Training @ Staburo: How to measure the abundance of mRNA, using Microarrays and Sequencing Technologies

The normal function of cells depends on accurate expression of a large number of proteins. As it is difficult to measure the number of thousands of proteins simultaneously, a pre-state of them – the so called protein coding RNAs (messenger RNAs; mRNAs) – are normally measured.
Staburo GmbH Bioinformatician Dr. Janine Roy started this talk with an introductory overview of protein synthesis, to answer the question – How is the information coded in the DNA translated to functioning proteins? Therefore, the structure of a cell with its organelles, Translation from DNA to pre-mRNA, splicing as well as the genetic code was profoundly explained.
Afterwards she moved to (DNA-)Microarrays and RNA-Sequencing.
Microarrays are used to measure the expression levels of large numbers of genes simultaneously. The composition of a Microarray and the general workflow of an experiment was shown on an example.
RNA-Sequencing uses next-generation sequencing techniques to reveal the presence and quantity of RNA. As many sequencing techniques exists, the technique of Sequencing by Synthesis was explained exemplary on a more detailed level.
The talk finished with a rigorous comparison of (dis-) advantages of (DNA-)Microarrays and RNA-Sequencing.

Staburo @ BIO-M Workshop: Start thinking with the end in mind: Using the right Data in Clinical Development and Market Access

Staburo’s Managing Director Roland Stieger attended the BioM seminar with the topic “Using the right Data in Clinical Development and Market Access” in Munich.
The main topic at this seminar was the future of Clinical Trial Designs, Real World Evidence Plus, further Market Access – study requirements and strategic insights in context of the patient related data to facilitate clinical development. Integrated, patient centered thinking may grant additional opportunities to develop better solutions faster in the clinical field.
Speakers were Dr. Ute Simon, Medical Director at the Novartis Pharma GmbH, Dr. Timm Volmer, Founder from SmartStep Healthcare & Market Access Consulting GmbH and Dr. Reiner Lehmann, Founder from DontBePatient Intelligence GmbH.

Novartis Pharma is one of the largest pharmaceutical companies. Novartis uses science-based innovation to address some of society’s most challenging healthcare issues. The talk was about the future of clinical development and the clinical trial designs.

SmartStep Healthcare & Market Access Consulting provides individualized and specialized consulting for the pharmaceutical and medical device industry, in order to achieve a rapid and effective market access for their products. Dr. Volmer’s topic was the integrated Market Access planning with questions like how to obtain advice from HTA institutions.

DontBePatient Intelligence generates Real World Insights derived from patients. Dr. Reiner Lehmann talked about how to identify and engage patients in the digital space and how to generate data to inform target population selection, trial design and choice of endpoints through patient derived information.

We thank BioM for the organisation and the speakers for their expert insights!

Training @ Staburo: Adaptive Enrichment Design Biostatistics

Due to the growing interest in personalized medicine, where patients receive individually tailored therapies, the application of adaptive enrichment designs becomes increasingly more important.

In standard approaches, the confirmatory clinical trial is run in the full population and patients who are more likely to benefit are identified in post-hoc subgroup analyses. However, disregarding the heterogeneity in the treatment effect, can lead to an erroneous stop of the development, as the effect may be diluted by the low efficacy in the overall population. In situations with a prior confidence about a benefit, only in a subset of patients, a further option is to start the trial with a broad range of patients and to sequentially change inclusion criteria, based on the data of the ongoing trial. After pre-planned interim analyses, these so-called adaptive enrichment designs allow the further recruitment of only the targeted subgroup(s). Depending on the selection rule at the interim analyses, an early stop for futility is also possible. In case the first-stage data indicates a promising benefit only in the subgroup, the trial is enriched by allocating the remaining sample size only to this patient subset. If the interim data fulfills the selection criterion for all subgroups, the original study plan is maintained and the null hypotheses, regarding all subgroups, are tested at the final stage.

In research, it has been shown that adaptive enrichment designs can obtain higher power than fixed parallel group designs or adaptive designs without enrichment, when the same sample size is used. Hence, adaptive enrichment designs are a meaningful contribution in the context of precision medicine.

Staburo supports OncologyInformationService in Data Analytics 

Staburo recently started a successful collaboration with OncologyInformationService – O.I.s)! Staburo supports O.I.s) in the analysis of Real World Data in oncology.

O.I.s) has been providing an innovative, proprietary and tailor-made methodology and expertise in the field of Real World Data for oncology and hematology for over 20 years. O.I.s) supports the majority of specialized pharmaceutical companies in market access and market development across Europe. In addition, the company and its founder Lenka Kellermann, are members of several medical associations, such as the “Deutsche Krebsgesellschaft” (DKG), DGHO and ASCO, bringing together patients, physicians and researchers into an environment designed to improve the outcomes. We are looking forward to a great sustainable cooperation!

Training@Staburo: clustering in the context of precision medicine

This presentation about clustering, differentiated between supervised and unsupervised methods, and introduced clustering as an important tool for subgroup identification, in the context of precision medicine and clinical trials.

Precision medicine means tailoring the treatment to specific patient subgroups, i.e. patients characterized by specific genetic alterations, or similar biomarker profiles. Clustering, as an unsupervised technique for subgroup identification, groups patients e.g. based on similarities in biomarkers, rather than on a given knowledge, like tumor type.

The importance of clustering for precision medicine and clinical trials was illustrated, based on two well-known examples of high clinical importance in oncology.

Hierarchical clustering was used to identify several patient subgroups in gene expression data of breast cancer patients. Those subgroups are characterized by different gene expression patterns, as well as different prognosis, regarding clinical endpoints, e.g. overall survival. Especially the HER2 gene is now a well-established prognostic marker, associated with poor survival in breast cancer.

The Consensus Molecular Subgroups in colorectal cancer are cluster-based subgroups with high clinical relevance, as well. Those subgroups were characterized by several expert groups, based on different supervised and unsupervised methods, e.g. hierarchical clustering, or partitional clustering with k-means, as unsupervised techniques. The experts identified 4 subgroups of which one is characterized by poor prognosis in patients with BRAF mutations and MSI.

During this talk, the concepts of both hierarchical and partitional clustering with k-means, were introduced and illustrated based on mentioned examples.

Staburo at the 12th IGSEE Forum

Staburo participated at the career fair that was organised by the International Graduate School of Science and Engineering (IGSSE), at the TUM Science and Study Center in Raitenhaslach. The IGSSE, which has won the German Excellence Initiative twice, stands for innovative research and has very close contacts to international research partners.

Dr. Michael Matiu introduced Staburo to the plenum and presented our biostatistics focus topics. Michael was afterwards available, as discussion partner at the fair. The exposition was organised, to provide network opportunities for highly qualified young researchers within academia and with industry partners, like biostatistics expert company Staburo.