Omics Analysis Services

Multi-omics analysis has transformed how researchers decode the molecular complexity of cancer, enabling the simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic layers within tumor systems. At Alfa Cytolog, we bridge cutting-edge omics technologies with robust preclinical tumor models to deliver actionable molecular insights that drive smarter therapeutic decisions.

Overview of Omics Analysis

Cancer is fundamentally a disease of molecular dysregulation, where genetic mutations, epigenetic reprogramming, and metabolic rewiring converge to drive uncontrolled proliferation and therapeutic resistance. Multi-omics approaches—encompassing genomics, transcriptomics, proteomics, metabolomics, and increasingly spatial and single-cell resolution methods—provide a holistic framework for dissecting these layered biological processes. By integrating data from multiple molecular dimensions, researchers can move beyond isolated gene-phenotype correlations to construct systems-level models of tumor behavior, revealing how driver mutations alter signaling networks, how the tumor microenvironment reshapes immune landscapes, and how metabolic dependencies create exploitable vulnerabilities.

Fig 1. Single-cell technologies for dissecting tumor heterogeneity across the tumor microenvironment. (Le, Jiayuan, et al., 2025)

In preclinical oncology research, the convergence of high-throughput sequencing, mass spectrometry-based proteomics, and advanced bioinformatics has made it possible to profile tumor samples with unprecedented depth and precision. Genomic profiling through whole-exome or targeted next-generation sequencing identifies somatic mutations and copy number alterations; transcriptomic analysis via bulk or single-cell RNA sequencing captures dynamic gene expression programs; proteomic and phosphoproteomic surveys map functional protein states and post-translational modifications; and metabolomic profiling reveals the biochemical fluxes that fuel tumor growth. When these datasets are integrated—often through machine learning and network-based algorithms—they yield composite biomarker signatures, mechanistic insights into drug action, and predictive models of therapeutic response that are far more powerful than any single-omics approach alone.

Spatial Multi-Omics: Mapping the Tumor Ecosystem at Single-Cell Resolution

Our Services

Alfa Cytolog integrates multi-omics profiling directly into our preclinical tumor model workflows, offering end-to-end molecular characterization services that span from sample processing and high-throughput sequencing to advanced bioinformatics and data interpretation. Whether you are seeking to validate a therapeutic target, identify a predictive biomarker signature, or understand the mechanism of drug resistance in your candidate compound, our team combines deep expertise in oncology animal models with state-of-the-art omics platforms to generate publication-quality datasets and clinically translatable insights.

Our Omics Analysis Services

Genomic Profiling

• Whole-exome sequencing (WES) and targeted NGS panel analysis for mutation detection, copy number variation (CNV) profiling, and microsatellite instability assessment in tumor models.
• Tumor-normal paired sequencing to distinguish somatic driver mutations from germline variants, enabling precise target identification.
• Comparative genomic analysis across treatment cohorts to identify resistance-conferring mutations and clonal evolution patterns.

Transcriptomic Analysis

• Bulk RNA sequencing (RNA-seq) for comprehensive gene expression profiling, differential expression analysis, and pathway enrichment in tumor and stromal compartments.
• Single-cell RNA sequencing (scRNA-seq) to deconstruct intratumoral heterogeneity, identify rare subpopulations, and map cell-state transitions under therapeutic pressure.
• Immune profiling panels and T-cell receptor (TCR) repertoire analysis for immuno-oncology studies, quantifying immune cell infiltration and activation status.

Proteomic & Phosphoproteomic Analysis

• Mass spectrometry-based proteomics (DIA, TMT, 4D-proteomics) for global protein expression quantification and post-translational modification mapping.
• Phosphoproteomic profiling to capture dynamic signaling pathway activation states, particularly relevant for kinase inhibitor and combination therapy studies.
• Multiplex immunoassays (Luminex, MSD, ELISA) for targeted cytokine, chemokine, and growth factor quantification in tumor lysates and serum.

Metabolomic & Lipidomic Profiling

• Untargeted and targeted metabolomics via LC-MS/MS to profile small-molecule metabolites, identify metabolic vulnerabilities, and track pathway fluxes.
• Lipidomics analysis for comprehensive characterization of lipid species, membrane composition, and lipid-mediated signaling in tumor models.
• Isotope tracing studies to measure metabolic flux and quantify substrate utilization rates in glycolysis, glutaminolysis, and fatty acid oxidation pathways.

Spatial Multi-Omics

• Spatial transcriptomics and spatial proteomics on fresh-frozen or FFPE tumor sections to preserve tissue architecture while capturing molecular profiles.
• Multiplex immunofluorescence (mIF) and in situ hybridization (RNAscope) for validation of spatial omics findings at protein and RNA levels.
• Integration of spatial data with digital pathology and AI-based image analysis for automated quantification of cellular neighborhoods and interaction networks.

Bioinformatics & Data Integration

• Multi-omics data integration using MOFA2, DIABLO, and network-based algorithms to identify cross-layer biomarkers and mechanistic pathways.
• Machine learning-driven drug response prediction models trained on integrated genomic, transcriptomic, and proteomic features.
• Customized data visualization, pathway analysis, and publication-ready figure generation with full methodological documentation.

Applications of Omics Analysis Services

Why Choose Alfa Cytolog?

Selecting the right partner for omics-integrated preclinical research can mean the difference between generating data and generating insight. Alfa Cytolog offers a distinctive combination of tumor model expertise, advanced analytical platforms, and scientific rigor.

• Integrated Model-to-Omics Pipeline — We eliminate the fragmentation of outsourcing by performing tumor model generation, treatment studies, sample collection, and molecular profiling under one roof.
• Deep Oncology Expertise — Our scientific team brings decades of combined experience in cancer biology, pharmacology, and computational genomics, ensuring biological relevance in every analysis.
• Platform Versatility — From bulk RNA-seq to single-cell multi-omics and spatial transcriptomics, we offer a comprehensive technology stack tailored to your specific research questions.
• Custom Bioinformatics Solutions — We do not apply one-size-fits-all pipelines; our bioinformatics team customizes analysis frameworks, integration algorithms, and visualization strategies to match your program objectives.
• Accelerated Turnaround — By co-locating animal facilities with molecular profiling laboratories, we minimize sample transit time and deliver faster results without compromising data quality.

Contact Us

Ready to unlock the molecular landscape of your preclinical tumor models? Whether you need a comprehensive multi-omics profiling package or a targeted biomarker analysis, our team is here to design a solution tailored to your therapeutic program. Reach out to us today to discuss your project requirements, and let Alfa Cytolog transform your tumor model data into actionable scientific insights.

For research use only. Not intended for any clinical use.