Author Archives: Genie

25.04.2016 | Publication: SimLoRD – Simulation of Long Read Data

Bianca Stöcker; Johannes Köster; Sven Rahmann
Bioinformatics 2016;
10.1093/bioinformatics/btw286

SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Third generation sequencing methods provide longer reads than second generation methods and have distinct error characteristics.
In a SMRT library the sequenced DNA fragments are circular with adapter sequences between forward and backward strand, and a fragment may be sequenced multiple times in a single run. For a single pass through the sequence (subread), the error rate is high, but it is possible to calculate a consensus after multiple passes (circular consensus sequence read, CCS). Thus the error rate of CCSs decreases with the number of passes.

We analyzed public data from Pacific Biosciences (PacBio) SMRT sequencing, developed an error model and implemented it in a new read simulator called SimLoRD. Reads are simulated from both strands of a provided or randomly generated reference sequence. It offers options to choose the read length distribution and to model error probabilities depending on the number of passes through the sequencer. The new error model makes SimLoRD the most realistic SMRT read simulator available.

SimLoRD is available open source at http://bitbucket.org/genomeinformatics/simlord/ and installable via Bioconda.

Poster about the EAGLE tool at University Hospital Essen Science Day 2015

Exome Analysis GraphicaL Environment (EAGLE)

Christopher Schröder, Christoph Stahl, Felix Mölder, André Janowicz, Jasmin Beygo, Marcel Martin, Sven Rahmanneagle

The Exome Analysis GraphicaL Environment (EAGLE) combines a best practices variant calling workflow, with a web frontend. By storing the called information in speficially structerd hdf5 files, EAGLE allows filtering and parameter tuning in almost real time. This enables iterative tuning of thresholds, or the selection of different samples for filtering by non computer scientists via the web interface.

06.11.2015 | Publication: Human TLR8 senses UR/URR motifs in bacterial and mitochondrial RNA

EMBO Reports 2015 Dec; 16(12): 1656–1663.
doi:10.15252/embr.201540861

Toll‐like receptor (TLR) 13 and TLR2 are the major sensors of Gram‐positive bacteria in mice. TLR13 recognizes Sa19, a specific 23S ribosomal (r) RNA‐derived fragment and bacterial modification of Sa19 ablates binding to TLR13, and to antibiotics such as erythromycin. Similarly, RNase A‐treated Staphylococcus aureus activate human peripheral blood mononuclear cells (PBMCs) only via TLR2, implying single‐stranded (ss) RNA as major stimulant. Continue reading

November 2015 | Neue Mitarbeiterin in Essen

Seit November 2015 arbeitet Bianca Stöcker bei uns in Essen. Bianca wird zunächst an ihrem Simulator für lange Reads weiterarbeiten, den sie während ihrer Masterarbeit entwickelt hat. Außerdem arbeitet sie zusammen mit Johannes Köster (Dana-Farber Cancer Institute, Boston) und Eli Zamir (MPI, Dortmund) an Protein-Hypernetzwerken.
Herzlich Willkommen, Bianca!

Poster at GCB 2015 on mutational landscapes of relapsing neuroblastoma

Bioinformatics Analysis of Heterogenous Data Reveals Characteristic Mutational Landscapes of Neuroblastoma Relapses, GCB 2015 in Dortmund

Marc Schunb-posterlte, Johannes Köster, Daniela Beisser, Corinna Ernst, Christopher Schröder, Alexander Schramm and Sven Rahmann

Neuroblastoma is a malignancy of the developing sympathic nervous system that causes 15% of childhood cancer-related mortality. However, in the vast majority of cases death results not from the initial disease manifestation but rather from metastasis or recurrence.

Systematic search for genomic alterations in primary neuroblastomas has shown low genetic complexity, with significant mutations in only a very few genes. This study explored the genomic landscape of relapsing neuroblastoma in order to evaluate ‘driver’ mutations to be exploited as therapeutic targets.

