Whole Exome Sequencing (WES)

Whole Exome Sequencing

Protein-coding region sequencing for rare disease research, cancer genomics and population-scale variant studies.

Whole exome sequencing (WES) focuses on the protein-coding regions of the genome, where many functionally important variants are found. It provides a targeted and cost-effective approach for studying genetic variation in human disease research, cancer genomics, complex disease studies and population genetics.

Novogene Europe supports WES projects as part of its broader multi-omics service portfolio, combining exome capture, high-throughput sequencing, quality control and bioinformatics analysis to help researchers generate reliable data for genomics studies.

Service Highlights

Focused Exome Analysis

Target protein-coding regions of the genome to study variants associated with disease mechanisms, inherited conditions, complex traits and biological function.

Proven Capture Panels

Commercial exome capture panels, including IDT, Agilent SureSelect and Twist, support human WES studies and selected model organism applications.

Consistent Data Quality

High-throughput sequencing workflows and quality control processes support reliable data generation for downstream WES analysis.

Clear Variant Annotation

Bioinformatics analysis supports exon-based variant detection, annotation and reporting for disease-focused, cohort-based and exploratory genomics studies.

Applications

Disease Variant Research

WES supports exon-based variant analysis for studies of inherited disease, complex disease and disease-associated genomic variation, helping researchers focus on functionally relevant coding regions.

Cancer Genomics

Exome sequencing can support tumour-focused research by identifying somatic variants, copy-number changes and genomic alterations associated with cancer biology, progression and treatment response.

Population Studies

WES provides efficient coding-region data for studying genetic variation across cohorts, populations and ancestry-related research questions.

Model Organism Research

Selected exome panels can support mouse and other model organism studies, helping researchers investigate genetic variation, disease models and genotype–phenotype relationships.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Sample Type	Amount (Qubit®)	Volume	Concentration	Purity (NanoDrop™/Agarose Gel)
Genomic DNA	≥300 ng	≥20 ul	≥15 ng/uL	OD260/280 = 1.8-2.0; no degradation, no contamination Fragments longer than 3000 bp
FFPE DNA	≥300 ng	≥20 ul	≥15 ng/uL	Fragments longer than 1000 bp
cfDNA/ctDNA	≥30 ng	-	≥0.5 ng/μL	Fragments of 170 bp or its multiples, no genomic DNA contamination

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Sequencing Depth	For Mendelian disorder/rare disease: effective sequencing depth above 50× (6G)
Sequencing Depth	For tumor sample: effective sequencing depth above 100× (12G)
Data Analysis	Data quality control Alignment to a reference genome SNP and InDel calling Somatic SNP/InDel/CNV mutation detection (tumor-normal paired samples)

Resources

Example Analysis Output

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Chromosome Depth Coverage

Visualise sequencing depth across chromosomes to assess coverage distribution, capture consistency and regions with uneven read support.

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Sequence Depth Distribution

Review read-depth distribution across target regions to evaluate sequencing consistency and support reliable downstream variant analysis.

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Mutation Spectrum

Summarise mutation types and base-substitution patterns to support interpretation of variant profiles across samples or study groups.

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Mutated Gene Landscape

Display recurrently mutated genes and sample-level mutation patterns to explore key genomic features across a cohort.

Webinars

Getting Started with Genomics: Next Generation Sequencing Essentials for 2024

Discover the fundamentals of Next-Generation Sequencing (NGS) and learn how leading technologies such as Illumina, PacBio, and Oxford Nanopore are advancing genomic research and unlocking new possibilities in DNA analysis.

Learn More

Frequently Asked Questions

What types of variants can WES detect?

WES detects SNVs and small insertions/deletions (InDels) within protein-coding regions. Exon-level copy number variation (CNV) analysis is also available.

How does WES differ from whole genome sequencing?

What sequencing depth do WES projects use?

Which exome capture panels does Novogene support?

What DNA quality does WES require?

Is WES suitable for rare disease research?

Can WES scale to large studies?

Explore Genomics Insights

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

Speak with a Specialist

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