Whole Exome Sequencing for Brain Tumors

The human exome contains important information about protein synthesis and is the most direct manifestation of the functions performed by genes. Although it represents only 1-2% of the genome, it contains about 85% of the known disease-associated variants. Whole exome sequencing (WES) is a method that uses sequence capture technology to capture and enrich exonic regions and non-transcribed regions of important regulatory functions for high-throughput gene sequencing. WES allows for more precise identification of disease-associated mutant loci and is cost-effective and economical.

The WES Service for brain tumors we offer

Mutations in whole exome regions are most likely to affect the development of brain tumors. Alfa Cytology provides a reliable method for brain tumor genomic research by accurately detecting SNV and InDel through WES, which can efficiently resolve cancer susceptibility and pathogenicity genes. Our WES service helps researchers to find meaningful biomarkers indicating efficacy and has become the method of choice for comparing brain tumors with normal samples.

• Deeper sequencing depth facilitates the identification of low-abundance mutations in brain tumors.
• Smaller and more manageable data set compared to whole genome sequencing (WGS).
• Comprehensive coverage of coding regions narrows the scope of concern, allowing in-depth study of coding mutations that affect brain tumor biology.
• Not only the CDS region can be evaluated, but also can be extended to the UTR region and miRNA binding sites, allowing a comprehensive view of gene regulation to be obtained.

Services flow

The information analysis service we provide includes, raw downstream data filtered out connectors, low-quality bases, and unmeasured bases, compared to the reference genome for SNV, InDel, and CNV analysis, and then annotated by the database. To ensure high-quality sequencing data, we have set up a strict data quality control system throughout the analysis process.

Bioinformatics analysis projects we offer

Sample type and delivery requirements

• Frozen fresh tissue. Fresh tissue > 5 mg, immediately frozen in liquid nitrogen for half an hour. Store at -80 °C and transport on dry ice.
• FFPE tissue. 3-5 FFPE sections, 4-5 um, 0.6 mm³. please provide H&E stained slices. FFPE sections shipped at room temperature.
• Cells. After centrifugation of >5×10⁵, collected cells are washed twice in PBS buffer and immediately frozen in liquid nitrogen for half an hour. Store at -80 °C and transport on dry ice.
• Plasma/serum. Total volume > 2.5 mL, sodium citrate tubes or EDTA tubes are recommended, heparin anticoagulation tubes are not recommended. Store at -80 °C and transport on dry ice.
• Blood. Total volume > 7.5 mL, sodium citrate tubes or EDTA tubes are recommended, heparin anticoagulation tubes are not recommended. Store at -80 °C and transport on dry ice.
• gDNA. DNA dissolved in TE buffer, total volume > 300 ng, concentration 20-100 ng/μL, volume > 10 μL.

The low cost and high yield of WES have become a clear advantage over WGS technology. Alfa Cytology uses WES to reveal variant features at the gene level in brain tumors, including data indicators such as tumor mutational load, mismatch repair defects/microsatellite instability, and copy number variation. This may offer new hope in the search for predictive markers for immunotherapy. Please feel free to contact us for more information and to better utilize WES for brain tumor susceptibility, pathogenesis, heterogeneity, metastasis and recurrence, and drug efficacy studies.