Whole Genome Sequencing for Brain Tumors

Genomic data has revolutionized the identification of genetic diseases, pinpointing mutations propelling brain tumor progression and monitoring tumor outbreaks. Whole-genome sequencing (WGS) offers precise single-base resolution of the entire genome. This capability enables the identification of potentially pathogenic variants, guiding researchers to investigate gene expression and regulatory mechanisms of brain tumors in greater depth. Alfa Cytology offers advanced whole genome sequencing specially designed for brain tumor research.

Fig.1 Whole-genome sequencing (WGS) data reveal diverse forms of genomic alteration. (Zhao EY., et al., 2019)

Whole Genome Sequencing in Brain Tumors

Whole genome sequencing (WGS) promises to deliver precise and comprehensive analyses of the brain tumor genome in its entirety, covering coding mutation regions and non-coding regions such as introns, regulatory elements and intergenic regions. Leveraging next-generation sequencing, WGS can uncover structural variants (SVs) and copy number variants (CNVs) across extensive genome segments during brain tumor development, capturing even subtle variants that might otherwise be missed in one sequencing run. Hence, WGS serves as a potent tool to unveil the impact of non-coding regions on brain tumor progression, offering a comprehensive view of the driver mutations in brain tumors.

Our Services

The comprehensive insights provided by whole genome sequencing combined with in-depth sample data analyses highlight whole genome sequencing as a powerful tool for foundational brain tumor research. Alfa Cytology offers advanced whole genome sequencing services that cater to brain tumor research, enabling our clients to achieve a deeper understanding of brain tumor advancement. Our whole genome sequencing services include but are not limited to the following contents.

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 tissues, FFPE samples, blood samples, etc.

Workflow of WGS

Sample Preparation

Library Construction

Sequencing

Data Analysis

Advantages of Our WGS

In addition to capturing data on gene expression regions, whole genome sequencing can also reveal insights into introns and intergenic regions.
WGS can be conducted on diverse brain tumors for bioinformatic analyses at both individual and group levels.
WGS allows for the thorough identification of various variants like single nucleotide variations (SNVs), copy number alterations (CNVs), insertions and deletions (InDels) and structural variations (SVs) from the genome.

Contact Us

Whole genome sequencing plays a crucial role in screening susceptibility genes related to brain tumors, exploring pathogenesis and genetic mechanisms, and identifying potential molecular targets associated with brain tumor development. Alfa Cytology provides advanced and comprehensive whole genome sequencing services tailored to brain tumors. If you have any other questions about our whole genome sequencing services, please do not hesitate to reach out to us.

Reference

Zhao EY.; et al. (2019). Whole-Genome Sequencing in Cancer[J]. Cold Spring Harbor perspectives in medicine. 9(3), a034579.

All of our services and products are intended for preclinical research use only and cannot be used to diagnose, treat or manage patients.