Genomnia is a SME established in October 2008 with the aim of offering Next Generation Sequencing and Bioinformatic Analysis services. Recently we have progressed from the SOLID to the Ion Torrent technology, with which we are able to offer to Universities and Public or Private Research Centres in Italy and abroad a wide range of services, which include exome and genome analysis, personalized gene panels, transcriptome analysis, genome-wide epigenetic analyses (Chip-Seq and Methyl-Seq) and metagenomic analyses. In addition to the wide experience in molecular biology, the Company know-how extends to the sectors of bioinformatic analysis of massive sequencing data and high-throughput PCR applied to biomedical or to molecular genetics research projects.

Genomnia has adopted a new sequencing platform, Thermo Fisher/Life Technologies Ion Torrent, acquiring the Ion Personal Genome Machine® (PGM™) and the Ion S5. This platform of new technological conception is very flexible, with a production ranging from a minimum of 100 Meagbases to a maximum of 16 Gigabases of sequence for run. Its main application fields range from the study of mutations and gene alterations, with single-gene or disease-specific gene panels resequencing; to the human whole exome study; to the de novo sequencing or the resequencing of bacterial and viral genomes; to the study of transcriptome (RNA-seq, miRNA-seq, etc) and of epigenome (ChIP-seq, MBD-seq, Methyl-seq, etc.); till the study of the metagenomics of human microbiome and of other microbiomes using the 16S or whole-genome sequencing.

The laboratories are specifically organized according to the ThermoFisher/Life Technologies guidelines for a deep sequencing facility with the Ion Torrent platform, minimizing or zeroing the dangers of cross-contamination.

Library preparations laboratory

In this laboratory we perform the extraction, preparation and quality control of the samples delivered to Genomnia. In order to fulfill these activities the laboratory is fitted out with:

  • Nanodrop™ Spectrofotometer and Invitrogen Qubit™ fluoremeter for an accurate quantitifcation of nucleic acids, single or double stranded, even in minimal quantities.
  • Bioanalyzer Agilent, on-chip capillary electrophoresis system for the evaluation of the dimension, quantity and hence of integrity of the nucleic acids contained in the samples and of the quantity and quality of the libraries.
  • Eppendorf Concentrator Plus: Vacuum device to concentrate samples for excessively diluted samples
  • Devices for analysis, visualization and purification of nucleic acids with agarose or acrylamide gels
  • Covaris™ Sonicator for DNA and chromatin shearing
  • Thermomixer, ABI 9700 thermocyclers, centrifuges and stirrers for sequencing libraries preparation

Laboratory for the preparation of emulsions(e-PCR)

In this laboratory we prepare, through emulsion-PCR, the templated beads which will be loaded on the sequencing chips where the sequencing reaction will take place.

Deep sequencing laboratory

It is the laboratory where we perform the actual sequencing. It is fitted out with:

  • ION PGM™ Sequencer
  • ION S5 Sequencer
  • ION servers, one for each sequencer, for collection and primary analyses of sequencing data
  • ABI 7900HT Fast Thermocycler for Real-Time PCR
  • Verity Thermocycler and Applied Biosystems QuantStudio® 3D, for Digital PCR

Bioinformatics unit

The aim of the Bioinformatics Analysis Unit at Genomnia is in a first instance the delivery to the scientific partners of high quality ION PGM™ and S5™ sequence data, unambiguously mapped to the reference genome, annotated and classified with the maximum level of precision and information content and counted with precision. Current bioinformatic analysis skills include the coding and non-coding human and model organisms transcriptome analysis, with focus on circulating or tissue microRNAs; analysis of human exome variants or insertions/deletions for the identification of putative disease genes, including the "trio" experiment analysis; the identification and differential analysis of regulatory regions using the interpretation of ChIP-Seq; assembly and primary annotation of small genomes; analysis of metagenomic or differential methylation experiments (MBD-Seq). In addition we offer a range of quantitative PCR analysis services. For detailed descriptions please consult the Service Sheets for the ION PGM™ and S5™ applications. The available harware is as follows:
  • Shared memory Linux 64 bit server with 24 processors (dual-Xeon esacores) and around 130 Gb of RAM;
  • Linux 64 bit distributed memory cluster composed of seven compute nodes with 8 processors and 32 Gb of memory each and a frontend with 40 cores
  • 85 Terabytes of globally shared disk space
  • High speed Infiniband communication switch