The National University Complex for Biomedical and Translational Research (NUCBTR) is a strategic network of infrastructures for fundamental and translational biomedical research and includes partners from two of the largest medical universities in Bulgaria, the Medical University of Sofia and the Medical University of Plovdiv, as well as a number of hospital and research centers. At the core of the University Complex is the unification of the largest biobanks for the storage of biological material and clinical data in the country.
NUCBTR links existing resources, achieving a critical mass of expertise and technological opportunities, creating conditions for developing research in the field of molecular medicine, genetics and epidemiology in Bulgaria in the post-genomic era. The purpose of creating and developing the University Complex is to accelerate the transition between fundamental research and clinical practice in order to improve the prevention, diagnosis and treatment of the most important diseases for society.
Based on the international expert assessment, NUCBTR has been assessed as one of 4 infrastructure complexes, which are nationally significant infrastructures and have the potential to participate in pan-European research infrastructures. MMC and NUCBTR are included in the National roadmap of the scientific infrastructure in Bulgaria from its creation in 2010.
Molecular Medicine Center
The Genomic Core at MMC is equipped with state-of-the-art equipment, which allows us to face the challenges of modern biomedical research and provide special services in genetics/ genomics.
Equipment:
The sector is equipped with:
ABI Prism 3130xl Automated sequencer(16 capillary array) (Thermo Fisher Scientific)
ABI 3500Xl Генетичен анализатор (24-capillary array) (Thermo Fisher Scientific)
7900HT Real-time PCR System (Applied Biosystems) PCR System (384-well plate) with SDS Enterprise Database, RQ Manager software and SNP Manager software,
EcoTM Real-time PCR System (Illumina)
Rotor-Gene Q (Qiagen) for SNP genotyping, gene expression and High Resolution Melting Analysis (HRM);
QuantStudio 3D digital PCR system for highly sensitive and specific amplification of DNA in microvolume for quantification of nucleic acids without the need for standards and the use of chips without the need for emulsion PCR and with the ability to: Quantify rare mutations; Analysis of copy number variants (CNV); Detection of pathogens and determination of the load; Absolute quantification of the exact number of copies of the target nucleic acids; Quantifying next-generation sequence libraries; Characterization of small changes (up to 5%) in mRNA and miRNA expression.
The new Next Generation Sequencing Laboratory is equipped with next-generation sequencing platforms of Thermo Fisher Scientific and Illumina.
Ion Torrent PGM™ (Thermo Fisher Scientific) use emulsion PCR (emPCR) using a unique combination of fluidics, micromachining, and semiconductor technology that allows the direct translation of genetic information (DNA) to digital information (DNA sequence), rapidly generating large quantities of high quality data.
The Ion PGM™ Sequencer produces the fastest results of any benchtop next-generation sequencer, offering a one-day workflow for most applications. Because of the rapid cycle times possible with semiconductor sequencing, Ion PGM™ Sequencer runs are complete in as little as 30 minutes for 35 base runs on an Ion 314™ Chip, and only 4.5 hours for up to 1 Gb, 200 base run on a Ion 318™ Chip. Ion fragment libraries can be prepared in as little as 2 hours.
The instrument allows the following applications:
Small RNA and miRNA Sequencing
Chromatin Immunoprecipitation Sequencing
Ion GeneStudioTM S5 Prime System (Thermo Fisher Scientific) The Ion GeneStudio S5 system uses semiconductor chip sequencing to allow for flexibility in analysis, from gene panels to exomes, from gene expression to transcripts or microbial genomes to microbiomes. Technology based on massive parallel synthesis of DNA fragments (from 2 million to 130 million) using unlabeled nucleotides. Detection of DNA synthesis by detecting the release of protons by semiconductor technology without the use of optical modules. Allows control of the capacity to generate sequential data in the range from 0.3 Gb to 25 Gb by using performance-specific sensors. Works with reagents and consumables marked with a radio frequency identifier for automatic recognition by the device and time to obtain a result - 6.5 hours. Allows whole exomic sequencing of up to 4 exomas simultaneously
Ion GeneStudio S5 Prime System Applications:
DNA sequencing - target sequencing,
de novo sequencing,
Chip sequencing,
DNA methylation analysis,
16s sequencing,
RNA sequencing - gene expression analysis,
small-RNA sequencing,
complete transcriptome (Whole –transcriptome) analysis
sequence analysis with a minimum amount of material - 1 nanogram of DNA or RNA from FFPE samples.
whole exome sequencing
Ion Chef ™ Instrument (Thermo Fisher Scientific) is an automated sample preparation system for NGS sequencing, compatible with the Ion PGM system available in the laboratory.
MiSeq sequencing system (Illumina) delivers the fastest time to answer, a revolutionary workflow, and the widest breadth of sequencing applications, all in a compact and economical instrument. It integrates the functions of cluster generation, Sequencing by Synthesis (SBS), and data analysis in a single instrument and can go from sample to analysed data within a single day (as few as 8 hours).
The highest integrity data and broader range of applications, listed below are outstanding parts of MiSeq:
Whole genome resequencing
Target resequencing using enriched targets or custom selected amplicons
Sequencing of or „Long-range” PCR
Sequencing of molecular inversion probes
De novo sequencing
ChIP-Seq analysis of specific DNA binding proteins
ChIP-Seq analysis of modified histones and epigenetic markers
ChIP-Seq analysis of specific protein-DNA sequence interactions
Sequencing of treated with bisulfite DNA for studies of methylation
16S рРНК sequencing (Metagenomics)
mRNA sequencing
mRNA sequencing in both directions
Taq-based sequencing
Sequencing of small RNAs
Ribosomal profiling
DNase I hypersensitivity mapping
Nucleosome mapping and studying the chromatin structure
CNV-Seq analysis for measurement the copy number variatins
GRO-Seq analysis for investigation of the RNA polymerase initiation events
Sequencing of ancient DNA samples
DNA fingerprints and allele specific expression analysis
NovaSeq 6000 (Illumina) is a next generation sequencing technology with the possibility of simultaneous sequencing from 1 to 384 samples; or sequencing 48 human genomes simultaneously in a single run of the apparatus. The system has a capacity of 160 Gb to no less than 6000 Gb with 20 trillion reads in less than 2 days.
Applications:
whole genome sequencing
whole exome sequencing
target re-sequencing
de novo sequencing
sequencing of bisulfite-treated DNA (methyl-seq)
RNA sequencing
ChIP-Seq analysis
The system is equipped and works with a server bioinformatics platform for ultra-fast secondary analysis of next-generation sequencing data (NGS) Illumina DRAGEN Bio-IT platform, which uses algorithms for genomic analysis, including BCL conversion, mapping and alignment, sorting and determination of haplotype variants; analyzes new generation sequential (NGS) data from entire genomes, exomas and RNA sequencing; it is possible to process sequential data from the whole human genome at 30 × coverage in about 25 minutes and from whole human exome at 100 × coverage in about 8 minutes.
The NGS Laboratory is equipped with software packages for data analysis: NextGene Software, NG Browser/ viewer (Soft Genetics LCC), VarSeq (Golden Helix), DRAGEN server (Illumina)