NGS Analysis Services

Next-generation sequencing (NGS) has fundamentally reshaped how researchers interrogate the genomic architecture of cancer, moving from single-gene assays to comprehensive molecular portraits that capture mutations, copy number alterations, gene fusions, and transcriptomic shifts in a single experiment. At Alfa Cytolog, we translate this genomic depth into actionable preclinical intelligence—our NGS Analysis Services are architected to support every stage of oncology drug development, from target validation through resistance monitoring, with turnaround times and data quality that keep your program moving forward.

Overview of Next-Generation Sequencing in Oncology Research

Next-generation sequencing refers to a family of high-throughput technologies capable of determining the order of nucleotides across millions of DNA or RNA fragments in parallel. In oncology, this capability has transitioned tumor characterization from hypothesis-driven, single-analyte testing to unbiased, genome-scale discovery. Whole-exome sequencing (WES) captures coding mutations across approximately 20,000 genes, while targeted gene panels focus on clinically actionable loci with deeper coverage and faster turnaround. RNA sequencing (RNA-Seq) complements DNA-based approaches by quantifying gene expression, detecting novel transcripts, and revealing fusion events that drive oncogenesis. Together, these modalities provide a multidimensional view of tumor biology that is essential for identifying therapeutic vulnerabilities and understanding drug response.

Fig 1. In vitro characterisation of theMCF-7-luc cell lines edited for mCAIX expression. (Ghoreyshi, Nima, et al., 2025)

The preclinical application of NGS extends far beyond simple mutation cataloging. In patient-derived xenograft (PDX) models and genetically engineered mouse models (GEMMs), longitudinal NGS profiling can track clonal evolution under therapeutic pressure, revealing emergent resistance mechanisms before they appear in clinical settings. Liquid biopsy approaches using circulating tumor DNA (ctDNA) enable non-invasive monitoring of tumor dynamics in vivo, capturing spatial and temporal heterogeneity that static tissue biopsies often miss. Furthermore, the integration of NGS with functional assays—such as CRISPR/Cas9 screening or pharmacogenomic profiling—allows researchers to move from correlation to causation, linking specific genomic alterations to measurable phenotypic outcomes in both in vitro and in vivo systems.

The Convergence of Genomic Profiling and Targeted Radiopharmaceutical Development

Our Services

Alfa Cytolog delivers end-to-end NGS analysis services tailored specifically for preclinical oncology programs. Whether you are profiling a novel patient-derived xenograft bank, validating a genetically engineered model, or tracking clonal dynamics under therapeutic pressure, our integrated platform combines robust nucleic acid isolation, customized library preparation, high-depth sequencing, and expert bioinformatics interpretation. We understand that preclinical timelines are unforgiving—our workflows are optimized to deliver publication-grade genomic data with the speed and consistency your drug development program demands, bridging the gap between bench discovery and clinical translation.

Our NGS Analysis Services

Comprehensive Tumor Genomic Profiling

• Deep targeted panel sequencing covering hotspot mutations, copy number variations, and structural rearrangements
• Whole-exome and whole-transcriptome profiling for unbiased discovery of novel drivers and resistance mechanisms
• Tumor mutational burden (TMB) and microsatellite instability (MSI) calculation to support immunotherapy biomarker strategies
• Cross-platform compatibility with FFPE, fresh-frozen, and liquid biopsy specimens from in vivo model systems

RNA Sequencing & Transcriptomic Analysis

• Strand-specific mRNA sequencing for differential expression, pathway enrichment, and drug-response signature detection
• Fusion gene detection via hybrid-capture RNA panels to identify actionable oncogenic rearrangements
• Single-cell RNA-Seq for resolving intra-tumoral heterogeneity and rare subpopulation dynamics
• Small RNA and non-coding RNA profiling to explore epigenetic and post-transcriptional regulatory layers

Liquid Biopsy & Circulating Tumor DNA Analysis

• Ultra-deep sequencing of ctDNA from plasma or serum for non-invasive tumor monitoring
• Digital PCR and NGS-based minimal residual disease (MRD) detection in hematologic and solid tumor models
• Serial sampling workflows to capture temporal evolution of resistance mutations during long-term in vivo studies
• Correlative analysis between tissue-based and liquid biopsy genomic profiles

Bioinformatics & Variant Interpretation

• Custom pipeline development for somatic variant calling, annotation, and clinical-tier classification
• Tumor-normal paired analysis with rigorous germline filtering and artifact suppression
• Pathway and network analysis to contextualize genomic findings within oncogenic signaling frameworks
• Interactive data visualization and report generation tailored for regulatory submission and publication

Model Characterization & Quality Control

• STR profiling and NGS-based authentication to confirm model identity and detect cross-contamination
• Comparative genomic analysis between patient tumors and their derived in vivo or in vitro models
• Passage-dependent drift monitoring to ensure longitudinal genomic stability across study duration
• Human-mouse genomic deconvolution for accurate variant calling in xenograft and humanized systems

Workflow of NGS Analysis Services

Our NGS workflow is designed as a seamless, end-to-end pipeline that transforms raw biological specimens into interpretable genomic insights. Each stage is quality-controlled and documented to ensure reproducibility, traceability, and regulatory readiness for preclinical oncology studies.

Step 1: Sample Receipt & Nucleic Acid Extraction

Upon receipt, all specimens undergo rigorous quality assessment including histopathology review, tumor purity estimation, and integrity scoring. DNA and RNA are extracted using platform-optimized protocols tailored to the input material—whether fresh-frozen tissue, FFPE blocks, cell pellets, or plasma-derived ctDNA. Purity and concentration are verified by spectrophotometry and fluorometry before proceeding.

Step 2: Library Preparation & Target Enrichment

Extracted nucleic acids are fragmented, adapter-ligated, and amplified to create sequencing-compatible libraries. For targeted applications, hybridization capture or amplicon-based enrichment is performed to focus sequencing depth on regions of therapeutic relevance. Unique molecular identifiers (UMIs) and sample-specific barcodes are incorporated to enable multiplexed sequencing and suppress PCR artifacts.

Step 3: High-Throughput Sequencing

Libraries are loaded onto state-of-the-art sequencing platforms configured for the required read length, depth, and throughput. Sequencing-by-synthesis chemistry generates massive parallel read data with high base-call accuracy. Real-time quality metrics monitor run performance, and failed reads are flagged for downstream filtering.

Step 4: Bioinformatics Processing & Variant Calling

Raw sequencing data undergoes a structured computational pipeline: quality trimming, adapter removal, alignment to reference genomes, duplicate marking, local realignment, and variant detection. Somatic mutations, indels, copy number alterations, and structural variants are called using validated algorithms. Tumor-normal subtraction and population frequency filtering minimize false positives.

Step 5: Annotation, Interpretation & Reporting

Detected variants are functionally annotated using curated oncology databases and in silico prediction tools. Biological significance is assessed in the context of the therapeutic hypothesis, and actionable findings are highlighted. Deliverables include interactive variant reports, raw data files (BAM, VCF), coverage metrics, and publication-ready visualizations.

Applications of NGS Analysis in Preclinical Oncology

Contact Us

Ready to integrate high-resolution genomic profiling into your preclinical oncology program? Reach out to us today to discuss how Alfa Cytolog's NGS Analysis Services can illuminate the molecular drivers of your model systems, accelerate target validation, and de-risk your path to the clinic. Our team is standing by to design a sequencing strategy tailored to your specific therapeutic area, sample types, and decision milestones—so contact us now and let's turn genomic data into drug development momentum.

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