Whole Exome Sequencing (WES)

Service Overview

Whole exome sequencing (WES) refers to sequencing of genome-wide exons, which can be enriched by sequence-based capturing. Although exon only takes up approximately 1% of whole genome, it represents the profile of total protein functions directly. In human genome, it has been reported that more than 85% of disease related mutations occur in protein coding region.

Service Workflow

Experimental Design / Sampling guidance
Sample quality control
WES Library Construction
HiSeq sequencing/Data quality control
Data analysis/After-sale technical support
Sample type: Whole blood, PBMC, frozen tissue, FFPE samples, plasma, amniotic fluid cells, etc.

Sequence library: Single cell library (in pg), ordinary library (1 μg), low in-put library (30-100 ng) DNA extraction and library construction kits are selected based on types of samples.

Exon capturing platform: SureSelect Human All Exon v6

Bioinformatic analysis

Results Demo

Mapping against reference genome

Clean data is mapped against reference genome to evaluate similarity of sequencing data and reference, which is presented as mapping ratio. Sequencing depth refers to the ratio between mapped data over reference genome size. Coverage refers to the percentage of mapped length in that of whole genome.

SNV Identification

SNV and Indel are identified by mapping against reference genome. Different types of SNV are counted in different coding regions.

Mutational Signature NMF clustering analysis

Different mutagenesis processes such as DNA replication infidelity, genotoxin exposures, etc. during DNA replication may lead to specific types of mutations, which are known as mutational signatures. According to the bases next to SNV (±1 bp), SNV can be classified into 96 types. NMF (non-negative matrix factorization) clustering analysis is processed based on the frequency of these types and classified SNV into different mutational signatures.

Distribution of driver genes/ Mutation spectrum

Significantly mutated genes (SMGs) are identified by analyzing gene mutation rate and background mutation rate with MutSigCV software. SMGs are more likely to be driver genes.

Highly frequent CNV analysis (GISTIC recurrence analysis)

Copy number variation (CNV) refers to the changes in copy number of a certain DNA fragment on genome. The lost fragments in somatic CNV may contain tumour suppressor genes, while added fragments may introduce oncogene. GISTIC is employed here to analyze the distribution of somatic CNV and identify highly frequent CNV.

Tumour purity analysis

Clinical tumor samples are mixture of tumor cells and normal cells. The purity of tumor can affect the identification of somatic mutations. ABSOLUTE is employed to calculate tumor purity and ploidy based on copy number of the genome and somatic CNV frequency.

Service Advantages

50+ skilled experts in analysis
Diverse successful cases
Highly-experienced technical team
3 distributed computer cluster servers
In-depth data interpretation
Optimized reports delivery
Professional after-sale support
Rapid analysis


1How to decide sequence depth in whole exome sequencing?
Answer: In disease research, i.e. germline variation research, 10 Gb/sample is recommended. In Tumor somatic mutation research: 15-20 Gb/sample is recommended for tumor tissue. (More data might be required for tumor with low purity.) For control samples: 10 Gb/sample is recommended.
2What is WES capture efficiency? How to calculate sequencing depth?
Answer: Capture efficiency refers to the ratio between sequences mapped to targeting region (valid sequences) and total sequence mapped to reference genome. Capture efficiency won't affect quality of data, but valid mapping ratio. Normally, capture efficiency of targeting region is approximately 60% - 70%. The size of targeting region defined by exon capturing kits, e.g. Roche and Agilent, is approximately 60 Mb. In this case, sequencing depth=10G*60%/60 Mb=100X.
3DNA extracted from FFPE samples is usually heavily degraded and of low amount. Is it still suitable for WES?
Answer: FFPE samples are very common in clinical samples. We strongly recommend to send FFPE sample to Biomarker Technologies for DNA extraction. Our molecular lab has accumulated massive experience in DNA extraction from abnormal samples, including degraded samples at different levels, cfDNA, etc. For FFPE samples, we have specific kit to correct C-T substitution caused by chemical decoration. Moreover, our technical team is highly-skilled in low in-put library construction.