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Research Services

Human Whole Exome Sequencing

Introduction to Human Whole Exome Sequencing

Human whole exome sequencing (WES) is a technique used to sequence all the protein-coding regions of the human genome, known as exome. The exonic region constitutes about 1-2% of the human genome but contains approximately 85% of the known disease-related variants. By targeting these regions, human whole exome sequencing (hWES) allows one to analyse various genomic variants, germline mutations and somatic mutations. It is a cost-effective alternative to human whole genome sequencing and has applications in diverse areas such as identifying genetic disease-related variants, discovering biomarkers and therapeutic targets, studying complex diseases, cancer research, or human population genetics.

Novogene has extensive experience with human whole exome sequencing with a variety of commercial WES panels from leading providers such as IDT, Twist, Agilent etc. Our hWES service is complete with high-quality data, bioinformatics analysis with variant annotation and “publication-ready’’ figures accompanying the analysis.

Applications of Human Whole Exome Sequencing

Human whole exome sequencing has applications in several fields such as:

  • Detection of genomic variants for research and/or diagnostics 
  • Cancer research 
  • Clinical research 
  • Evolutionary biology 

Benefits of  Novogene’s Human Exome sequencing service

  • Extensive Experience: Novogene has extensive experience with human whole exome sequencing using variety of mainstream WES panels such as from IDT, Agilent, Twist etc. 
  • Choice of WES panels: We support projects using WES panels from variety of commercial vendors such as IDT, Twist, Agilent etc. Our Twist WES data is complete with mtDNA panel, providing you with insights regarding mitochondrial variants. 
  • High-Quality Data: We deliver high-quality sequencing data that meets leading industry standards.   
  • Bioinformatics Support: We provide comprehensive bioinformatics support, including SNV, InDel, CNV analysis, complete with ‘publication ready’ figures using your data base of choice.  
  • Short Read and Long Read Sequencing: Novogene provides the option of carrying out your sequencing projects with your choice of sequencing strategy, short read and long read, using the latest sequencing platforms on the market.   
  • Fast Turnaround Times: Our sequencing labs are located near you, in Germany and the UK, allowing for reduced shipping times. With our large sequencing capacity, automated and streamlined workflows, we ensure that you receive your data promptly without compromising on quality   
  • Customer Service System (CSS): Novogene’s Customer Self Service System (CSS) is an online project management portal that streamlines project management and provides direct access to all your sequencing projects in one place. You can view your sequencing project(s), track their progress, access reports, collaborate with your team members, and obtain other useful information at one place. 

Whole Exome and Target Region Sequencing Service Flyer

Whole Exome Sequencing provides a cost-effective alternative to whole genome sequencing, as it targets only the protein coding region of the human genome responsible for the majority of known disease-related variants. Whether you are conducting studies in rare mendelian disorders, complex disease, cancer research, or human population studies, Novogene’s comprehensive human whole exome sequencing service provides a high-quality, affordable, and convenient solution. Target region sequencing focuses on gene subsets related to a certain disease or phenotype and is even more cost-effective than WES when investigating regions of interest, achieving delivery of much higher coverage and identification of rare variants.

Download the Service Flyer

On-demand Webinar

Getting Started with Genomics: Next Generation Sequencing Essentials for 2024

This webinar will provide an accessible introduction to NGS principles and its pivotal role in decoding the secrets of DNA. It will explore the basics of DNA sequencing applications and provide insights into the array of technological platforms available, including Illumina, PacBio, and Oxford Nanopore. Whether you’re a beginner or an experienced professional, this webinar is set to offer a foundational understanding of NGS that will enhance your journey with genomic technologies.

The session will also touch upon Novogene’s contributions to the genomics field and detail the expanded services available for European customers that have contributed to this.

Learning Objectives:

  • Gain foundational knowledge of NGS principles
  • Understand the basics of DNA sequencing applications and technologies
  • Learn about recent developments in NGS technology and services.

Watch Now

hWES Specifications: DNA Sample Requirements

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

*Formalin-Fixed, Paraffin-Embedded; cell-free DNA, circulating-tumour DNA

Project Workflow of Novogene hWES Services

From sample preparation, library preparation, DNA sequencing and data quality control, to bioinformatics analysis, Novogene provides high-quality products and professional services. Each step is performed in agreement with a high scientific standard and meticulous design to ensure high-quality research results.

