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 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 softwares 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.
- Agilent SureSelect Human All Exon V6 Kit
- 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 Type||Amount (Qubit®)||Volume||Concentration||Purity (NanoDrop™/Agarose Gel)|
|Genomic DNA||≥ 1 μg||≥ 20 μl||≥ 20 ng/μl||No degradation, no contamination|
|Genomic DNA (PCR-free)||≥ 1.5 μg||≥ 20 μl||≥ 20 ng/μl||No degradation, no contamination|
|DNA products of single-cell whole genome amplification||≥ 1 μg||≥ 20 μl||≥ 20 ng/μl||Fragments should be longer than 500 bp|
|FFPE*||≥ 1.5 μg||-||-||Fragments should be longer than 1500 bp|
- Within 25 working days after verification of sample quality for 6G data without data analysis (depending on sample numbers)
- 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×
Monogenic disorders1. Variant filtering 2. Analysis under dominant/recessive model (Pedigree information is needed) 2.1 Analysis under dominant model 2.2 Analysis under recessive model 3. Functional annotation of candidate genes 4. Pathway enrichment analysis of candidate genes 5. Linkage analysis 6. Regions of homozygosity (ROH) analysis
Complex/multifactorial disorders1. Variant filtering 2. Analysis under dominant/recessive model (Pedigree information is needed) 2.1 Analysis under dominant model 2.2 Analysis under recessive model 3. Functional annotation of candidate genes 4. Pathway enrichment analysis of candidate genes 5. De novo mutation analysis (Trio/Quartet) 5.1 De novo SNP/InDel detection 5.2 Calculation of de novo mutation rates 6. Protein-protein interaction (PPI) analysis 7. Association analysis of candidate genes (at least 20 trios or case/control pairs)
Cancer (for tumor-normal pair samples)1. Screening for predisposing genes 2. Mutation spectrum & mutation signature analyses 3. Screening for known driver genes 4. Analyses of tumor significantly mutated genes 5. Analysis of copy number variations (CNV) 5.1. Analysis of CNV distribution 5.2.Analysis of CNV recurrence 6. Fusion gene detection (for WGS project only) 7. Purity & ploidy analyses of tumor samples 8. Tumor heterogeneity analyses 9. Tumor evolution analysis 10. Display of genomic variants with Circos
Customer ServiceAt Novogene, we consider a successful project to be one in which we have generated publication-ready data efficiently, effectively in a short time-frame and gives our customers what they need to aid in the research success.
- In the design and development phase of your project, a team consisting of a Project Manager and Technical Support member will work with you to ensure that we understand your needs and design the project to meet those needs.
- Thoughout the project, the Project Manager and scientific team work closely to ensure that the project proceeds as expected/needed and keeps you updated. At each step along the way, you will be contacted by Novogene team member and given the status of your project and its disposition
- Upon completion of the project we continue to support your needs via scientists at Novogene who are available to answer your questions and assist you in reviewing the information that we have generated. Our support scientists will give you feedback on any inquiry that you have within 24 hours and we provide support on your project for up to one year after project completion.
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 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.
Figure. Identification of driver genes in renal cell carcinoma stem cells via single-cell exome sequencing.
Simultaneous evolutionary expansion and constraint of genomic heterogeneity in multifocal lung cancer
Nature Communications 8:823 (2017)
Tumors are genetically unstable, providing the potential to accumulate novel mutations for expansion; however, their heterogeneity can also be constrained by their functionality as they adapt to environmental pressures. This study explored the simultaneous evolutionary expansion and constraints of tumor genomic heterogeneity in a cohort of multiple synchronous lung cancers (MSLCs). Independent clonality and profound genomic heterogeneity at each multicentric primary tumor, and novel mutations with therapeutical potential, are revealed by Novogene’s whole exome sequencing (WES) when comparing tumors with matched adjacent normal lung DNA. Independent validation of oncogenic pathway convergence with whole genome sequencing (WGS) also indicates that selection for functional convergence plays a significant role in the constraints of new mutations and genomic heterogeneity during oncogenesis. The paper provides exciting insights into utilizing WGS and WES as tools in understanding tumor evolution and finding novel mutations that are therapeutically targetable for further studies.
Figure. Mutational landscape of all 16 sequenced tumor regions. Putative driver genes with somatic mutations were classified according to the functional categories.