Service portfolio

The Alacris team has long-standing expertise in next generation sequencing technologies, large-scale operations, data management, high-dimensional data analytics and bioinformatics systems, allowing us to offer a wide range of cutting-edge services. Our staff is dedicated to excellence, providing quality-certified, personalized services to our customers.

Certified NGS Services

We offer a variety of NGS sequencing services to suit a broad range of applications and customer requirements. With our closed, confidential and secure IT infrastructure operating with ISO9001, Illumina CSPro and Agilent Service Provider certified sequencing pipelines, we can guarantee our customers high-quality results. All NGS procedures are operated according to strict quality control standards.

We deploy our NGS expertise within a number of research projects and translational activities, with a strong focus on technology development. One of our patented sequencing protocols has been licensed by NGS market leaders.

Our NGS service list:

  • Whole genome sequencing (WGS)
  • Shallow WGS for CNV analysis
  • Whole exome sequencing (WES)
  • Targeted sequencing
  • Strand-specific RNA sequencing (mRNA and ribo-depleted)
  • Small RNA /microRNA sequencing
  • ChIP-Seq (Chromatin Immuno Precipitation DNA-Sequencing)
  • MeDIP-Seq (Methylated DNA  Immuno Precipitation Sequencing)
  • Immune repertoire sequencing

Focus on High-Resolution Transcriptomics

We are inventors of a strand-specific RNAseq protocol (Parkhomchuk et al. 2009, Sultan et al. 2012), used by market leaders in the NGS field. We were first to publish the benefits of RNAseq as compared to microarrays (Sultan et al. 2008). We know what matters.

Strand-specific high-resolution transcriptomics provides an essential data layer for:

  • Identifying cancer driving fusion genes
  • Quantitative gene expression
  • Validating variants identified by WGS/WES
  • Gene variant allele-specific expression
  • Detecting long non-coding RNAs
  • Identifying differentially spliced transcripts isoforms
  • Identifying novel transcription units
  • Analyzing eRNAs
  • Analyzing eQTLs
  • Identifying specific signatures and biomarkers

NGS-Associated Services

Project planning:

  • Selection of the optimal cost-efficient sequencing strategy
  • Assistance in experimental design

Sample processing:

  • Isolation of nucleic acids from different samples (cell cultures, frozen tissue, blood, FFPE, etc.)
  • DNA and RNA quantification and quality control

Sequencing libraries:

  • Standard and project-specific library preparation
  • Protocols with built-in QC steps
  • Quality check of libraries

NGSight & Oncovar: Integrated Genomic/Transcriptomic Analysis

Alacris Theranostics offers one of the most comprehensive NGS analysis pipelines available on the market today.

NGSightTM: we have developed a highly efficient analysis pipeline for NGS data that can be tailored to the needs of each project. The use of multiple mapping algorithms, project-specific data pre-processing, output filtering and data integration make NGSightTM a powerful and flexible analysis system for all NGS applications.

OncovarTM is the specialized NGSightTM analysis pipeline developed by cancer research experts at Alacris. OncovarTM extracts the most relevant information for the therapy decision process.

CMTA: Comprehensive Molecular Tumor Analysis

A unique personalized solution for cancer patients

Cancer is a complex and heterogeneous disease. Every tumor is unique and demands individual molecular analyses to comprehend its complexity. We offer a highly comprehensive integrated NGS genomic and transcriptomic analysis of tumors that fulfills the highest demands for quality. CMTA is one of the most comprehensive precision medicine products on the oncology market today.

A key strength of the CMTA is the use of quantitative, high-resolution transcriptome data to enhance the quality and value of the molecular profiling conducted.

Based on our unique OncovarTM pipeline specially developed for NGS-based molecular oncology, the CMTA provides a personalized approach to cancer management and beyond, delivering an ultra-deep, fully annotated analysis of the patient’s tumor and reference genome that goes beyond the state of the art.

Biomarker identification

Alacris has established and developed methodologies for complex (omics-driven) biomarker identification that facilitates (i) the selection of patients or biomarker sets to stratify patients for targeted clinical trials and (ii) biomarker identification as companion diagnostics for personalized oncology. We carry out statistical analyses of genomic and other omics data for the identification of predictive and prognostic biomarkers. The methods used for identification of biomarkers range from basic statistical tests, e.g. Mann-Whitney-U-test, to more sophisticated classification algorithms, e.g. logistic regression, support vector machines, random forests. Our biomarker analysis expertise was successfully used in the framework of the IMI Oncotrack project, leading to the identification of novel predictive signatures of cetuximab and 5-FU response in colon cancer (Schuette et al. 2017).

In clinical trial scenarios, the patients that are most likely to benefit from a particular drug/drug combination can be selected based on biomarkers identified, for inclusion in smaller and less expensive clinical trials.

ModCell

Our proprietary ModCellTM technology is a new, revolutionary systems medicine modeling tool for optimizing predictive personalized medicine and drug development.  A simulation tool that provides a gateway to the complex molecular processes occurring within each of our cells, fostering insight and discovery for clinical application and in silico testing of therapy response.

Virtual clinical trials

ModCellTM facilitates applications for the pharmaceutical/biotechnology industry, virtualizing a range of developmental pipelines.

Virtual clinical trial technology finds applications in:

Drug response testing (single and combinatorial) within large patient groups, e.g. clinical trials for drug approval or for the identification of patient cohorts, including biomarkers, for companion diagnostics.

Repurposing (repositioning) drugs from other disease indications for the treatment of cancer.

Rescuing drugs that have failed in stage II and III of clinical trials due to low-efficiency rates rather than non-tolerable side effects. These drugs can be approved for particular (responding) patient groups.

To conduct virtual clinical trials, we use a range of data sources, including the ever-expanding data sets being generated on cancer patients from large, international research projects (e.g. the International Cancer Genome Consortium, ICGC), our own project generated data sets or dedicated data sets provided by our customers and collaboration partners.

Using our virtual clinical trial system, patients who would benefit from a specific new or ‘rescued’ drug or drug combination can be identified; information that can be subsequently exploited to enable approval of the drug in a smaller, more efficient and targeted real-life clinical trial.