[1]https://www.nature.com/articles/jhg2013114

Publications of Human Whole Exome Sequencing

Human whole exome sequencing (hWES) enables researchers to cost-effectively unveil protein-coding variants in rare Mendelian disorders, complex disease, cancer, or human population studies. Here we summarized some outstanding academic publications that have used Novogene hWES services.

Data Quality Control

Sequencing Error Rate Distribution

The sequencing error rate is the major confounding factor of precise detection of low-frequency variations by deep sequencing. It determines the quality of the sequencing data. The sequencing error rate is highly associated with the sequencing cycle, escalating towards the end of each read because of the consumption of chemical reagents, which is a common feature of the Illumina high throughput sequencing platform.

Novogene hWES Error Rate Distribution

Note: The x-axis represents the position in reads, and the y-axis indicates the average error rate of bases of all reads at a position.

GC Content Distribution

GC content distribution aims to check the potential of AT/GC separation. Sample contamination, sequencing bias, and errors during library preparation can impact on the sequencing results.

Note: The x-axis represents the position in reads, and the y-axis indicates the percentage of each type of bases (A, T, G, C); different bases can be distinguished by different colors.

Alignment to Reference Genome

Sequencing Depth & Coverage Distribution

Sequencing depth and coverage illustrate the average number of pair-end clean reads which are aligned to the known reference nucleotides. The sequencing coverage distribution determines whether the identification of variations can be done with a certain degree of confidence at specific base positions.

Novogene hWES Sequencing Depth & Coverage Distribution

Average sequencing depth (bar plot) and coverage (dot-line plot) in each chromosome

Note: The x-axis represents the chromosome; the left y-axis indicates the average depth; the right y-axis shows the coverage (proportion of covered bases).

SNP and InDel Calling, Annotation and Statistics

Single nucleotide polymorphisms (SNPs), also known as single nucleotide variants (SNVs), constitute the largest class of genetic variants in the genome. Another class of genetic variations includes small insertions and deletions (InDels) which are <50 bp in length. The InDels present in the coding region or splicing sites may cause changes in mRNA transcripts and proteins.

Novogene hWES SNP Detection

The number of SNPs/inDels in various genomic regions

Novogene hWES SNP Detection

The number of different types of SNPs/InDels in the coding region

Advanced Analysis

Driver Gene Analysis

Heatmap of significantly mutated genes

Only a few mutations related to cancer can drive tumorigenesis by affecting genes. Significantly mutated genes (SMGs) refer to those mutations that show a significantly higher mutation rate than the background mutation rate (BMR), thus indicating a positive selection during tumorigenesis. Analysis of SMGs helps us pinpoint the key genes that are critical for cancer initiation and progression.

Novogene hWES Heatmap of Significantly Mutated Genes

Heatmap of significantly mutated genes (SMGs) across samples

Note:
The bar plot at the top shows the mutation rate of each sample (Mutations/Mb). The heatmap in the center shows the mutation types of each SMG across samples. The horizontal axis represents samples, and the vertical axis represents SMGs. Different mutation types are distinguished by different colors. The bar plot on the left side of the heatmap shows the percentage of samples affected by mutations in each SMG, and the plot on the right side shows p values of SMGs.

Tumor Heterogeneity Analysis

Intra-tumor Heterogeneity Analysis

Intra-tumor heterogeneity refers to the heterogeneous composition of tumor cells. Deciphering the intra-tumor heterogeneity and clonal architecture may contribute towards the understanding of therapeutic resistance.
The number and content (subclonal somatic mutations) of tumor subclones were identified by analyzing the variant allele frequencies of somatic mutations.

Novogene hWES Heatmap of Significantly Mutated Genes

Note:
The horizontal axis of each panel represents variant allele frequency(VAF). A cluster of mutations with relatively low VAF represents a subclonal population. The top panel shows kernel density of VAFs across regions with copy number one, two, or three, posterior predictive densities summed over all clusters for copy number neutral variants, and posterior densities for each cluster/component. The panels below the top panel show read depth versus VAFs for each class of copy number regions.

*Please contact us to get the full demo report.

More Research Services

Target Region Sequencing (TRS)

Mouse Whole Exome Sequencing

Clinical Whole Exome Sequencing (CLIA/CAP)