Print

Bioinformatic Analysis

With the advent of next generation sequencing, the bottleneck of biomedical discovery has shifted from data generation to the bioinformatic analysis and interpretation of large-scale genomic datasets. Indeed, the cost of performing a meaningful bioinformatic analysis now often exceed the cost of data generation (http://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-8-125). It is therefore critical to plan the bioinformatic analyses early on in the project. To maximize the quality and impact of the research that is supported by the BSF, users need to show that an appropriate bioinformatic analysis plan is in place in order to be eligible for sequencing on the subsidized "Collaborative Sequencing" framework.

Importance of an Analysis Plan

For clinical trials it is good scientific practice to write a detailed statistical analysis plan prior to data collection, which minimizes three important risk factors: (i) costly production of data that are conceptually insufficient for answering the scientific question of interest; (ii) lack of access to statistical expertise for analyzing the data once it has been generated; and (iii) inflated false positive rates due to arbitrary changes in the analysis strategy until statistical significance is found. In the same way, the writing an analysis plan can substantially contribute to the likelihood of success of sequencing-based studies. Those users who plan to perform their analysis themselves (or together with bioinformatic collaboration partners that are not associated with the BSF) are requested to submit their analysis plan (or a short summary of it) for a plausibility check in order to be eligible for the subsidized "Collaborative Sequencing" option.

Bioinformatics and Biostatistics Consulting

To help users with limited bioinformatic experience, the BSF is associated with a network of bioinformatics and biostatistics experts, who can give advice on the analysis plan and on a case-by-case basis enter into more extensive collaborations. This service is provided under the umbrella of the Bioinformatics Support Group of the Medical University of Vienna. To request bioinformatics and biostatistics consulting, the user should send an e-mail with a brief summary of the planned study to the following e-mail address: This email address is being protected from spambots. You need JavaScript enabled to view it.. The user will then be assigned a 30-minute time slot to present and discuss the study design with bioinformatics and biostatistics experts from the following groups:

  • Arndt von Haeseler (This email address is being protected from spambots. You need JavaScript enabled to view it.) at CIBIV
  • Martin Posch (This email address is being protected from spambots. You need JavaScript enabled to view it.) at CeMSIIS
  • Wolfgang Schreiner (This email address is being protected from spambots. You need JavaScript enabled to view it.) at CeMSIIS (focus on clinical data integration)
  • Christoph Bock (This email address is being protected from spambots. You need JavaScript enabled to view it.)

In-depth Analytical Support

Projects that involve large amounts of next generation sequencing require substantial bioinformatic contributions in order to obtain the expected biological insights. Certain parts of these analyses are relatively standardized, such as the initial quality control, short read alignment, mutation calling for exome sequencing, quantification of gene expression levels for RNA-seq and the submission of sequencing data to the relevant public repositories to fulfill journal requirements. These services are routinely provided in a centralized manner by the BSF team, and for collaborative sequencing the associated costs are heavily subsidized by CeMM. However, this basic support does not include project-specific analyses or additional support with data processing and presentation. It is therefore strongly recommended that users identify suitable collaborators already during the design phase of a project (e.g. by presenting in the Bioinformatics Support Group) and to make sure to allocate sufficient funding e.g. as part of an FWF grant application. As a role of thumb, the costs of performing in-depth analyses (i.e. the salary of a bioinformatics postdoc for a given amount of time) tend to be in the same order of magnitude as the sequencing costs.