Discovery of Novel Biomarkers
Genes, genomic DNA sequences, DNA methylation status, and gene expression levels are all important indicators of normal and pathological processes. These biomarkers are valuable tools to determine the efficacy of therapeutic agents, to identify patient subpopulations that may experience the greatest benefits of a treatment, and to establish the presence or severity of a disease. Profiling strategies that identify diagnostic, prognostic, or screening markers can include genomic, transcriptomic, or proteomic profiling approaches. Often combinatorial studies will interrogate multiple biomolecule types to best understand the bioactivities associated with a disease and/or treatment1-5. Subsequent confirmation studies are critical to accurately identify reliable biomarkers that overcome the inherent variability between patients.
ORB has supported initiatives to establish markers in the neurology, oncology, cardiovascular, and gastrointestinal disease areas. ORB’s wet lab and in silico analysis services are designed to reduce attrition and accelerate the drug discovery and development process. Because the implementation of biomarker driven strategies do not stop in the lab, ORB also provides support for patent and FDA applications as well as publications for each project. Client records are maintained with strict confidentiality.
ORB Platforms to Enable Biomarker Discovery
ORB scientists are highly experienced with the identification of markers using a variety of platforms including Illumina sequencing, microarray, and immunoassays. ORB’s biomarker discovery workflow is optimized and validated with non-invasive sample types such as biofluids as well as FFPE tissues due to their ideal storage parameters. Repeatedly, ORB has demonstrated the detection and confirmation of microRNA, proteins, and exosomal RNA. Genomic and epigenetic analyses can also be utilized to identify germane oncogenes or genetic variants in cancer research as well as the analysis of methylation patterns using cell-free DNA bisulfite sequencing. After candidate selection, ORB provides GLP microRNA or analyte confirmation with real-time qPCR or single-plex protein assays.
In addition to standard statistical analyses, ORB provides predictive modeling services, which employ advanced statistical learning techniques such as logistic regression analyses, support vector machines, and K-nearest neighbors, to accurately identify an actionable candidate multivariate marker set.
ORB offers analysis of 6 biomolecules from biological fluids: mRNA, long non-coding RNA, small RNA, oncogenes, methylated cfDNA, and proteins. For most biofluid studies, starting materials are often extremely limited, therefore ORB incorporates pilot studies wherever possible to optimize the sample dilution and promote judicious use of biofluid samples. ORB scientists are highly experienced with a wide variety of circulatory, excreted, and secreted biofluids.
ORB’s small RNA sequencing and microRNA microarray services are optimized for degraded RNA in order to provide researchers tools to identify biomolecular markers formalin-fixed, paraffin-embedded tissues.
To facilitate the identification of circulating exosomal RNA biomarkers, ORB offers long and small RNA extraction from biofluid-based exosomes as well as the analysis of these molecules and their respective roles in cell-to-cell communication using RNA sequencing and microarray technologies .
ORB's RNA sequencing enables predictive modeling analyses to identify potential genetic biomarkers, e.g. mRNA, long non-coding RNA, and small RNA molecules, using the Illumina NextSeq 500, HiSeq 2500 and HiSeq 4000 instruments. ORB workflows are optimized for ultra-low and degraded input to facilitate analysis for studies with limited starting material.
ORB offers microRNA microarray services using Affymetrix industry standard arrays and miRBase 19 high sensitivity microarrays which are proprietary to ORB. ORB’s mirBase 19 microarray process is optimized for low input biofluid samples and is available at the lowest price in the industry.
A complete service for the accurate and sensitive quantification of proteins in a wide variety of samples including plasma, serum, cerebrospinal fluid, urine, and breast milk. Custom panels can be designed to evaluate up to 60 analytes in parallel, and markers are available for numerous disease areas including oncology, cardiology, diabetes, obesity, and autoimmune disorders.
Cell-free DNA Bisulfite Sequencing
Characterize methylome patterns in circulating cell-free DNA (cfDNA) to identify biomarkers from blood-based biofluids.
