High content genomics and bioinformatics

The facility has several computer workstations dedicated to data analysis and makes use of the high performance computing facility housed in the IGTP data processing center. In addition to our internal laboratory infrastructure to carry out sample quality control and preparation for high-content genomic analysis assays, the unit is coordinated with centralized genomics facilities such as the CRG-CNAG. Automated Illumina Infinium test platform HiScan Illumina Infinium Assay Platform: Used for genome-wide SNP genotyping based on matrix-based, number-copy and LOH analysis, and DNA methylation profiles. The HiScan (Illumina) matrix scanner is a confocal scanner with a spatial resolution of 0.375 microns and two lasers at wavelengths of 532 and 660 nm. It allows the extraction of images and data for Infinium beadray assays to measure the fluorescent signal of probes profiling up to 5,000,000 genomic positions per sample simultaneously. The Evo-150 liquid handling robot (Tecan) is equipped with 8 fixed tips and is configured for the automated processing of samples for Illumina infinium tests. It allows the parallel manipulation of up to 384 samples. Robotic handling of liquids Sciclone NGS liquid handling robot (PerkinElmer). Robot with disposable tip head 96 and plate clamp. Protocols for automated execution of molecular biology applications, especially for next-generation sequencing (NGS). It allows the parallel manipulation of up to 96 samples simultaneously. It is used for the preparation and quantification of the NGS library and the qPCR configuration of 384 microwell plates. Quantification and shear of nucleic acids Qubit (Thermofisher): Single tube fluometer. It is used for the precise quantification of nucleic acids from 1 to 20 µl of sample. It discriminates single-stranded DNA and RNA. Ultrasonic S2 (Covaris). Ultrasonic mechanical processor based on adaptive focused acoustics. It is used for the fragmentation of genomic DNA and chromatin, the extraction of nucleic acids from paraffin-fixed tissue. Process one sample at a time. Bioinformatics data analysis computing HP xw8600, xw4600, Z600, Z440 Workstations (Hewlet Packard): High-performance computer workstations with Linux operating system. Used for local computing or remote access to centralized nodes and storage systems hosted at the IGTP Scientific Computing Data Processing (HPC) center for bioinformatics analysis of matrix-generated genomic data and NGS. Dell Precision T7500 (Dell) – PGM Ion Server: High-performance computer server with Linux operating system and Ion Torrent Suite software for controlling the execution and analysis of next-generation Ion Torrent sequencing data Automated nucleic acid analysis and size selection Bioanalyzer 2100 (Agilent): Automated laboratory microfluidic chip nanoelectrophoresis system. It is used for the analysis of the integrity and evaluation of the size of DNA and RNA, and for the qualitative profile of small RNA. It can process up to 11-12 samples per run. Pippin Prep (SAGE): Gel electrophoresis and automated elution system. It is used to select the size of DNA libraries in next-generation sequencing application libraries. It allows the simultaneous separation of up to 4 library clusters per run and the avoidance of fractions of predefined size using independent configurations per cluster. Next generation sequencing Ion Torrent PGM (Personal Genome Machine, ThermoFisher) next generation sequencer: Massively parallel sequencing instrument based on miniaturized fluid proton detection sensors placed in microchips. It can generate up to 5,000,000 sequencing readings up to 400 nt in length per roll from up to 384 samples grouped simultaneously. It is used for RNA and DNA sequencing applications on 314, 316, and 318 ion chips. Prior to execution, clonal amplification of the sequencing libraries by emulsion PCR is performed in the PCR system. of automated emulsion Ion Torrent One Touch2 (ThermoFisher) followed by the enrichment of positive microspheres of template by means of the instrument of manipulation of liquids Ion Torrent ES (Enrichment System, ThermoFisher).

The unit offers its services directly (in coordination with the Translational Genomics Unit of the IGTP) or through external providers. We offer comprehensive support from experimental design to interpretation of results and offer additional support for outsourcing and outsourcing. We have experience in many global genome, transcriptome, and epigenome analysis methodologies that allow the discovery of new molecular markers applicable to many diseases. The services currently offered include: consultation, sample quality control, sample processing for next-generation sequencing (Illumina, Ion Torrent) and microarray-based assays (Illumina Infinium), automation of liquid handling for to sample preparation and configuration of high-performance PCR assays and bioinformatics data analysis. Aplications qPCR (high performance automated testing) Gene expression (mRNA, ncRNA, miRNA) SNP genotyping Quantification of the NGS library Microarrays: Detection of DNA variants (SNP, CNV) DNA methylation Gene expression (mRNA, ncRNA, miRNA) Massively parallel sequencing: Genomes (WGS) Exomes Specific panels (subxomes, hotspot, liquid biopsy) Metagenomes (16S rRNA, shotgun) Transcriptomes (mRNA-seq, total RNA-seq, small RNA-seq) ChIP-seq Attention to specific needs Special samples (low entry, partially degraded, FFPE, biofluids) Essay customization Test automation Data analysis settings for new applications Bioinformatics support Experimental design Sample size estimates Quality control of raw data (global evaluation, detection of atypical effects and batches) Data preparation (reformatting, re-annotation, metadata curing) QPCR data analysis (efficiency correction, selection of normalizers, relative quantification) Preprocessing of microarray data (background correction, normalization) NGS data preprocessing (demultiplexing, adapter and base quality trimming) Mapping of NGS data to the reference genome (removal of duplicates, coverage analysis, reading count by biotype, gene, region, promoter, enhancer, chromosome segment) De novo NGS assembly (whole genome, transcriptome) Call and annotation of sequence variants (SNV / indels in genomes, exomes, panels, transcriptomes) Chromosomal localization analysis (structural variations, LOH, chromatin peak, gene fusions, chromatin interactions) Differential statistical analysis (expression, methylation, copy number) Functional genomic analysis (GO, pathway, TF or miRNA binding, resistance, pathogenicity) Classification and prediction construction Survival analysis Viral insertion analysis RNA soformes analysis (splicing, editing, iomiR) Analysis of genetic variation (analysis of associations throughout the genome, microbial typing, typing of viral quasi-species, phylogeny of epidemic outbreaks) Metagenomic analysis (taxon distribution, enrichment of metabolic functions) Visualization of genomic data (genome browser traces, graphics) Help for publishing and sending data to repositories Help to access protected datasets

GINYS-IGTP-006

Open