BIOINFORMATICS

With the advent of new sequencing technologies, research and clinical studies often generate large volumes of data, making the analysis stage very long and discouraging.
We know our clients’ needs very well and it is for this reason that we have recruited a very skilled team of bioinformaticians that can process data generated from the majority of Next Generation Sequencing (NGS) technologies regardless of their amount and complexity. To give the best answer to your research’s question.

All Platforms and Data Types

We can analyse data from all of the major technology platforms (eg Illumina, Ion Torret, PacBio) for a wide range of applications:

• Genome-wide association studies (GWAS), whole genome sequencing (WGS) analysis, SNP detection and haplotype analysis to facilitate the discovery and/or typing of SNPs implicated in disease
• RNA-Seq data analysis (quality control, alignment, quantification, and differential expression): whole transcriptome analysis for differential gene analysis, to compare gene expression between conditions, such as a drug-treated vsnon-treated and up- or down-regulated genes
• ChIP-Seq data analysis: sequencing depth selection, data quality check, mapping, data normalisation, assessment of reproducibility, etc.
• Methyl-Seq data analysis: Bisulfite sequencing analysis for epigenetic studies
• Exome sequencing analysis for the identification of known and novel SNPs and indels etc
• CNV analysis.
• Metagenomic Analysis: publication ready Phylogenetic trees, Alpha and beta-diversity, rarefactions, rank abundance plots, relative abundance bar plots, with integration of meta-data, etc.

DNA Xperts offers cost-efficient, rapid turnaround, high-throughput microarray data analysis services.

Our team can perform differential gene expression analyses using data generated from major commercial microarray providers such as Affymetrix, Illumina and Agilent.

Our approaches mean you can go wider and deeper in the scope of the analysis and cover all array types such as genotyping, gene expression and DNA methylation.

Our microarray analysis services include:

Gene Expression Analysis

We can analyse gene expression profiling data for all the major commercial microarray providers (Affymetrix, Illumina, Agilent) as well custom microarray platforms and exon arrays. We offer computationally innovative solutions to help you overcome challenges in genomic microarray analysis.

SNP Genotype Analysis

We offer a full range of SNP genotyping services which can include:

• SNP filtering,
• Linkagedisequilibrium,
• Haplotypeanalysis,
• Genome-wide association studies (GWAS),
• Copy number variation (CNV)

Proteomics is the study of the full repertoire of proteins encoded by the genome in a given cell, tissue or organism. It is used to further our understanding of protein structure and function and how these change in response to a disease.

Proteomics research is particularly applied in Oncology, Microbiology, Virology, Toxicology, Antibody Profiling and Biomarker Discovery research.

DNA Xperts  can analyse data generated by state-of-the-art proteomics technologies, such as:

• ShotgunLC-MS/MS, SELDI-TOF MS,
• MALDI-TOF MSand protein arrays.

Applications

Our team has a broad knowledge of proteomics technologies and great expertise in the computational sciences: for this reason, DNA Xperts  can provide unparalleled services for the analysis and interpretation of proteomics data.

We offer the below data analysis services:

• Identification of biomarkers that are biologically relevant and for prognosis or diagnosis
• Protein discovery & sequence identification
• Protein quantification.

As part of our metabolomic analysis service, we can simultaneously analyse large parts of the metabolome. This allows us to provide information not only on specific metabolites of interest but also on interactions taking place in the biochemical networks.

Our metabolomics services include:

• Metabolite profiling& identification,
• Metabolite quantification.

Alongside our Metabolomics service, we also offer Lipidomics as part of our bioinformatics solutions. Our workflows can identify and quantify lipids in tissues or at a cellular level for different applications such as biomarker identification.

Applications

Metabolomic and Lipidomic analysis can help with different purposes in research:

• Insights into drug discovery, developmentand mode-of-action
• Disease diagnosticsand mechanisms
• Evaluation of new therapies
• Personalised medicine.

We can help you to investigate disease mechanisms and develop targets therapying the epigenome.  Understanding epigenetic processes has an important role in human cancers, metabolic syndromes and brain disorders amongst other areas.

DNA Xperts provides a range of analysis services and solutions for epigenetic research, including:

• Methylation analysis (NGS and arrays)
• chip-seq to identify histone modification patterns
• miRNA analysis (NGS and arrays)
• DNA-Protein Interaction analysis.

Bioinformatics Solutions for CRISPR

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) sequences are specialised sections of DNA, playing a key role in antiviral defences.

Our team at DNA Xperts are well-placed to help you get the most out of your CRISPR-generated data, as our approaches allow you to go deeper into the analysis of data produced. We can help at any stage of your study, from the design through to the analysis of on- and off-target effects.

CRISPR Services:

DNA Xpertscan help with a range of CRISPR-generated data such as:

• Gene expression and GWAS
• Epigenetics
• Microbiome
• Metabolomics and proteomics

We can analyse data taken from publicly available data sources in addition to datasets provided by clients.

With large amounts of data being created from biological datasets, the process of finding meaningful information hidden within has become more challenging. In a scenario where datasets come in large quantities, discovering patterns and use those patterns for research is a challenge. Data mining becomes then crucial in the healthcare industry: digging data from the public domain allows to identify inefficiencies and best practices that improve care whilst dramatically reducing costs.

How it works

Our team can mine data from a range of sources such as publicly available data sources and databases, or from datasets provided by clients. Our tools and methods allow to go deeper into data already produced and ensure that our clients get the best answer to the research’s question.

A typical data landscaping project involves identifying suitable data sets for further analysis. These can take many forms; it could be gene expression datasets in a specific disease, or datasets showing that a mutation is present in a given gene. Our analysis team use public resources, keyword searches and manual curation to identify relevant datasets, which are then presented back to the client using our custom report formats.

Data mining projects take a set of public data (either from a data landscaping study, or from a list of already identified datasets) and analyse them. We can perform data mining by using standard or suggested workflows. Some analysis projects can also include meta-analysis where our team combine outcomes from several studies (and therefore datasets) to increase the overall analysis power and impact on your research.