Services
Advanced processing and analysis methods are applied to all types of data generated.
Our team supports standard processing and custom analysis as well as data transfer tailored to the specific project needs.
We developed bio-IT pipelines for :
We provide secure, scalable solutions for raw or processed data transfers. Data transfers can be executed using AWS S3 exchange buckets for efficient, high-throughput data delivery. SFTP transfers or proprietary platforms are also possible when preferred.
We facilitate the transfer of raw sequencing data, pipeline outputs, downstream processed results, and customizable metadata, ensuring timely, reliable delivery aligned with your specifications. Additionally, our internal archiving policy allows us to securely store and retrieve project data for up to 25 years, providing the flexibility to access or reshare data long after initial delivery.
RNA-Seq Data Analysis – Pipelines for Comprehensive Transcriptome Profiling
Our bioinformatics pipeline for transcriptomic data focusses strongly on generating extensive and detailed quality metrics and visualizations presented in a QC report.
The initial analysis includes read alignment and transcript quantification. Optional modules include splice variant detection, fusion detection and tumor immune cell fractions. More advanced capabilities include the quantification of the expressed tumor mutation burden (eTMB) through somatic variant calling of tumor RNA-seq data and the establishment of microsatellite instability (eMSI) through repeat analysis of the RNA-seq reads. These additional analyses workflows are based on proprietary machine learning algorithms and enable a comprehensive characterization of tumor samples.
Our team provides expert support in differential gene expression (DGE), gene set enrichment analysis (GSEA), pathway analysis, and more. With a flexible, project-driven approach, and building on our in-house developed machine learning models that incorporate proprietary features as described above, we can tailor each analysis to specific research questions, such as investigating disease mechanisms, treatment response, or biomarker candidates.
Whether you’re conducting biomarker discovery, pathway analysis, or treatment response profiling, our RNA-seq data analysis service delivers customizable outputs and expert analytical support—scalable for both small studies and large cohorts.
NanoString nCounter® – Targeted Gene Expression
We offer end-to-end support, from panel design (custom or predefined) to high-throughput sample processing and advanced data analysis. Our bioinformatics pipeline includes extensive quality control, background correction and normalization. Our NanoString service incorporates strategies to control sources of variability, such as batch effects and lot-to-lot variability, ensuring fast, reproducible and interpretable results.
We provide differential gene expression (DGE) analysis and pathway enrichment analysis interpreted through robust statistical modeling for confident discovery of regulated pathways.
Our quantitative PCR workflows are optimized for high-throughput screening based on peer-reviewed quantification models for efficiency data correction, error propagation, inter-run calibration, and statistics across large sample sets.
For digital PCR , we use advanced data processing tools that allow us to go beyond classic assay validation. When testing linearity and accuracy we use generalized mixed linear models and reliable error propagation, e.g. when using multiple replicates and reference genes.
Both platforms are fully integrated into our data analysis infrastructure, providing validated, auditable outputs suitable for regulatory submissions and translational research. Whether supporting CAR-T development, viral vector quantification, or genome editing control, data from our PCR-based assays provide the accuracy and scalability your program demands.
Our robust bioinformatics pipelines support both platforms, generating extensive and detailed quality metrics and visualizations presented in a QC report and delivering high-throughput data processing from alignment and variant calling to more specific analyses. The pipeline ensures high-quality analysis across diverse experimental setups.
The WGS pipeline provides unbiased, genome-wide coverage, enabling the detection of both coding and non-coding variants, large structural variants, copy number changes, mitochondrial variants, and repeat expansions. WGS is the gold standard for projects requiring full genomic context, complex variant discovery, or pan-genomic biomarker analysis.
The WES pipeline focuses on the coding regions of the genome, capturing over 95% of known disease-associated variants with efficient sequencing depth and cost-effectiveness. It is ideal for identifying SNVs, indels, CNVs in clinically relevant genes and detecting microsatellite instability (MSI), and tumor mutational burden (TMB). Both tumor-only and tumor/normal paired analysis are available. These readouts support applications from rare disease research to oncology and pharmacogenomics.
We offer cohort-level analysis of coding mutations, including SNVs, indels, CNVs, and clinically relevant splice variants. Our interpretation pipelines support variant filtering, annotation with population databases, and integration with expression or phenotypic data for biomarker or candidate gene discovery.
With scalable infrastructure and flexible reporting formats, our WES and WGS offerings are designed to meet the demands of both discovery research and clinical-grade projects.
TSO500 HT & ctDNA – Comprehensive Genomic Profiling for Solid Tumors and Liquid Biopsies
Our TruSight Oncology 500 High Throughput (TSO500 HT) assay delivers broad, hybrid-capture–based genomic profiling of solid tumors, covering over 500 cancer-related genes.