Poster about dinopy at GCB 2015

Henning Timm and Till Hartmann
dinopy
Dinopy (Dna INput and Output in PYthon) is a Python package that aims to simplify the development of bioinformatics applications by providing efficient facilities for DNA input and output.
At the time of writing, there is no library for I/O of DNA specific files available which makes full use of the potential of Cython. Dinopy exports Cython level API bindings which can be used by other Cython applications for increased speedup.

29.06.2015 | Publication: Mutational dynamics between primary and relapse neuroblastomas

A. Schramm, J. Köster, Y. Assenov, K. Althoff, M. Peifer, E. Mahlow, A. Odersky, D. Beisser, C. Ernst, A. G. Henssen, H. Stephan, C. Schröder, L. Heukamp, A. Engesser, Y. Kahlert, J. Theissen, B. Hero, F. Roels, J. Altmüller, P. Nürnberg, K. Astrahantseff, C. Gloeckner, K. De Preter, C. Plass, S. Lee, H. N. Lode, K. Henrich, M. Gartlgruber, F. Speleman, P. Schmezer, F. Westermann, S. Rahmann, M. Fischer, A. Eggert, J. H Schulte

Nature Genetics 47, 872–877 (2015)
doi:10.1038/ng.3349

Neuroblastoma is a malignancy of the developing sympathetic nervous system that is often lethal when relapse occurs. We here used whole-exome sequencing, mRNA expression profiling, array CGH and DNA methylation analysis to characterize 16 paired samples at diagnosis and relapse from individuals with neuroblastoma. Continue reading

Christopher Schröder contributed to an article on the origin of human intronic CpG islands that are not present in mouse

Evolutionary Origin and Methylation Status of Human Intronic CpG Islands that Are Not Present in Mouse

Rademacher, K., Schröder, C., Kanber, D., Klein-Hitpass, L., Wallner, S., Zeschnigk, M., Horsthemke, B.

Genome Biol Evol 6, 1579–1588 (2014), doi:10.1093/gbe/evu125

Imprinting of the human RB1 gene is due to the presence of a differentially methylated CpG island (CGI) in intron 2, which is part of a retrocopy derived from the PPP1R26 gene on chromosome 9. The murine Rb1 gene does not have this retrocopy and is not imprinted. We have investigated whether the RB1/Rb1 locus is unique with respect to these differences.

Continue reading

Poster on Exomate at GfH 2014 in Essen

exomate-posterExomate: an easy to use exome sequencing analysis pipeline

Christopher Schröder, Johannes Köster, Christoph Stahl, Sebastian Venier, Sven Rahmann, Marcel Martin

Exomate is an exome-sequencing pipeline with a web frontend. It automates most steps needed to go from FASTQ files to variant calls, puts the calls and metadata about patients, samples, etc. into a database and then allows interactive analysis via a web frontend. It is primarily designed for easy use and has already been used in various studies [1,2,3].

[1] Martin, M. et al., 2013. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat. Genet. 45, 933–936.

[2] Czeschik, J.C. et al., 2013. Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome. Hum. Genet. 132, 885–898.

[3] Voigt, C., et al., 2013. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies – expanding the phenotypes associated with EFTUD2 hfg mutations.
Orphanet J Rare Dis 8, 110.

 

Christopher Schröder presents a poster at Science Day 2013, University Hospital Essen

Target identification for metabolic engineering,

Christopher Schröder, Sven Rahmanntarget-poster

In metabolic engineering by gene knockouts, one searches for genes controlling metabolic reactions that should be removed from a metabolic network in order to optimize the yield of a desired metabolite.

In a conservative way, this is done by undirected mutagenesis selection of the population with best efficiency.

Unrean et al. developed a simple algorithm to directly predict reaction targets, to save the high costs of this uncontrolled expensive process. It is based on elementary modes, undecomposable sequences of metabolite transformation flows in the network.

We substantially improved the algorithm and applied it to a network of Escherichia coli to show the improved results.