Leading Edge Genomic Services & Solutions

Clinical-Grade Whole Exome Sequencing

Service Overview
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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 a 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, performed in our US lab, provides a high-quality, affordable, and convenient solution.

Novogene’s bioinformatics analysis includes data QC, mapping with reference genome, SNP/InDel, somatic SNP/InDel calling, statistics, and annotation. Novogene utilizes internationally recognized software in bioinformatics analysis, e.g. BWA, SAMtools, GATK, etc.

In particular, Novogene's bioinformatics pipeline includes annotation with the exome aggregation consortium (ExAC). ExAC dataset spans 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. This population scale database greatly facilitates research of disease pathogenesis.

The Novogene Advantage

  • Unsurpassed data quality: We guarantee a Q30 score ≥80%, exceeding Illumina’s official guarantee of ≥75%. See our data example.
  • State-of-the-art exome capture: Agilent SureSelect Human All Exon V6 (58 M) is used.
  • Accurate variant calling with longer read length up to 150 bp.
  • Extraordinary informatics expertise: Novogene uses its cutting-edge bioinformatics pipeline and internationally recognized best-in-class software to provide customers with publication-ready data.

Project Workflow

Exome Sequencing Service Project Workflow

Exome Capture

  • Agilent SureSelect Human All Exon V6 Kit

Sequencing Strategy

  • 180-280 bp insert DNA library
  • HiSeq platform, paired-end 150 bp

Data Quality Guarantee

  • We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, which exceeds Illumina's offical guarantee of ≥75%.

Sample Requirements

  • Input DNA:
    • For fresh sample: ≥ 1.0 μg (a minimum of 200 ng can be accepted with risk)
  • DNA concentration: ≥ 20 ng/μl
  • DNA volume: ≥ 10 μl
  • OD260/280 = 1.8-2.0 without degradation or RNA contamination

Turnaround Time

  • Within 22 working days after verification of sample quality (without data analysis)
  • Additional 5 working days for data analysis

Recommended Sequencing Depth

  • For Mendelian disorder/rare disease: effective sequencing depth above 50×
  • For tumor sample: effective sequencing depth above 100×

Analysis pipeline

Exome Sequencing Service Analysis Pipeline

Novogene provides the highest quality NGS services. We guarantee that over 80% of bases will have a sequencing quality score ≥ Q30 on Whole Exome Sequencing (WES). Based on our clinical validation using the NovaSeq platform, Novogene achieves an average Q30 of approximately 95%, exceeding Illumina’s official guarantee of ≥ 75%.

The following table demonstrates some of the performance characteristics of our WES assay. Sequences aligned to human reference genome (UCSC hg19) showed an average mapping ratio of 99%.

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. Base calling quality score.
5 Percentage of reads with an average quality greater than Q30. Base calling quality score.
6 Percentage of G and C bases from total bases.
7 Percentage of total reads that mapped to the reference human 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 ≥ 10x.
11 Percentage of bases in target region with a sequencing depth ≥ 20x.
12 Transition/Transversion ratio.

Examples of Publications Using Novogene’s Services

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.
Gastroenterology, 153(1):166-177 (2017)Genetic alterations as esophageal tissues from squamous dysplasia to carcinoma.
Nature Communications 8:823 (2017)Simultaneous evolutionary expansion and constraint of genomic heterogeneity in multifocal lung cancer.
Cancer Research 77:23 (2017)Clonality, heterogeneity, and evolution of synchronous bilateral ovarian cancer.