For liquid biopsy applications, our TSO500 ctDNA v2 workflow enables sensitive detection of tumor-derived alterations from plasma cell-free DNA. Using the same comprehensive gene content, the ctDNA v2 version is optimized for ultra-low input and variant detection down to 0.5% allele frequency, enabling longitudinal monitoring, minimal residual disease (MRD) assessment, and non-invasive tumor profiling.
At CellCarta, our TSO500 workflows are deployed on Illumina Connected Analytics (ICA), ensuring secure, scalable, and streamlined data processing. This setup includes read alignment, variant calling, annotation, QC metrics, and biomarker computation, all within a secure, scalable informatics infrastructure.
OncoRevealTM Assay – Comprehensive Genomic Profiling
The OncoReveal™ assay is a targeted NGS-based solution designed for the detection of clinically relevant somatic mutations in solid tumors. Built on Pillar Biosciences’ proprietary SLIMamp® technology, it offers high specificity, uniform coverage, and compatibility with low-input FFPE samples.
The assay is fully supported by Pillar’s integrated software ecosystem:
ASPYRE™ Lung – Ultra-Sensitive, Targeted Mutation Detection with Integrated ASPYRE Lab Analysis
Data generated with ASPYRE™ is seamlessly processed through ASPYRE Lab, Biofidelity’s dedicated cloud-based analysis platform. ASPYRE Lab automates data QC, variant calling, and quantification, providing clear, intuitive reports with actionable mutation results. This eliminates the need for complex in-house bioinformatics and ensures consistent, validated analysis across projects and sites.
HLA Genotyping – High-Resolution Typing
Our HLA genotyping service provides high-resolution typing of class I (HLA-A, -B, -C) and class II (HLA-DRB1, -DQB1, -DPB1) loci using NGS, and is optimized for both research and clinical trial support.
We leverage advanced data processing pipelines to handle complex allele phasing, alignment, and ambiguity resolution, ensuring consistent and confident calls even in highly polymorphic regions. Automated QC metrics, annotation, and customizable output formats make integration with downstream analysis workflows seamless. Our scalable infrastructure enables high-throughput processing for large cohorts with fast turnaround, without compromising on data quality or resolution.
At CellCarta, we provide tailored analysis services for high-resolution transcriptomic data generated with the 10x Genomics Chromium Next GEM Single Cell 5′ assay. We support studies focused on gene expression, immune repertoire profiling, and cellular heterogeneity.
Our Single-Cell RNA-Seq pipeline incorporates the Cell Ranger software suite to streamline data processing (demultiplexing, alignment, quality filtering, normalization, dimensionality reduction, clustering) and supports the analysis of diverse library types, including 5′ gene expression, T and B cell V(D)J libraries, and feature barcode (antibody) libraries. The pipeline is designed to be scalable and reproducible, making it suited for a wide range of single-cell applications, such as cell-type annotation, trajectory inference, and pathway enrichment, providing comprehensive biological interpretation.
Furthermore, our cloud-based CellEngine software replicates the traditional flow cytometry workflow, allowing scientists to work with familiar, interactive visualization tools. Researchers can use population gating guided by tSNE and UMAP clustering to identify cell types, then visualize individual genes, proteins, or gene signature scores on a per-cell basis using histograms, dot plots, and contour plots. They can carry out secondary analysis using bar charts, line graphs, and heatmaps to look across patients, time points, or treatment conditions.
With scalable processing and expert bioinformatics support, our scRNA-seq service delivers high-quality insights from even the most complex samples.
GeoMx ® Spatial Biology – High-Plex, Region-Specific Profiling
Our data analysis pipeline includes ROI selection, quality control and integration with digital pathology. We provide comprehensive bioinformatics support, from raw data processing to unsupervised analysis and differential expression, ensuring biological insights are both localized and actionable.
Visium & Visium HD – Spatial Transcriptomics with Tissue-Level Precision and High-Resolution Insight
Our pipeline based on the 10x Space Ranger software includes spatial alignment, quality filtering, normalization, clustering, and spatial domain detection. We also integrate histological images with transcriptomic data for precise interpretation of spatial patterns. The pipeline has been engineered and validated as a scalable and reproducible workflow to generate spatially resolved gene expression data.
Our spatial analysis capabilities include batch correction across slides or tissue types, cell type deconvolution using reference single-cell atlases, spatial domain detection, and gene signature enrichment. We integrate transcriptomic data with histological images for spatial mapping of biological processes with tissue context preserved.