Data Annotation and Analysis
The Syngene Data Annotation and Analysis teams provide a range of services to aid early discovery, target indentification and validation and biomarker discovery. This includes preparation of pharmacogenomic target reports, data analysis of high throughput genomic & proteomic data, pathway annotation & knowledgebase curation, and clinical relevance of NGS data.
Pharmacogenomic Target Dossiers
Target dossiers built around a target or interest includes data compiled from various public databases and an exhaustive literature survey, providing an integrated pharmacogenomic report on the target, as well as the suggested methods for target validation, categorized under the following sections:
- Gene Summary
- Protein Domains
- Alternate Transcripts
- Promoter Analysis
- Gene summary
- Polymorphisms with potential functional implications (NCBI-dbSNP)
- Variations in Minor Allele Frequencies in Caucasian population
- Sites of polymorphisms on the protein sequence/ structure
- Literature reported polymorphisms
- Other Genetic Alterations
- Somatic Mutations
- Chromosomal Aberrations
- Methylation and Acetylation
- miRNAs targeting the gene
- Mouse ortholog
- Gene-Disease Association
- Functional role in normal tissue
- Role in human diseases/disorders
- Effect of inhibition/activation
- Target Validation
- Experimental assays for the genetic confirmation of the functional role of the target
- Experimental assays to validate the role of the target in disease and the effect of inhibition/activation
- Experimental assays to validate the targeting potential of likely inhibitors/activators
Data Analysis and Pathway annotation
High throughput genomic data can be used to derive insights into genes and pathways that are altered either in a disease or upon treatment with a drug or NCE either in vitro or in vivo. This can lead to a better understanding of the biology behind the observed phenotypes, targets that may be valuable, actions of a drug or a drug class and surrogate markers of interest. Our team can analyze these data sets efficiently to provide:
- An understanding of the significant differential gene expression patterns relative to the condition of interest.
- An association of the gene expression signature obtained with the most relevant signalling pathways that may be impacted.
- A review of the published literature for each relation to obtain a precise and succinct pathway annotation that may be represented as curated pathway figures.
Knowledge Base Curation
Our team can create knowledge bases and annotated interaction networks in a specific disease area or organ of interest. These curated pathways can be used to overlay data from experiments, derive therapeutic hypotheses, generate mechanism of action and compare compounds based on their biological effects.
Clinical Relevance of NGS Data
Clinical interpretation of variants identified via NGS is crucial in applying the knowledge obtained from the mutation profile for better health care. Scientists in the bioinformatics team are experienced in interpreting NGS data obtained from sequencing of germline/somatic mutations in several disease areas including genetically defined diseases, cardiac disorders and cancer.