Investigate the mutational status of cancer patients, using either liquid biopsies or tumor samples for isolation of cfDNA or cellular DNA respectively. ORB offers ultra-high coverage sequencing of gene panels available from Swift Biosciences, Illumina, and other manufacturers. ORB provides library preparation, sequencing on the NextSeq 500, and a full analysis of genetic variation to enable the detection of known variants as well as discovery of novel variants in patient samples.
ORB’s well-researched algorithms are designed to search for predictive biomarkers that are clinically relevant for diverse purposes.
Real-Time qPCR Assays
Real-time qPCR assays provide precise discrimination and quantitation of genes and mature microRNAs. This method provides the ultimate customization to support confirmation studies that follow broader examinations using RNA sequencing or microarray assays. ORB can provide GLP ABI Taqman assays upon request to support the development of your therapeutic and/or companion diagnostic.
Acceptable Sample Types
Scientists at ORB are experienced with the isolation of RNA, DNA, and protein from a variety of biofluid, cellular, and tissue biopsy samples.
- Whole Blood
- Cell-free DNA
- Genomic DNA
- Cerebrospinal Fluid
- FFPE tissue
- Lymphatic Fluid
- Ascites Fluid
- Synovial Fluid
- Buccal Swabs
- Dried Blood Spots
Biomarkers are widely utilized in most disease areas to assess the presence or severity of pathologies, to determine the optimal treatment course based a patient’s genetic composition, and to monitor the efficacy of a drug therapy. Common disease areas or conditions where biomarkers are frequently employed for screening, prognostic or diagnostic purposes are listed below:
- Metabolic Diseases
- Infectious Diseases
- Neurological Diseases
- Reproductive Health
- Prenatal Testing
Biomarker Utility in Drug Discovery and Development Process
Potential biomarkers with demonstrated reproducible association with a disease can be used to support drug discovery and development programs from the initial identification of a candidate through the production of FDA applications. Established uses of biomarkers include:
- Efficacy testing
- Differentiation of drugs within a structural or functional class
- Examining toxicity
- Disease screening prior to trial commencement
- Patient stratification
- Identification of non-responders
- Prognostic markers to encourage behavior modification or preventative therapies
Companion diagnostics are designed to advance personalized medicine programs and establish treatment-specific biomarkers. These assays are often run in conjunction with the administration of a particular drug therapy in order to determine appropriate dosages and treatment effectiveness. ORB is an experienced service provided of the open-ended transcriptomic, genomic, and protein investigations often employed when developing a companion diagnostic assay.See more details on these applications
Click on the links above to explore ORB’s biomarker discovery capabilities.
- Resl, M., M. Clodi, G. Vila, A. Luger, S. Neuhold, R. Wurm, C. Adlbrecht et al. "Targeted multiple biomarker approach in predicting cardiovascular events in patients with diabetes." Heart 102, no. 24 (2016): 1963-1968.
- Chen, Xueping, Yongping Chen, Qianqian Wei, Ruwei Ou, Bei Cao, Bi Zhao, and Hui-Fang Shang. "Assessment of a multiple biomarker panel for diagnosis of amyotrophic lateral sclerosis." BMC neurology 16, no. 1 (2016): 173.
- Somlo, George, Sean K. Lau, Paul Frankel, H. Ben Hsieh, Xiaohe Liu, Lixin Yang, Robert Krivacic, and Richard H. Bruce. "Multiple biomarker expression on circulating tumor cells in comparison to tumor tissues from primary and metastatic sites in patients with locally advanced/inflammatory, and stage IV breast cancer, using a novel detection technology." Breast cancer research and treatment 128, no. 1 (2011): 155-163.
- Scher, Howard I., Glenn Heller, Arturo Molina, Gerhardt Attard, Daniel C. Danila, Xiaoyu Jia, Weimin Peng et al. "Circulating tumor cell biomarker panel as an individual-level surrogate for survival in metastatic castration-resistant prostate cancer." Journal of Clinical Oncology 33, no. 12 (2015): 1348-1355.
- Weber, Georg F. "The cancer biomarker osteopontin: combination with other markers." Cancer Genomics- Proteomics 8, no. 6 (2011): 263-288.