- Drug R&D
- Animal / Plant
Cancer initiation and progression are driven by a series of genetic and epigenetic alterations that cause either activation of oncogenes or inactivation of tumor suppressor genes, both accompanied by broad alterations in genome utilization and gene expression programs. Cancer research has shifted from a pure genetic to a mixed genetic/epigenetic approach. The emergence of powerful technologies such as next-generation sequencing for genome-wide analysis of genetic, epigenetic or other mechanistic alterations has also impacted the field. These changes will have far-reaching implications for our capacity to understand the causes of cancer, to decipher the pathways and molecules involved and to devise new strategies for prevention and treatment. BGI is part of several cancer research projects and collaborations including the International Cancer Genome Project (ICHG), some of which can be reviewed by visiting our cancer research related publications page.
Building on the expertise that developed from its involvement in these research projects, BGI is able to offer the Cancer Research community comprehensive and innovative Service Solutions including the distinctive ability to perform Single Cell Sequencing and de novo Cell Line Sequencing.
- Sequencing and Analysis – BGI provides whole exome sequencing using NGS platform. Data analysis is performed using BGI’s proprietary software. We screen multi-type mutations and identify their relationship to cancer biology. BGI also offers services to identify copy number variations (CNV) and structure variation (SV) by low depth whole genome resequencing.
- RNA – Transcriptome analysis is performed by RNA-seq. BGI also offers small RNA and microRNA sequencing.
- Single Cell Sequencing – BGI provides an innovative and proprietary approach that utilizes whole genome amplification and next generation sequencing to obtain sequence data at the level of single-cell genomes. It can be applied to discover genetic information in single cells, and allows for the differentiation of those mutations that coincide with the development of cancerous cells and those that spur the cancer’s progression. BGI has sequenced hundreds of cells and the results from applying the new single-cell sequencing method to identify the genetic characteristics of essential thrombocythemia and clear cell renal cell carcinoma have recently been published in Cell journal.
- De novo Cell Line Sequencing – Human immortal cancer cell lines serve as an accessible and often used biological model for investigating basic cancer biology and the efficacy of anticancer drug candidates. The genomes of cell lines may contain large-scale rearrangements. Clear understanding of the genomic background of clonal populations and cell lines is important for proper cell line selection. Selecting the proper cell line increases the relevance of the results and impacts the ability to interpret the validity of results in the context of the Test System. Existing re-sequencing-based methods for calling structural variations from short sequencing reads have limitations: 1) they favor discovery of particular limited length or types of SVs, 2) they are unable to identify SVs at single nucleotide resolution, and 3) they provide low accuracy and validation rate of SV identification. BGI has been able to successfully overcome these obstacles with de novo cell line sequencing and now offers this capability as a service. To learn more, download the De novo Sequencing of Cell Line brochure.
- Bioinformatics – Proprietary software developed by BGI is used to perform analysis to identify somatic mutations, including SNP/InDel/SV/CNV.
|Scientific Research Endeavor||Solution||Technology|
|Detect common gene mutations and variants for tumors or metastasis cells at the genome level||Whole genome research of tumors or metastasized cells||
-Whole genome sequencing: 30X Coverage
|Detect driver genes, germ line, or somatic mutations||Exome analysis to detect oncogenes and disease-related mutations||
-Exome sequencing: 50X Coverage
|Identify cancer-specific small RNAs as biomarkers||Discovery of small RNA biomarkers in cancer||-Small RNA sequencing|
|Study gene differential expressions, novel transcripts, alternative splicing, gene fusion, RNA editing, etc.||Transcriptome research for cancer||-Transcriptome sequencing|
|Determine genetic difference between cancer cell types (primary tumor, metastasis and xenograft or cells from different periods or different subtypes) at the level of single-cell genomeAnalyze cancer-cell evolution during tumor progression||Evolution study of cancer cell based on single-cell Sequencing||-Single cell whole genome amplification|
|Determine cancer subtypes and stagingDiscover biomarkers in response to treatments||Biomarker discovery based on cell line sequencing||-Transcriptome sequencing
-Small RNA sequencing
-Whole genome bisulfite sequencing
Study the pathogenesis of the hereditary cancers and epigenetics effects
Discover oncogenes from germ line and somatic mutations, as well as methylation modifications
|Hereditary study of cancer||-Whole genome sequencing
-MeDIP (or RRBS)