Exome & Target Region Sequencing
Technical Information
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Exome sequencing is an innovative technique that selectively targets the most functionally relevant DNA sequences that encode proteins. Human exome sequencing can identify novel genes associated with both Mendelian disorders and common diseases. Target region capture means enriching specific regions (e.g., HLA region) or specific genes, by microarray hybridization (NimbleGen Sequence Capture Array) or solution hybridization (Agilent Sure-Select™ system) based on probes designed according to the sequences of interested regions.

To date, BGI has sequenced 14,000 human exomes and 6,200 human target region samples. BGI also has rich experience in exome sequencing for plants and animals. For example, we provide mouse exome sequencing service using Agilent Mouse All Exon kit. In addition, we initiated the Chinese rhesus macaque and Cynomolgus macaque genome project and, based on the data from this study, designed the exome capture array and developed the exome sequencing platform for monkey to facilitate biomedical research.



  1. Most disease-related variations are located within exons
  2. Capture both common and rare variants missed in traditional GWAS studies
  3. 150 next-generation sequencers assures rapid turnaround
  4. 1000 bioinformaticians generate high-quality, reliable data

Target Region sequencing:

  1. Focused and in-depth investigation on genetic variants of interest
  2. Suitable for large sample sizes with high throughput
  3. More cost effective than PCR
  4. Rapid turnaround time to accelerate publication & application

Customer Testimonial:

"We use BGI as a NGS service provider for many of our targeted region re-sequencing projects. BGI has consistently provided high-quality data with a very quick turnaround time. I know exactly what to expect in terms of delivery time and data quality, which is vital for our business operations."
- Dr. Eric Lin, Chairman of the Board, Otogenetics Corporation

BGI has successfully completed numerous exome sequencing projects, including a Danish study of 1000 patient samples and 1000 controls with the aim of finding rare SNPs associated with metabolic disorders such as obesity and hypertension.

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude.
Science 329, 75 (2010)


50 exomes of ethnic Tibetans were sequenced for 18X per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This research can help us to prevent and cure the disease of plateau anoxia.

Frequent Mutations of Chromatin Remodeling Genes in Transitional Cell Carcinoma of the Bladder. Nature Genetics. 7 Aug 2011.

Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP- EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC.

Bioinformatics Analysis

  1. Data filtering (removing adaptors contamination and low-quality reads from raw reads)
  2. Alignment and summary of data production
  3. Assembly of consensus sequences
  4. SNP, Indel, CNV, and SV detection and annotation

Advanced Analysis:

  1. Population analysis
  2. Cancer advanced bioinformatics analysis
  3. Complex diseases advanced bioinformatics analysis
  4. Mendelian disorders advanced bioinformatics analysis

Custom Bioinformatics Analysis:

In addition to our Advanced Analysis, we offer customized bioinformatics analysis based on your particular research needs. Ask us how to get started!

Exome Capture Arrays

BGI currently has the capacity to process 800 samples of exome capture per week. There are mainly two exome capture strategies which both deliver a high-level performance and substantial savings on sequencing. Both NimbleGen SeqCap EZ (Biotinylated DNA oligonucleotide probes) and Agilent SureSelect system (Biotinylated RNA probes) can capture all exons in solution via a simple, scalable workflow and stringent built-in quality controls.

Exome capture arrays that we perform are as follows:


Human Exon Capture Array:

Design Capture Targets (Mb) (Regions Covered by Probes) Database Used to Select Primary Targets

NimbleGen SeqCap EZ Exome V2.0


CCDS Sep 2009+miRBase V14, Sep 2009+ RefSeq Jan 2010

Agilent SureSelect Human All Exon V2 (developed with Broad)


V1 + additional RefSeq contents including CCDS sep 2009

Agilent SureSelect Human All Exon 50 Mb (developed with Sanger)


CCDS sep 2009 + miRBase V14 + GENCODE + Sanger

Agilent SureSelect Human All Exon V1 (developed with Broad)*


CCDS Sep 2008 + miRBase V13

*Limited Quantity

Mouse Exome Capture Array:

Exome capture kit Insert size

Agilent SureSelect Mouse
All Exon

450 Mb

150-200 bp

NimbleGen Maize All

36 Mb

200-300 bp

Sample Requirements:

Human Exome Sequencing:

For the genomic DNA samples you will provide us:

  1. Purity: OD260/280=1.8-2.0, without degradation and RNA contamination.
  2. Concentration: ≥50ng/μl
  3. DNA amount: single library preparation starts from at least 10μg, the more the better.

Human Target Region Sequencing:

For the genomic DNA samples you will provide us:

  1. Purity:OD260/280=1.8-2.0, without degradation and RNA contamination.
  2. Concentration: ≥50-200ng/μl
  3. DNA amount: single library preparation starts from ≥30μg (using NimbleGen Sequence Capture Array, targeted region>17Mb) or ≥6μg (using Agilent SureSelect System/NimbleGen Sequence Capture Array when the targeted region is smaller than 17Mb).

Mouse Exome/Target Region Sequencing:

  1. Sample purity: OD260/280=1.8~2.0.
  2. Sample condition: DNA samples without degradation and RNA contamination
  3. Sample quantity demanded: ≥ 30 μg (using NimbleGen Sequence Capture Array when the targeted region is larger than 17 Mb) or ≥ 6 μg (using Agilent SureSelect System or using NimbleGen Sequence Capture Array when the targeted region is smaller than 17 Mb)
  4. Sample concentration: ≥ 50 ng/μl.

Monkey Exome Sequencing:

  1. Condition: DNA samples without degradation and RNA contamination
  2. Quantity demanded: ≥ 6 μg (for two times library construction in case there is a failure)
  3. Concentration: ≥ 50 ng/μl
  4. Purity: OD260/280 =1.8~2.0.