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Genomic information has been used to identify genetic diseases, find mutations that drive brain tumor development and track brain tumor outbreaks. Whole-genome sequencing (WGS) provides single-base resolution of the entire genome. In a single run, structural variants (SV) can be identified for large segments of the genome and also include variants that are small enough to be potentially missed. Potentially pathogenic variants can be identified, thus allowing researchers to target further studies of gene expression and regulatory mechanisms.
The ability of WGS to provide a comprehensive view of the entire genome and the ability of Alfa Cytology to handle large sample data make WGS a powerful tool for basic brain tumor research. We can provide WGS services for brain tumor research areas, which can help our clients to obtain more information about brain tumor diseases.
No. | Items |
1 | Data quality control to remove junction contamination and low-quality data |
2 | Comparison with reference sequences, statistical sequencing depth, and coverage |
3 | Somatic SNP / InDel / SV / CNV detection, annotation and statistics (paired samples) |
4 | Susceptibility gene screening |
5 | High-frequency mutation gene statistics and pathway enrichment analysis |
6 | NMF mutation characterization and mutation spectrum analysis |
7 | NovoDriver Known driver gene screening |
8 | Genomic variant Circos map display |
9 | MRT high-frequency mutation gene correlation analysis |
10 | Synergistic analysis of high-frequency mutant genes |
11 | Mutual exclusion analysis of high-frequency mutant genes |
12 | OncodriveCLUST driver gene prediction |
13 | Mutation site distribution analysis |
14 | High-frequency mutant gene SNP/InDel mutation site display |
15 | Predicted driver gene SNP/InDel mutation site display |
16 | High commonness CNV analysis |
17 | CNV distribution analysis |
18 | CNV reproducibility analysis |
19 | Fusion gene detection and Circos map display |
20 | ABSOLUTE tumor purity and ploidy analysis |
21 | Loss of heterozygosity (LOH) analysis |
22 | Intratumor heterogeneity and clonal structure analysis |
23 | Single sample clonal structure analysis (Pyclone) |
24 | Somatic mutation CCF calculation |
25 | NovoDrug high-frequency mutation gene targeted dosing prediction |
26 | NovoDR drug resistance mutation screening |
27 | NovoNoncoding high-frequency mutation analysis of non-coding regions |
28 | Tumor evolutionary tree analysis |
29 | NovoVirus viral integration analysis |
30 | Multi-region sampling clone structure analysis for the same patient |
31 | Multi-sample inter-clonal structural evolution analysis (Pyclone) |
32 | Brain tumor microsatellite analysis |
33 | Brain tumor rearrangement characterization |
34 | Brain tumor telomere length analysis |
35 | Brain Tumor Kataegis analysis |
36 | Neoantigen prediction |
37 | Driver gene prediction |
38 | Mutation spectrum 3D display map |
39 | Conpair analysis of inter-sample concordance and contamination levels |
Sample types: fresh frozen tissue, FFPE samples, blood samples, etc.
With WGS, Alfa Cytology can provide clients with a comprehensive view of the various alterations in a given brain tumor sample, including variants contributed by surrounding normal tissue and tumor clonality, by comparing DNA from a brain tumor and normal samples. Our WGS service also reveals the molecular abnormalities that drive brain tumor development, revealing targets that may help develop new therapies that target only cancer cells while not damaging healthy cells. Please feel free to contact us to learn which genes are mutated and drive the development of brain tumors so that you can select therapies that are best suited to attack specific molecules of cancer and thus provide more effective treatment options to your patients.