Benchtop sequencers

Learn more about how Illumina benchtop sequencers are cost-efficient solutions for low and mid-throughput applications and for library quality control (QC) prior to large-scale studies.

16S rRNA sequencing on NextSeq 1000 and NextSeq 2000 Systems

This application note demonstrates comparable performance using the NextSeq 2000 and MiSeq Systems for sequencing the V3 and V4 variable regions of the 16S gene.

Small whole-genome sequencing on NextSeq 1000 and NextSeq 2000 Systems

This application note compares the performance of the NextSeq 1000 and NextSeq 2000 Systems to that of the MiSeq System for WGS. The NextSeq 1000 and NextSeq 2000 Systems are excellent choices for labs interested in WGS of small to medium-size genomes.

Want to discuss benchtop sequencing options?

Speak to sales today about choosing the right benchtop sequencer based on your needs.

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For every lab, everywhere

NextSeq 1000 and NextSeq 2000 Reagents

NGS Workflow Finder

DRAGEN v4.3 now available on-premises and on-cloud

Illumina Proactive Instrument Performance Service

Do more, faster than ever

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

For every lab, everywhere

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For every lab, everywhere

For every lab, everywhere

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For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

Applications of NGS

NGS methods and applications

The discovery power of NGS provides untapped insights into biological phenomena, pathways, and systems across a broad spectrum of research areas

What is NGS used for?

Using NGS in key research areas

Popular NGS methods and applications include:

Cancer research

Microbiology and infectious diseases

Genetic and rare diseases

Further reading: New to NGS eBook

Key NGS applications in various fields

NGS Workflow Finder

Featured workflows

Prep

Sequence

Analyze

Featured workflow: Illumina RNA Prep with Enrichment