Genomnia is a start-up SME founded in October 2008 with the aim of offering deep sequencing and bioinformatic services and collaborations with private and public institutions, covering genomics, transcriptomics and epigenetics projects.

We have relevant experience in molecular biology and bioinformatic analysis of deep sequencing data applied to biomedical projects: transcriptome qualitative and quantitative analysis, miRNA identification and profiling, ncRNA identification and annotation, mutation detection, targeted genome resequencing and analysis.

Our experienced personnel takes care of the planning, optimization and analysis of your sequencing projects. We have upgraded our platform to the Applied Biosystems SOLID™ 5500XL-s with EZBead™ enrichment system, generating up to 180Gb per run . Fragment sequencing range from 25 up to 75bp, PE sequenging up to 75x35bp and mate paired sequencing up to 60x60bp.

Two base encoding system combined with the use of ECC (Exact Call Chemistry) Module allow a level of accuracy of 99.99% which makes it particularly suitable for genomic studies such as variation detection, especially for low frequency variants. The efficient barcoding system up to 96, permits safe and cost-effective multiplexing of large sample size projects. The wide dynamic range and sensitivity make it particularly suitable for measuring accurate fold changes at the low expression levels of RNA.

Genomnia has acquired a new sequencer, Thermo Fisher/Life Technologies Ion Personal Genome Machine® (PGM™). With this system of new technological conception it is possibile to produce up to 2 Gb of sequence per daily run. Its main application fields are: genome resequencing, for targeted genome regions or for disease-specific panels; metagenome analysis; small genome (viral or bacterial) resequencing, and the targeted resequencing of transcripts of interest.
The 300sq Genomnia laboratories are organized following the ABI guidelines for a SOLiD™ ™ deep sequencing facility:

Library preparations laboratory

- Agilent Bioanalyzer for evaluation of sample acid nucleic integrity and quantification even at picomolar scale
- Syngene G:Box electronic imagines system for any kind of gel
- Nanodrop™ spectrophoto- and Invitrogen Qubit™ fluoro-meter for miniscale quantification of biological materials, including nucleic acids
- Hydroshear® apparatus for nucleic acid fragmentation
- Agarose and acrylamide gel apparatus, including Ambion FlashPage™ system for smallRNA purification.
- ABI 9700 PCR Systems

E-PCR laboratory

- Eppendorf Microfuge
- Thermo Scientific Refrigerated centrifuge Multifuge® 3 Plus
- Eppendorf Refrigerated centrifuge 5417R
- Eppendorf Thermomixer
- Covaris™ sonicator
-EZBead™ Enrichment system
- ABI 9700 PCR system

Deep sequencing laboratory

- ABI SOLiD™ 5500 XL-s Sequencer
- ABI 7900HT Fast Real-Time PCR apparatus

Bioinformatics unit

- shared memory Linux 64 bit server with 24 processors (dual-Xeon esacores) and around 130 Gb of RAM;
- Linux 64 bit distributed memory cluster with seven compute nodes with 8 processors and 32 Gb of memory each and a frontend with 40 cores
- 75 Terabytes of globally shared disk space
- High speed Infiniband communication switch
- shared access to an external HPC facility, for the most compute intensive tasks
The aim of the Bioinformatics Analysis Unit at Genomnia is in a first instance the delivery to the scientific partners of high quality SOLiD™ 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 are strongly focused on sequence identification and annotation. This includes transcriptome analysis, both coding and non coding, of human and model organisms. Quantitative analysis skills (exploratory data analysis; univariate and multivariate approaches; linear model building) and genome-based approaches (mutation analysis; promoter recognition; correlation with gene structure; signal recognition) are also available in house and in partnership with external companies (see Bionformatic Services Brochure).