“We did whole genome sequencing plus advanced bioinformatics analysis using Novogene earlier this year. I am very satisfied with their professional, skillful and high-quality services. In particular, the bioinformatics knowledge and expertise in the project team were very impressive. They provided great support, rapid turn-around, and pricing that enables us to do more science with our limited budget. I really appreciate their willingness and ability to explore more advanced bioinformatics analysis to meet the specific requirements of my projects. With these in mind, I have initiated two additional RNA-Seq projects with them and recommended two collaborators to use Novogene’s sequencing service.”
“I am extremely satisfied with the quality and turn-around of the WGS results Novogene delivered. They have outstanding informatics/analysis, highly responsive and effective support, advanced Illumina technology (such as the X Ten), all at highly competitive prices.”
The Novogene Advantage
- State-of-the-art NGS technologies: Novogene is a world leader in sequencing capacity using state-of-the-art technology, including Illumina HiSeq X and NovaSeq 6000 Systems.
- Highest data quality: We guarantee a Q30 score ≥ 80%, exceeding Illumina’s official guarantee of ≥75%. See our data example.
- Extraordinary informatics expertise: Novogene uses its cutting-edge bioinformatics pipeline and internationally recognized, best-in-class software to provide customers with highly reliable, publication-ready data.
- 350 bp insert DNA library
- HiSeq X platform or NovaSeq 6000 platform, paired-end 150 bp
Data Quality Guarantee
- We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, which exceeds Illumina’s official 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|
- 18 working days after verification of sample quality without data analysis (depending on sample numbers)
- Additional 8 working days for data analysis
Recommended Sequencing Depth
- For tumor tissues: 50×, adjacent normal tissues and blood 30×
- For rare diseases: 30-50×
Bioinformatics Analysis includes:
- Data quality control: filtering out reads containing adapters or with low quality
- Alignment with reference genome, statistics of sequencing depth and coverage
- SNP/InDel/SV/CNV calling, annotation and statistics
- Somatic SNP/InDel/SV/CNV calling, annotation and statistics (paired tumor samples)
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 5.3 De novo CNV/SV and De novo SV/CNV detection 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 porject only) 7. Purity & ploidy analyses of tumor samples 8. Tumor heterogeneity analyses 9. Tumor evolution analysis 10. Display of genomic variants with Circos
Project ExampleThe following studies utilized Novogene's expertise in whole genome sequencing on HiSeq X Ten. Genetic alterations in esophageal tissues from squamous dysplasia to carcinoma Gastroenterology 153:166-177 (2017) Esophageal cancer is a major worldwide health threat, and intraepithelial neoplasia (IEN) is considered to be a precancerous lesion of esophageal squamous cell carcinoma (ESCC), one subtype of esophageal cancer. This study incorporated Novogene’s whole genome sequencing, together with whole exome sequencing and targeted sequencing, to track genetic changes in patients during development of ESCC. The study revealed significant similarities in the types and frequency of mutations between IEN and ESCC, including similarity in the DNA damage mutation signature. Mutations in the CCND1, CDKN2A, and FGFR1 genes were also revealed as the early driver events from phylogenetic and clonal analysis. However, the number of non-overlapping SNVs in tissues taken from the same individuals indicated that various lesions formed independently and that there was independent clonal expansion of mutations. As shown in this study, using multiple NGS applications provides novel approaches for exploring early diagnostics and treatments for cancer.
Examples of Publications Using Novogene’s Services
|Gastroenterology, 153(1), 166-177 (2017)||Genetic alterations in esophageal tissues from squamous dysplasia to carcinoma.|
|Oncogene, 36: 746-755 (2017)||Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions.|
|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.|
|Molecular Psychiatry, doi: 10.1038/s41380-018-0020-x (2018)||A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development.|