Genomics and Epigenetics Unit

Introduction

The Genomics and Epigenetics Section of the Central Research Unit of the Faculty of Medicine of Valencia provides advanced technological infrastructure aimed at developing highly complex biomedical research projects, supporting both research groups from the Universitat de València/INCLIVA and public and private institutions.

The Section is equipped with state-of-the-art technological platforms for genomic, transcriptomic, and epigenetic analysis, offering comprehensive solutions for the study of genetic variability, gene expression regulation, and epigenetic modifications associated with physiological and pathological processes.

Among its resources is the Affymetrix GeneChip® technology, which enables simultaneous and quantitative analysis of thousands of genes through expression, exon, and microRNA microarrays. This platform also allows studies of SNPs, loss of heterozygosity (LOH), mosaics, copy number variations (CNVs), as well as transcription factor binding analysis and characterization of new transcriptional elements.

The Section also features the Illumina NextSeq™ 550 sequencing platform, a highly flexible NGS system capable of adapting to multiple applications, including whole exome sequencing, transcriptomes, small and medium genomes, targeted panels, and amplicon-based studies. NGS technology enables detection of genomic alterations at nucleotide-level resolution, including SNPs, indels, CNVs, and chromosomal aberrations without prior knowledge of the target sequence.

In the transcriptomics field, the Unit develops RNA-seq studies aimed at global gene expression analysis, identification of new isoforms, gene fusions, low-abundance transcripts, and non-coding RNAs including long non-coding RNAs and antisense RNAs. Gene expression and miRNA studies are also performed in multiple model organisms and plant species.

The technological infrastructure is complemented by the MassARRAY® CPM platform from AGENA Bioscience, specialized in high-precision multiplex genotyping and quantitative DNA methylation analysis. This technology combines base extension chemistry with MALDI-TOF mass spectrometry, allowing simultaneous analysis of multiple genomic regions with high sensitivity, specificity, and reproducibility. Applications include SNP and genetic variant analysis, pharmacogenetics studies, epigenetic analysis using EpiTYPER® technology, molecular biomarker validation, and detection of low-frequency somatic mutations in tumor samples.

The Section also incorporates the PyroMark Q48 Autoprep pyrosequencing system from QIAGEN/Werfen, an automated platform designed for quantitative DNA methylation analysis and genetic variant validation. This system precisely and reproducibly determines methylation levels at specific CpGs and performs targeted short DNA sequence analysis. Its capacity to process up to 48 samples simultaneously improves efficiency, traceability, and analytical reproducibility, providing fast and highly sensitive results especially suited for epigenetic and oncological studies.

Thanks to the integration of microarray, next-generation sequencing, mass spectrometry, and pyrosequencing technologies, the Genomics and Epigenetics Section provides an advanced technological environment for research projects in genetics, molecular biology, epigenetics, molecular oncology, and personalized medicine.

Services

• Gene expression arrays for traditional expression pattern analysis.
• Whole-transcriptome arrays for in-depth differential expression and non-PolyA transcript analysis (lncRNA, lincRNA).
• Arrays for splicing variant studies and exon-level expression analysis.
• Arrays for small RNAs (miRNAs, pre-miRNAs, snoRNAs, scaRNAs).
• Arrays for transcriptomic mapping.
• Arrays for DNA/protein interaction and promoter analysis.
• Arrays for molecular cytogenetics studies (chromosomal aberrations, LOH, gains, losses, uniparental disomy, mosaics).
• Whole transcriptome sequencing (Total RNA-seq) and coding RNA (mRNA-seq).
• RNA sequencing in low-input and single-cell samples.
• Small RNA sequencing.
• Whole exome sequencing (WES).
• Whole genome sequencing (WGS).
• Targeted sequencing using commercial or custom panels, amplicons, and capture methods.
• High-sensitivity genotyping studies using MassARRAY® technology.
• Quantitative DNA methylation studies using MassARRAY® CPM and PyroMark Q48 pyrosequencing.
• Somatic mutation determination and tumor biomarker molecular analysis.
• Pharmacogenetics and epigenetics studies.
• Sequencing and arrays for methylation studies.
• Illumina Infinium Methylation EPIC and CytoSNP arrays.

Equipment

• NextSeq™ 550 (Illumina): NGS sequencing platform with chip scanning capability.
• MassARRAY® CPM (AGENA Bioscience): Genotyping and quantitative methylation platform based on MALDI-TOF mass spectrometry.
• PyroMark Q48 Autoprep (QIAGEN/Werfen): Automated pyrosequencing system for quantitative methylation and variant validation.
• Infinium Starter Pack: System for preparing Illumina Infinium BeadChips.
• GeneChip® Scanner 3000 7G: Confocal scanner developed by Affymetrix.
• Affymetrix GeneChip Fluidics Station 450: Automated system for chip staining and washing.
• GeneChip Hybridization Oven 640 and 645: Controlled hybridization systems.
• Agilent 2100 Bioanalyzer: Capillary electrophoresis system for DNA, RNA, and proteins.
• QuantStudio™ 5 (Applied Biosystems): Real-Time PCR system.