Leading Edge Genomic Services & Solutions

Whole Exome Sequencing

Service Overview
Novogene Data
Contact Us

Exome Sequencing ServiceNovogene’s comprehensive human Whole Exome Sequencing (WES) focuses on protein-coding genes to identify etiological variants in diseases such as hereditary genetic disorders and cancer. This service provides a cost-effective alternative to whole genome sequencing with a high-quality, affordable and convenient solution.

Our bioinformatics analysis workflow includes data quality control, alignment with human reference genome, SNP/InDel/CNV calling, statistics and annotation. This service utilizes internationally recognized bioinformatics analysis tools (BWA, SAMtools, GATK, etc.) with various annotation databases (ExAC, COSMIC, 1000 Genomes, etc.) to provide a robust and comprehensive analysis of human exomes.

The Novogene Advantage

  • State-of-the-art exome capture: Agilent SureSelect Human All Exon V6 Kit and Agilent SureSelectXT HS Reagent Kit
  • Unsurpassed data quality: Guaranteed Q30 score ≥80%, exceeding Illumina’s official guarantee of ≥75%
  • Accurate variant calling: Read lengths up to 150 bp
  • Extraordinary informatics expertise: Cutting-edge bioinformatics pipeline with internationally recognized best-in-class software, proving customers with “publication-ready data”

WES Service Overview

Exome Sequencing Service Project Workflow

Sample Requirements

  • For whole blood: Total volume ≥ 2 mL
  • For FFPE tissue: Approximately ten 4-μm sections, each with tissue area ≥ 25 mm2 and tumor content ≥ 20%
  • For extracted DNA: Total DNA ≥ 500 ng; DNA concentration (quantified by Qubit) ≥ 20 ng/μL, Total volume ≥ 10 μL; Purity: OD260/280 = 1.8-2.0 without degradation or RNA contamination

Exome Capture

  • Agilent SureSelect Human All Exon V6 Kit
  • Agilent SureSelectXT HS Reagent Kit

Sequencing Strategy

  • HiSeq X Ten or NovaSeq 6000, PE150

Recommended Sequencing Depth

  • Tumor sample: effective sequencing depth above 100X
  • Normal sample: effective sequencing depth above 50X

Data Quality Guarantee

  • Guarantee of ≥ 80% of bases with a sequencing quality score ≥ Q30, exceeding Illumina’s official guarantee of ≥ 75%.

Turnaround Time

  • Raw data delivery within 10 calendar days for blood or DNA samples, and 12 calendar days for FFPE tissue samples
  • Additional 7 calendar days for standard data analysis

Bioinformatics Analysis Workflow

WES Bioinformatics Workflow

Interested in learning more about our Whole Exome Sequencing service? Click on the link below to fill out a short form and download our informational brochure.

View brochure & validation reports

Novogene provides the highest quality NGS services. We guarantee that over 80% of bases will have a sequencing quality score ≥ Q30. In standard practice, Novogene achieves an average Q30 of 91.07%, exceeding Illumina’s official guarantee of 75%.

Additionally, an average of 98.3% of our raw sequencing data passes the quality control standards for effective clean data.

The following table includes data from our whole exome sequencing service projects, and demonstrates the quality of our sequencing. Alignment of the results to the reference genome (UCSC hg19) showed an average mapping ratio of 99.71%.

Table. Representative human whole exome sequencing data from Novogene
Table - Whole Exome Sequencing

1 Original sequencing data (in gigabases).
2 Percentage of clean reads from all raw reads.
3 Average error rate of all bases in read1 and read2.
4 Percentage of reads with an average quality greater than Q20.
5 Percentage of reads with an average quality greater than Q30.
6 Percentage of G and C bases from total bases.
7 Percentage of total reads that mapped to the reference genome.
8 Average sequencing depth (times coverage) per reference genome target region.
9 Percentage of target region covered by sequencing.
10 Percentage of bases in target region with a sequencing depth ≥ 4x.
11 Percentage of bases in target region with a sequencing depth ≥ 10x.
12 Percentage of bases in target region with a sequencing depth ≥ 20x.

Project Example

The following study utilized Novogene’s expert exome sequencing service.

Single-cell exome sequencing identifies mutations in KCP, LOC440040, and LOC440563 as drivers in renal cell carcinoma stem cells
Cell Research 1-4 (2016)

Renal cell carcinoma (RCC), the most common form of adult kidney cancer, has a low mutation rate. In this study, three novel renal cancer stem cell driver mutations were discovered using Novogene’s advanced single-cell exome sequencing technology. With over 140X coverage, 297 somatic SNVs were found, with 141 of these located in coding regions. Three missense mutations in the loci KCP, LOC440563, and LOC440040 were unique to CD133+ RCC cells and have not been reported in RCC before. This study suggests that these three novel mutations could play significant roles in RCC diagnostics and therapeutic treatment.

 

WES Project Example Fig 1

Figure. Identification of driver genes in renal cell carcinoma stem cells via single-cell exome sequencing

Examples of Publications Using Novogene’s Services

Journal Title
Molecular Neurobiology, 53:5097-5102 (2015) Identification of a novel mutation in the titin gene in a chinese family with limb-girdle muscular dystrophy 2J
Human Molecular Genetics, 25:1875-1884 (2016) Whole exome sequencing identifies lncRNA GAS8-AS1 and LPAR4 as novel papillary thyroid carcinoma driver alternations
The Journal of Pathology, 239:72-83 (2016) Clonality analysis of multifocal papillary thyroid carcinoma by using genetic profiles
Cell Research, 1-4 (2016) Single-cell exome sequencing identifies mutations in KCP, LOC440040, and LOC440563 as drivers in renal cell carcinoma stem cells
For Research Use Only. The content provided herein may relate to products that have not been approved for clinical use by the regulatory authorities of where this document is circulated. The application of such products should thus be limited to research only. The content of this document is subject to change without notice. © 2018 Novogene Co., LTD. All rights reserved. All trademarks are the property of Novogene Co., LTD and its subsidiaries unless otherwise specified.