Second-generation sequencing (SGS) is a family of new technologies which have dramatically increased the throughput and decreased the price of DNA sequencing. SGS has significantly extended the list of biological applications for sequencing. Now SGS is one of the most perspective and quickly developing technologies in basic biological research. Currently, two SGS platforms (synthesis-based Illumina GAII and ligation based ABI SOLiD 3) are available on the market and in the MPI for molecular genetics.

Our group specializes in technology development and bioinformatics related with SGS. We have a profound experience in application of SGS platforms for analysis of genome (resequencing) and transcriptome (gene expression profiling, splice junctions search, allele-specific expression, reverse transcription, etc.). Since SGS platforms became available in the MPIMG, several projects related with transcriptome analysis in different organisms (mammals, birds, fishes, plants, yeast) were successfully fulfilled.

Both for ABI and Illumina platforms, considerable efforts were invested in the improving and optimisation of sequencing library preparation protocols (optimization of fragmentation step, introduction of real-time library quality and concentration check, optimization of flowcell loading, etc.).

We have developed a SGS bioinformatics pipeline which brings together the information about the whole sequencing process from sample handling to analysis of results in genomic browser.

Recently we have published a method for strand-specific sequencing of cDNA. Knowledge of transcript orientation allows (i) to annotate novel genes correctly, (ii) to investigate antisense transcription, which plays an important regulatory role in all eukaryotes, (iii) to resolve colliding 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.

At present, main directions of the research activities of the group are the following.

• SGS based genotyping (wet procedure and accompanying analysis algorithm);

• SGS based methylation analysis(wet procedure and accompanying analysis algorithm);

• development of enrichment procedures for SGS;

• establishment of paired-end sequencing library preparation for SOLiD platform.

We are also involved in several biological projects requiring SGS for analysis of genome (resequencing) and transcriptome (gene expression profiling, splice junctions search, allele-specific expression, reverse transcription, etc.):

• 1000 Genomes project;

• Treat 1000 project;

• IMGuS staetohepatitis project ;

• FP7 ADAMS project;

• mouse transcriptional network studies;

• resequencing of the genome of the PWD mouse strain