Technology Development Group
Alexey V. Soldatov (06/07-07/12)
Phone: +49 (0)30 8413-1128
Fax: +49 (0)30 8413-1380
Email: soldatov@molgen.mpg.de
Till June 2007, A. Soldatov’s team was within Lehrach’s group and has specialised in the area of SNP genotyping and sequencing. A new SNP-genotyping method was developed, patented (PCT/EP2004/009546) and successfully applied for genotyping of Arabidopsis thaliana and human DNA samples. We have also worked on the development of new sequencing technologies in the frame of the European MolTools project: (i) microbead based sequencing (PCT/EP2006/008535) and (ii) ligation based sequencing in collaboration with U. Lan-degren laboratory (Uppsala University, Uppsala, Sweden).
Since June 2007, our group specializes in technology development and bioinformatics related with second generation sequencing (NGS). Till spring 2010 we were responsible for the NGS service in the department. We have set up the optimized laboratory workflows for both Illumina and ABI SOLiD sequencing platforms. We have developed a NGS bioinformatics pipeline, which brings together the information about the whole sequencing process from sample handling to results analysis. The system enables each authorized user (also external col-laborators) to track processing of samples, check the sequencing quality and view data in the genomic browser.
The group uses NGS platforms for analysis of genome (resequencing) and transcriptome (gene expression profiling, splice junctions search, allele-specific expression, reverse transcription, etc.). We have performed RNA-Seq, ChIP-Seq, MedIP-Seq and genomic DNA sequencing (including sequencing library preparation, sequencing and sometimes data analysis) for several groups within the MPIMG (AG Yaspo, AG Nietfeld, AG Himmelbauer, AG Schweiger, AG Hoehe, AG Lange, AG Krobitsch, AG Ralser, dept. Herrmann) and for external collaborators (Y. Shiloh (U. Tel Aviv), C. Koncz (MPI for Plant Breeding Research, Cologne), J. Klose (Charite, Berlin)).
We have developed, patented and published a convenient method for strand-specific sequencing of cDNA. The method is based on incorporation of uridine bases during first (or second) cDNA strand synthesis and subsequent destruction of this strand before sequencing. Knowledge of transcript orientation is important for transcriptome studies. It allows (i) to annotate novel genes correctly, (ii) to investigate antisense transcription, which plays an important regulatory role in all eukaryotes, (iii) to resolve transcript overlaps, which are abundant in compact genomes of prokaryotes and lower eukaryotes, and (iv) to correctly determine
gene expression levels in the presence of overlapping antisense transcription. The method is licensed by New England Biolabs company. We have developed and patented a method for preservation of information about spatial distribution of nucleic acid molecules transferred from a solid surface to another solid surface or into solution. This method permits to use a power of NGS for studying of two-dimensional distributions of nucleic acid molecules on tissue sections or other biological objects. Biological processes are spatially organized and rely upon the interplay of many different components forming an intricate structure of cells, tissues and organisms. Molecules participating in these processes have a certain spatial distribution. Understanding the biological processes is critically dependent on a detailed knowledge of this distribution.
At present, the group’s activities are focused on NGS-related technology development:
- early coding for parallel preparation of a number of sequencing libraries;
- RNA structural analysis;
- methylation analysis;
- preparation of NGS libraries from ultra small amounts of starting material;
- long-run NGS sequencing for haplotyping.