Genomics Area

Whole genome sequencing (WG-Seq) is the process of determining the complete DNA sequence of an organism's genome at a single time. It delivers a base-by-base view of all genomic alterations, including single nucleotide variants (SNVs), small insertions and deletions (indels), copy number changes (CNVs), and structural variations (SVs). It can also be used in metagenomic studies for accurate identification of species from environmental samples.

Whole genome sequencing with ONT technology produces reads that are several kilobases long. They are extremely useful to improve genome assemblies, to identify large structural variations and to phase alleles to their respective parental homolog.

Whole genome Enzymatic Methyl sequencing is a new method for identification of 5-mC and 5-hmC, in contrast to the traditional bisulfite sequencing (WGBS-Seq) which has been the gold-standard for DNA methylation at single-base resolution. Whole genome Enzymatic Methyl sequencing produces high quality libraries that enable superior detection of 5-mC and 5-hmC from fewer sequencing reads.

Whole exome sequencing is used to investigate all protein-coding regions of the genome with enhanced coverage for disease-associated genes. It is suitable to identify nucleotide variants across coding regions, being a cost-effective alternative to whole-genome sequencing, and producing smaller and more manageable data sets compared to whole-genome sequencing data.

Targeted sequencing is a highly directed approach that enables the analysis of genetic variation in specific genomic regions, using pre-designed gene panels, custom gene panels or amplicon sequencing. Potential applications are the discovery of rare mutations in complex samples (such as highly heterogeneous tumour samples) or sequencing the bacterial 16S rRNA gene across multiple species, a widely used method for phylogeny and taxonomy studies.

RNA sequencing is a sensitive and accurate method for determining the primary sequence and relative abundance of all RNA molecules. It provides strand-specific information that allows assigning transcripts to the corresponding DNA strand. Most common applications are differential gene expression, allele-specific gene expression, alternative splicing, fusion transcripts, de novo transcriptome assembly and genome annotation, and single nucleotide variant identification.

RNA sequencing with long reads allows full-length characterization of native RNA or cDNA, as well as the identification of complex transcript isoforms, and chimeric or gene fusion transcripts.

The three-dimensional configuration of the genome is complex, dynamic and crucial for gene regulation. Hi-C sequencing is a chromosome conformation capture technique that reveals the interactions between different pieces of DNA.

Single cell sequencing allows analyses of individual cells. Looking at both complex systems, such as tissues or organs, and at single-cell level, the cellular heterogeneity and the state of each cell type is revealed. Most common applications are Single Cell RNA sequencing, Single Cell ATAC sequencing, Single Cell immune profiling (BRC/TRC), CITE sequencing and Single Cell Multiome ATAC + Gene Expression.

Spatial transcriptomics allows to study gene expression within an unperturbed tissue microenvironment and architecture maintained. It  allows to study the processes that happen in whole organismal systems as realistic as possible.

The assay for transposase-accessible chromatin sequencing (ATAC-Seq) is a rapid and sensitive technique to assess genome-wide chromatin accessibility. It uses the Tn5 transposome to detect nucleosome-free regions of the genome. It is widely used for nucleosome mapping and to determine transcription factor occupancy.

Next-generation sequencing (NGS) has dramatically changed the molecular diagnostic area. Whole exome sequencing by NGS and confirmation of the reported candidate variants by Sanger Sequencing is a common practice in many clinical labs.

DNA fingerprinting enables identification of individuals using hair, blood, semen, or other biological samples, based on unique patterns (polymorphisms) in their DNA. It can be done by whole genome sequencing in the discovery phase and/or by amplified fragment length polymorphism (AFLP, detection of multiple DNA restriction fragments by means of PCR amplification) for larger number of samples.

Metagenomics is the study of genetic material recovered directly from environmental samples. Accurate identification of species is a major challenge and can be done by two complementary approaches: whole genome sequencing (WG-Seq) and 16S, 18S or ITS amplicon sequencing. The latest is a cost-effective approximation to study large number of samples although is limited to one specific gene, while the WG-Seq strategy can be applied to lower number of samples but works well for all organisms found in the same sample, prokaryotes and eukaryotes.

The Sanger method is based on sequentially synthesizing a strand of DNA complementary to a single strand (used as a template), in the presence of DNA polymerase, the four 2'-deoxynucleotides that make up the DNA sequence (dATP, dGTP, dCTP and dTTP) and four dideoxynucleotides. Using specific primers for known genes can detect different polymorphisms in the sequence.

Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have been popular markers due to their high polymorphism. The PCR reaction is performed with fluorescent dye-labelled primers, then the PCR fragments can be analysed on a capillary DNA sequencing machine, and the data is analysed using GeneMapperTM software.

Quantification of allelic expression of specific genes using TaqMan™ assays or SYBR Green intercalator assays can be performed using RT-PCR system.

TaqMan is a commonly used SNP genotyping method developed by Life Technologies, which is an advanced, mature, validated, and widely used technology using RT-PCR system. Each TaqMan genotyping assay contains two primers for amplifying the sequence of interest and two allele-specific and differently labeled TaqMan probes for allele detection. Each allele-specific MGB probe is labelled with a fluorescent reporter dye (either a FAM or a VIC reporter molecule) in the 5’ end and is attached with a fluorescence quencher to the 3’ end.

DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene. To perform a microarray analysis, RNA molecules (mRNA for gene expression and miRNA for miRNA analysis) are typically collected from both an experimental sample and a reference sample. The samples are then converted into complementary DNA (cDNA), and each sample is labelled with a fluorescent probe. The data gathered through microarrays can be used to create gene expression profiles, which show simultaneous changes in the expression of many genes in response to a particular condition or treatment.

Small organism whole genome sequencing can be performed using a next generation sequencing platform.

The small RNA sequencing service covers the existing small RNA molecule sequencing and novel small RNA discovery, mutation characterization, and expression profiling of small RNAs by leveraging advanced NGS technologies and the data analysis pipeline.

Mitochondria play a very important role in important cellular functions. Mitochondrial DNA sequencing is a useful tool for researchers studying human diseases, and can also be also in population genetics and biodiversity assessments

Imaging systems are used for the detection, quantitation, and analysis of proteins and nucleic acids in gels and on membranes. They can be used for detection and automated data analysis with all common modes of protein and nucleic acid staining and labelling: colorimetric, fluorescent and chemiluminescent.